MERCURY COMPUTER SYSTEMS INC
10-K, 1999-09-27
ELECTRONIC COMPONENTS & ACCESSORIES
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                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                    FORM 10-K
         (MARK ONE)
              [X] ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF
                       THE SECURITIES EXCHANGE ACT OF 1934
                     FOR THE FISCAL YEAR ENDED JUNE 30, 1999
                                       OR
              [ ] TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d)
                     OF THE SECURITIES EXCHANGE ACT OF 1934
                       COMMISSION FILE NUMBER - 000-23599

                                 ---------------

                         MERCURY COMPUTER SYSTEMS, INC.
             (Exact name of registrant as specified in its charter)

           MASSACHUSETTS                             04-2741391
  (State or other jurisdiction of                 (I.R.S. Employer
   Incorporation or organization)                Identification No.)

199 RIVERNECK ROAD, CHELMSFORD MASSACHUSETTS                       01824
  (Address of principal executive offices)                       (Zip code)

<TABLE>
<S>                                                             <C>
                (978) 256-1300                                         NASDAQ NATIONAL MARKET
(Registrant's telephone number including area code)             (Name exchange on which registered)
</TABLE>

             SECURITIES REGISTERED PURSUANT TO SECTION 12 (b) OF THE
                        SECURITIES EXCHANGE ACT OF 1934:
                                      None

             SECURITIES REGISTERED PURSUANT TO SECTION 12 (g) OF THE
                        SECURITIES EXCHANGE ACT OF 1934:
                     Common Stock, Par Value $.01 Per Share

Indicate by check mark whether the Registrant (1) has filed all reports required
to be filed by Section 13 or 15 (d) of the Securities Exchange Act of 1934
during the preceding 12 months (or for such shorter period that the registrant
was required to file such reports), and (2) has been subject to such filing
requirements for the past 90 days.

Yes  [X]  No  [ ]

Aggregate market value of Registrant's voting stock held by non-affiliates of
the Registrant as of August 31, 1999: $269,402,562.

Shares of Common Stock outstanding as of August 31, 1999: 10,361,637 shares

                       DOCUMENTS INCORPORATED BY REFERENCE

Excerpts from the Registrant's Annual Report to Shareholders for the year ended
June 30, 1999 is incorporated by reference into parts I and II of this report.

Portions of the Registrant's definitive Proxy Statement for its special meeting
in lieu of the 1999 Annual Meeting of Stockholders to be held on November 18,
1999 (the "Proxy Statement") are incorporated by reference into Part III of this
report.

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405
of Regulation S-K is not contained herein, and will not be contained, to the
best of registrant's knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this form 10-K or any amendment to this
Form 10-K. [ ]

                            Exhibits Index on Page 18


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                                     PART I

ITEM 1.  BUSINESS

OVERVIEW

    Mercury Computer Systems, Inc. (the "Company" or "Mercury") designs,
manufactures and markets high performance, real-time digital signal processing
computer systems that transform sensor generated data into information which
can be displayed as images for human interpretation or subjected to additional
computer analysis. These multicomputer systems are heterogeneous and scalable,
allowing them to accommodate several different microprocessor types and to
scale from a few to hundreds of microprocessors within a single system.
Mercury's system architecture is specifically designed for digital signal
processing ("DSP") applications, which are typically, computation intensive and
require I/O capacity and interprocessor bandwidth not available on a general
purpose PC or workstation.

    The two primary markets for Mercury's products are defense electronics and
medical diagnostic imaging. Both of these markets have computing needs which
benefit from the unique system architecture developed by the Company. Mercury's
computer systems are generally used on real-world signal data to enable a
military commander to "see" the battle space through natural barriers such as
clouds, darkness, water or foliage, so that the position and strength of the
enemy can be determined, or to enable a physician to "see" within the body
instead of performing invasive surgery.

    During the past several years, the majority of the Company's revenues
have been generated from sales of its products to the defense electronics
market, generally for use in reconnaissance and intelligence gathering systems.
The Company's activities in this area have focused on the proof of concept,
development and deployment of advanced military applications in radar, sonar
and airborne surveillance. The Company has established relationships with many
of the major prime contractors to the worldwide defense industry, including
Lockheed Martin Corporation, Hughes Aircraft Company, Raytheon Systems Company,
Northrop Grumman Corporation, MIT/Lincoln Laboratory, GEC Marconi Limited,
Ericsson Microwave Systems AB, MATRA Systems & Information, Mitsubishi Heavy
Industries, Ltd., British Aerospace and a prime contractor owned by the Israeli
Ministry of Defense.

    Medical diagnostic imaging is the other primary market currently served by
the Company. Mercury's computer systems are embedded in Magnetic Resonance
Imaging ("MRI"), Computed Tomography ("CT") and Positron Emission Tomography
("PET") machines. Mercury has supplied computer systems for use in several of GE
Medical Systems' diagnostic imaging systems since 1987, and has established
relationships with Siemens Medical Systems, Inc., and Picker International. The
major medical imaging manufacturers are currently developing the next generation
of MRI, CT and digital x-ray machines, which are expected to provide better
performance at lower cost. Mercury has secured design wins on programs with
certain of the major medical imaging manufacturers for their next generation
MRI, CT and digital x-ray machines.

    Mercury's computer systems are designed to process continuous streams of
data from sensors attached to radar, sonar, medical imaging equipment and other
devices. The resulting image is transmitted to the battlefield commander, pilot,
technician or physician in order to assist in the decision making or diagnostic
process. Due to the nature of the applications in which many of Mercury's
computer systems are embedded, they are frequently confined in limited spaces
and therefore are designed to generate a minimum amount of heat. The Company
employs the RACEway Interconnect, an industry standard system area network
developed by Mercury, which allows for high interprocessor bandwidth and I/O
capacity. The Company uses its proprietary ASICs to integrate microprocessors,
memory and related components into the RACEway Interconnect to provide optimum
system performance. The Company uses industry standard processors, such as
Motorola's PowerPC and Analog Devices' SHARC, in the same system. The Company
believes that the RACEway Interconnect and its proprietary ASICs, working
together with a group of mixed microprocessors in the same system, allow the
most efficient use of space and power with an optimal price/performance ratio.

    Since July 1996, Mercury has targeted the emerging shared storage market for
introduction of a new product which draws on the Company's core competencies in
systems engineering and the development of real-time software. This business
unit was created to exploit some of Mercury's innovative software developments.
It has evolved into software for use in applications and market segments that,
while exciting and potentially offering a large


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return, are outside of Mercury's core businesses and strengths. The Company has
therefore issued an offering memorandum seeking alternative ways to fund the
continuing development of this business.

INDUSTRY BACKGROUND

    Defense Electronics

    Digital signal processing computer systems are embedded into air, sea and
land-based platforms for processing radar, sonar and signal intelligence
applications. The Company believes that an important factor underlying the
development of this market is a continuing desire by military commanders for
increased battle space information, which can be obtained through radar, sonar,
signal intelligence and image intelligence systems. Military commanders also
need more powerful computers with similar attributes in order to conduct dynamic
battle simulations and mission planning tasks utilizing today's complex weapons
systems.

    Another important trend in the defense electronics marketplace is the
movement away from so-called "stove pipe" systems designed by prime contractors
with special purpose hardware specifically for a single application, largely
without regard to cost. The market is moving toward the use of systems which
incorporate selected commercial-off-the-shelf ("COTS") hardware and software
components in order to save money and development time. Recent Department of
Defense ("DOD") leaders and federal regulations have mandated widespread use of
COTS components in defense electronics applications. All of Mercury's computer
systems are eligible for use in defense electronics applications as COTS
components.

    Medical Imaging

    The principal modalities of medical diagnostic imaging systems include MRI,
CT, digital x-ray, PET, SPECT (single photon emission computed tomography) and
ultrasound devices. Although demand for medical imaging equipment has been
sluggish in recent years due primarily to cost containment pressures and
consolidation in the health care industry, the Company believes that demand for
medical diagnostic imaging equipment will increase modestly over the next three
years. The Company believes that this increase will be primarily due to the
introduction of next-generation devices, together with the anticipated future
development by the major medical imaging manufacturers of new international
markets for their diagnostic equipment. The Company believes medical imaging
equipment manufacturers will continue to replace in-house designed digital
signal processing systems with commercially available systems designed by the
Company and others.

    This industry's demand is driven in part by the need to provide physicians
with rapid, sharp and clear images of areas of a patient's body suspected to be
diseased or injured, while using the least intrusive means. These images provide
a significant diagnostic tool for the physician, who can more readily understand
the patient's malady and prescribe appropriate corrective action. In order to
provide such images, medical imaging machines must be capable of processing a
continuous stream of data on a real-time basis. A parallel concern in the health
care industry is the need to reduce costs. Hospitals, in particular, continue to
be under significant pressure to contain costs and, at the same time, maintain
quality of care. Such pressures are forcing hospitals to be as technologically
efficient as possible. Toward this end, hospitals seek to reduce the required
period of time a patient must spend in their medical imaging machines, which has
the added benefit of increasing the total number of patients who can be
diagnosed with this expensive equipment during a given period of time. One way
to reduce patient time in medical imaging machines and improve image quality is
to utilize more powerful signal processing computers, such as those supplied by
Mercury.

MARKETS AND CUSTOMERS

    Defense Electronics

    Mercury provides high performance embedded computer systems as standard
products to the defense electronics market by using commercial and selected
rugged components and by working closely with defense contractors to complete a
design which matches the specified requirements of military applications. The
Company engages in frequent, detailed communication with the end users of
Mercury's systems, military executives and program managers in government and
defense contractors regarding the technical capabilities of Mercury's advanced
signal processing computers and the successful incorporation of its computers in
numerous military programs.


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    Mercury employs industry specialist managers to monitor the defense programs
of each major branch of the United States armed services and additional managers
based in Europe and Japan to keep abreast of developments in their respective
regions. This approach provides relevant information to Mercury regarding major
military procurements worldwide. Mercury maintains sales and technical support
groups to service defense industry participants in six branch offices in the
United States, and through Mercury's subsidiary offices or distributors in 11
other countries. At Mercury's headquarters in Chelmsford, Massachusetts, a group
of systems engineers specializing in radar, sonar and surveillance problems
provides support on an as-needed basis to the remote offices to assist in
securing inclusion in targeted military programs.

    Medical Imaging

    Mercury strives to provide a superior combination of high performance and
competitively priced embedded computer systems to the medical imaging market.
The Company focuses on establishing strong relationships with its customers, the
medical equipment manufacturers. By maintaining frequent, in-depth
communications with its customers and working closely with their engineering
groups, the Company is able to understand their needs and provide appropriate
solutions. In addition, the Company intends to continue its efforts to install
its computer systems in place of alternative designs created by the in-house
design teams employed by the medical imaging equipment manufacturers.

    The Company currently is working closely with major medical equipment
companies to design the next generation of MRI, CT and digital x-ray systems,
which the Company believes will lead to faster time-to-market and competitive
advantages for the medical equipment companies that use Mercury's computer
systems for inclusion in their imaging machines. Mercury's industrial PC class
hardware system provides the medical imaging industry with increased performance
densities at lower costs and an architecture that accommodates performance
upgrades as new technology becomes available. Integrating the high-bandwidth
RACEway Interconnect system area network within the PCI environment results in
highly scalable systems. This allows medical equipment suppliers to design
systems that can satisfy a broad range of price/performance requirements and
meet the needs of global markets, all with the same Mercury architecture.

    Mercury's medical OEM customers consist of the leading manufacturers of
diagnostic imaging equipment. They include GE Medical, headquartered in
Wisconsin, GE Medical Systems Europe in France, GE Yokugawa Medical Systems in
Japan, Siemens Medical in Germany, and Picker International. These companies
have adopted Mercury's PCI or VME computer systems as part of their developments
in either MRI, CT, or digital x-ray systems and, in the case of some companies,
multiple types of systems. The Company has supplied GE Medical with computer
systems for use in three successive generations of MRI machines from 1987
through the present, as well as for use in other GE Medical equipment, such as
PET. In addition, GE Medical and Siemens Medical, the two leading global
suppliers of medical imaging equipment, have awarded contracts to Mercury to
design the signal processing system for the next generation of certain of their
CT medical diagnostic equipment.

    The Company is building systems based on Analog Devices' SHARC DSP processor
and Motorola's Power PC processor to fulfill design wins in CT. The Company also
is building a system based on the Power PC chip to fulfill a design win in
digital x-ray. The Company believes that the principal reason for its medical
imaging design wins is Mercury's experienced team of systems and applications
engineers who work closely with the medical equipment designers and with the
Company's product development engineers. This joint design effort frequently
precedes the first production orders by approximately two to three years.
However, once selected, the production contracts typically continue for the life
of the medical imaging system. In addition, the equipment manufacturers
typically offer computer system upgrades to their customers, potentially
resulting in additional sales of Mercury products.

    AgileVision

    On September 1, 1999, the Company formed a joint venture with the Sarnoff
Corporation referred to as AgileVision. The venture will use Mercury technology
to design, develop, and deliver products and solutions expected to dramatically
reduce the cost of digital TV infrastructure for the broadcast and cable
markets. The many business uncertainties that attend the new venture make
revenue projections at this time inappropriate. The joint venture does
anticipate it would begin to generate revenues during fiscal 2000. Mercury's
share of gains and losses will be reported as a separate line item in its profit
and loss statement.


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    Digital Wireless

    During the fourth quarter of fiscal 1999, the Company announced that it will
pursue the digital wireless communications opportunity internally, offering its
technology and expertise to manufacturers for incorporation within new
generations of base stations that require substantially more flexible and
powerful signal processing capabilities. Returns on Mercury's investments in
fiscal 2000 and 2001 would not begin before fiscal 2001. The market opportunity,
however, is very large, amounting to several hundred millions of dollars
annually, and it represents an OEM business model, which Mercury understands
well. In this past year, Mercury has carried out extensive activities creating a
business development plan that merges its future technology with the processing
requirements of the evolving wireless infrastructure.

KEY TECHNOLOGY COMPETENCIES

    Many of Mercury's customers share a common requirement: the need to process
high-volume, real-time data streams. Whether from an antenna in a defense
application or a medical scanner, the computer must have the ability to process
incoming data as quickly as it is received. Data rates can range from a few to
several hundreds of megabytes per second (or several billion bits per second).
The ability to process this continuous flow of high-bandwidth data is a
fundamental difference between the majority of computing systems in the world
(such as personal computers, workstations and servers) and the computers built
by Mercury.

    Mercury has developed a set of core technical strengths specifically
targeted to, and defined by, the application areas of signal, image and media
processing. These technical strengths are pivotal to Mercury's success in the
real-time market segments of the defense electronics and medical imaging
industries and have resulted in the following developments and capabilities:

    Heterogeneous Switched-Fabric Interconnects. Mercury connects different
microprocessor types (RISC, DSP and specialized computing devices) and I/O
devices in a bus-less, high-bandwidth manner based on multi-stage switches in
its system area network. Among the engineering developments which distinguish
Mercury's systems are the RACEway Interconnect built using the multi-port
RACEway crossbar chip which supports high bandwidth point-to-point data
transfers and fibre channel chassis-to-chassis extensions for RACEway in large
system configurations.

    Heterogeneous Processor Integration. Mercury has developed several ASICs
which integrate standard microprocessors and special purpose mathematics and
graphics processors into a single heterogenous environment. Mercury develops
systems consisting of different microprocessor types with a single-system
software model. Mercury's processor independent software offers a consistent set
of software tools and interfaces, which can drive a heterogeneous mix of
microprocessor types, such as Motorola's PowerPC processor and Analog Devices'
SHARC DSP processor.

    Performance Density. The Company has been using high performance packaging
technology such as multi-chip modules and ball grid arrays in its systems since
the early 1990's. The Company's thermal analysis expertise allows it to design
products that optimize the dissipation of heat from the system in order to meet
the environmental constraints imposed by many of its customers' applications.
The Company's modular hardware and software building blocks allow it to design
systems that best meet the application's specific data profiles. All together,
these attributes combine to deliver the maximum performance in processing,
reliability and bandwidth in the smallest possible space.

    Scalable Software. Mercury's software has been designed to scale to nearly
one thousand processors in real-time environments while maintaining a
high-bandwidth capability. Regardless of the number of processors, the Company's
software provides the same programming environment for a software developer
working with Mercury's computer systems, allowing faster time-to-market and
lower life cycle maintenance costs for its customers.

    Optimized Algorithm Development. Mercury specializes in algorithm
development for single and multi-processor implementations. The Company believes
that using the mathematical algorithms in Mercury's scientific algorithm library
significantly increases the performance of customers' applications, reduces
development time and minimizes life cycle support costs.


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    System Engineering Expertise. Mercury has established a core competency in
providing total system solutions to its customers. The Company has the knowledge
and technical staff to act as an extension of the customer's engineering
organization in order to fashion solutions to some of the world's most demanding
real-time, signal processing applications. Mercury has partnered with its
customers to understand and resolve the challenging problems encountered in
applications as diverse as radar, sonar and signal intelligence for the
military, and diagnostic imaging for MRI, CT, PET and digital x-ray in the
medical imaging market. The Company also provides an integration and development
service to meet the demands of its customers with advanced applications that
cannot be satisfied with standard products. This service combines the variety of
standard products with custom hardware and software to meet the specific
configuration demands of an application.

    Leverage and Create Standards. Mercury uses existing standards where
applicable and has been successful in developing new standards. For example,
Mercury adheres to VME and PCI standard bus interfaces and form factors. The
RACEway Interconnect system area network that Mercury developed was adopted as
an ANSI/VITA standard in 1995, and since then has been adopted by several
companies offering products and services for embedded real-time applications.

PRODUCTS

HARDWARE PRODUCTS

    Mercury offers three classes of systems for the Company's target markets.
Each class of product is scalable to meet the full range of requirements in
signal processing applications.

    High Performance Class. For the highest-performance applications, Mercury
offers a family of high performance systems for the most compute intensive and
I/O capacity and interprocessor bandwidth demanding applications in the defense
electronics market. These applications include space time adaptive processing,
ground-penetrating and foliage-penetrating radar and synthetic aperture radar.
These high-performance systems, known as MultiPort(TM), can scale to a thousand
processors and today include compute modules based on the SHARC and PowerPC
processors.

    VME Class. The VME bus has been the traditional standard for many embedded
applications. Mercury's VME systems each support RACEway Interconnect. Systems
contain modules based on the SHARC, PowerPC and i860 processors and can scale to
several hundred processors. The VME-based systems and components are primarily
used in the defense market where backward and forward compatibility is required
for the long system life cycles of military equipment. This class of RACE Series
systems meets the computing speed, bandwidth and scaleability requirements of
many of today's medium performance radar, sonar and signal intelligence
applications. Advanced and future radar systems are more likely to use the high
performance class systems.

    Industrial PC Class. Based on the PCI bus standard, these systems use the
RACEway Interconnect to provide the extended bandwidth required for real-time
applications. Currently Mercury provides compute modules based on the SHARC and
PowerPC processors. These systems scale to hundreds of processors and are
primarily directed to the medical imaging market, which is moving from VME to
PCI based designs.

SOFTWARE PRODUCTS

    Mercury has developed a comprehensive line of signal processing software
products for the defense and medical imaging markets. Certain of Mercury's
software products are included in a heterogeneous development software package
that enables customers to develop application software that will run on Mercury
hardware. The development software package includes the MC/OS operating system,
scientific algorithm libraries, debugging tools and compilers. License fees
range from $10,000 to $50,000 based on the number of seats chosen by the user
for its application, ranging from a single user license to a project license.

    Set forth below are certain signal processing software products offered by
the Company.

    MC/OS Version 4.X. The MC/OS runtime operating environment allows maximum
use of the RACE heterogeneous multi-computer architecture in a single-system
model incorporating a consistent set of system and application programming
interfaces, and a common development environment. MC/OS is supported on the high
performance, VME and industrial PC classes of Mercury hardware systems. MC/OS is
included in Mercury's


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development software package.

    Scientific Algorithm Library (SAL). Mercury's scientific algorithm library
consists of more than 400 assembly language routines developed by Mercury's
programmers and optimized for execution on Mercury's RACE architecture,
permitting extensive code reusability. The library encompasses a comprehensive
selection of functions including vector processing and data conversion commonly
performed by digital signal processing applications. SAL is included in
Mercury's development software package.

    Parallel Application System (PAS). PAS is a set of high performance
libraries which form a complete programming environment for developing parallel
applications in a distributed memory multicomputer system. The libraries speed
the development of advanced applications using many processors in parallel. PAS
is included in Mercury's development software package.

    SuperVision(TM). SuperVision(TM) is a state-of-the-art debugging tool for
observation and control of embedded, real-time multicomputing systems.
SuperVision(TM) speeds application development by selectively monitoring
individual and large groups of processors, while simultaneously performing
detailed process-level debugging. SuperVision(TM) is sold separately.

ENGINEERING, RESEARCH AND DEVELOPMENT

    The Company's engineering, research and development efforts are focused on
developing new products as well as enhancing existing products. Mercury's
research and development goal is to fully exploit and maintain the Company's
technological lead in the high performance, real-time, signal processing
industry.

    Mercury is involved with researchers from other companies and government
organizations to develop new signaling technologies using fiber optics. This has
the potential for providing more bandwidth per line than conventional techniques
and is directed at the 21(st) century challenges of the next generation of
advanced signal processing systems. Similar cooperative developments are
underway to develop open software solutions for code portability. This research
is focused on developing generic applications, which can be targeted to
Mercury's products through the use of industry standard tools with
Mercury-specific libraries. Some of these research areas benefit from cost
sharing through DARPA grants in those areas where the DoD will obtain benefit
from the development.

    As of June 30, 1999, the Company had 136 people primarily engaged in
engineering, research and development, including hardware and software
architects, design engineers and engineers with expertise in developing medical,
defense and shared storage software systems. During fiscal years 1999, 1998 and
1997, the Company's total research and development costs were approximately
$20.7 million, $14.5 million, and $12.8 million, respectively.

CUSTOMER SUPPORT AND INTEGRATION

    Mercury's Customer Services Group is engaged in a full range of support
functions, including training, technical program management, integration and
design services, host porting services and the traditional maintenance and
support services. The Company has invested in the range of tools, analyzers,
simulators, instruments and workstations to provide a rapid response to both
development and customer support requirements. Within the Customer Services
Group, the solutions systems department has developed many custom interfaces,
reviewed customers' designs, developed special hardware and software components
and provided program management on behalf of defense and medical customers. The
capabilities of this group enable the Company to respond to the demanding
individuality of many programs and have resulted in Mercury being selected for
both development, high volume production and deployed programs.

MANUFACTURING AND TESTING

    Mercury's strengths include the design, development and testing of products
which meet the exacting technology and quality expectations of the Company's
defense electronics and medical imaging customers. Board assembly is outsourced
to a number of electronic contract manufacturers. The supplier typically inserts
most of the components into a printed circuit board, solders the connections,
conducts preliminary testing and returns the boards to Mercury. The Company
conducts final assembly, burn-in and system level testing.


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    Mercury utilizes Optimal Supply Chain Management to provide highly flexible
manufacturing solutions which can be tailored to the specific needs of the
Company's customers, while maintaining the highest level of quality and control
of product assembly. This standard is maintained through demanding Quality
Assurance and Reliability Programs, such as Statistical Process Control, which
are integrated throughout the manufacturing process.

    The Company's outsourcing strategy provides maximum flexibility to respond
to customer requirements and schedule adjustments, with minimal asset investment
by Mercury. This outsourcing strategy also provides multiple sources of supply,
both to support the breadth and complexity of Mercury's product lines, as well
as to ensure continuity of supply. By outsourcing assembly to electronic
contract manufacturers, Mercury is able to focus its manufacturing efforts on
designing more reliable products, designing more efficient methods of building
its products, systems integration, testing and supply chain management.

    Mercury's manufacturing approach is based on a highly integrated process
that takes a product from concept through production. All products are required
to meet specified standards of performance, quality, reliability and safety. The
Company manufactures both commercial and ruggedized versions of its computer
systems. Extensive testing is a fundamental part of the Company's process.
Computer Integrated Manufacturing, Concurrent Engineering, Material Requirements
Planning and Just-In-Time techniques are also integrated into manufacturing
operations as part of an on-time delivery philosophy. Mercury has been ISO 9001
certified since 1995.

COMPETITION

    The markets for the Company's products are highly competitive and are
characterized by rapidly changing technology, frequent product performance
improvements and evolving industry standards. Competition typically occurs at
the design stage, where the customer evaluates alternative design approaches,
including those from internal development organizations. A design win usually
ensures a customer will purchase the product until their next generation system
is developed. Occasionally, the Company's computer systems compete with computer
systems from workstation vendors, all of whom have substantially greater
research and development resources, long term guaranteed supply capacity,
marketing and financial resources, manufacturing capability and customer support
organizations than those of the Company. The Company believes that its future
ability to compete effectively will depend, in part, upon its ability to
continue to improve product and process technologies and develop new
technologies in order to maintain the performance advantages of products and
processes relative to competitors, to adapt products and processes to
technological changes, to identify and adopt emerging industry standards and to
adapt to customer needs.

    The principal bases for selection in sales of digital signal processing
systems to the defense electronics industry are performance (measured primarily
in terms of processing speed, I/O capacity and interprocessor bandwidth,
processing density per cubic foot, power consumption and heat dissipation),
systems engineering support, overall quality of products and associated
services, use of industry standards, ease of use and price. Competitors in the
defense electronics industry include a relatively small number of companies that
design, manufacture and market DSP board level products and in-house design
teams employed by prime defense contractors. In-house design efforts
historically have provided a significant amount of competition to the Company.
However, competition from in-house design teams has diminished in significance
in recent years due to the increasing use of COTS products and the trend toward
greater use of outsourcing. Despite this recent change, there can be no
assurance that in-house developments will not re-emerge as a major competitive
force in the future. Prime contractors are much larger than Mercury and have
substantially more resources to invest in research and development. Increased
use of in-house design teams by defense contractors in the future may have a
material adverse effect on the Company's business, financial condition and
results of operations.

    In the medical imaging industry the principal bases for selection are
performance (measured primarily in terms of processing speed, I/O capacity and
interprocessor bandwidth and power consumption), price, systems engineering
support, overall quality of products and associated services, use of industry
standards and ease of use. Competitors in the medical imaging market include
in-house design teams, a small number of companies that design, manufacture and
market DSP board level products and workstation manufacturers. Workstations have
become a competitive factor primarily in the market for low-end MRI and CT
machines and, to date, have not been a significant factor in the
high-performance market, Mercury's primary focus. There can be no assurance that
workstation manufacturers will not attempt to penetrate the high-performance
market for medical imaging machines. Workstation manufacturers typically have
greater resources than Mercury and their entry into markets historically
targeted by Mercury may have a material adverse effect on the Company's
business, financial condition and results


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of operations.

    Some of the Company's competitors have greater financial and other resources
than the Company, and the Company may be operating at a cost disadvantage
compared to manufacturers who have greater direct buying power from component
suppliers or who have lower cost structures. There can be no assurance that the
Company will be able to compete successfully in the future with any of these
sources of competition. In addition, there can be no assurance that competitive
pressures will not result in price erosion, reduced margins, loss of market
share or other factors, that could have a material adverse effect on the
Company's business, financial condition and results of operations.

INTELLECTUAL PROPERTY AND PROPRIETARY RIGHTS

    The Company relies on a combination of patent, copyright, trademark and
trade secret laws to establish and protect its rights in its products and
proprietary technology. In addition, the Company currently requires its
employees and consultants to enter into nondisclosure and assignment of
invention agreements to limit use of, access to and distribution of, proprietary
information. There can be no assurance that the Company's means of protecting
its proprietary rights in the U.S. or abroad will be adequate. The laws of some
foreign countries may not protect the Company's proprietary rights as fully or
in the same manner as do the laws of the U.S. Also, despite the steps taken by
the Company to protect its proprietary rights, it may be possible for
unauthorized third parties to copy or reverse engineer aspects of the Company's
products, develop similar technology independently or otherwise obtain and use
information that the Company regards as proprietary. There can be no assurance
that others will not develop technologies similar or superior to the Company's
technology or design around the proprietary rights owned by the Company.
Although the Company is not aware that its products infringe on the proprietary
rights of third parties, there can be no assurance that others will not assert
claims of infringement in the future or that, if made, such claims will not be
successful. Litigation to determine the validity of any claims, whether or not
such litigation is determined in favor of the Company, could result in
significant expense to the Company and divert the efforts of the Company's
technical and management personnel from daily operations. In the event of any
adverse ruling in any litigation regarding intellectual property, the Company
may be required to pay substantial damages, discontinue the sale of infringing
products, expend significant resources to develop non-infringing technology or
obtain licenses to use infringing or substituted technology. The failure to
develop, or license on acceptable terms, a substitute technology could have a
material adverse effect on the Company's business, financial condition and
results of operations.

    The Company holds four issued United States patents covering aspects of the
RACE architecture, the SuperVision( debugging tool, and shared storage area
network technology. In addition, the Company has one pending United States
patent application covering additional aspects of the RACE architecture and the
Company's Parallel Application System. The Company may file additional patent
applications seeking protection for other proprietary aspects of its technology
in the future. Patent positions frequently are uncertain and involve complex and
evolving legal and factual questions. The coverage sought in a patent
application either can be denied or significantly reduced before or after the
patent is issued. Consequently, there can be no assurance that any patents from
pending patent applications or from any future patent application will be
issued, that the scope of any patent protection will exclude competitors or
provide competitive advantages to the Company, that any of the Company's patents
will be held valid if subsequently challenged or that others will not claim
rights in or ownership of the patents and other proprietary rights held by the
Company. Since patent applications are secret until patents are issued in the
United States or corresponding applications are published in international
countries, and since publication of discoveries in the scientific or patent
literature often lags behind actual discoveries, the Company cannot be certain
that it was the first to make the inventions covered by each of its pending
patent applications or that it was the first to file patent applications for
such inventions. In addition, there can be no assurance that competitors, many
of which have substantial resources and have made substantial investments in
competing technologies, will not seek to apply for and obtain patents that will
prevent, limit or interfere with the Company's ability to make, use or sell its
products either in the United States or in international markets.

BACKLOG

    As of June 30, 1999, the Company had a backlog of orders aggregating
approximately $52.1 million. The Company includes in its backlog, customer
orders for products and services for which it has accepted signed purchase
orders with assigned delivery dates within twelve months. Orders included in
backlog may be canceled or rescheduled by customers without penalty. A variety
of conditions, both specific to the individual customer and


                                       9
<PAGE>   10


generally affecting the customer's industry, may cause customers to cancel,
reduce or delay orders that were previously made or anticipated. The Company
cannot assure the timely replacement of canceled, delayed or reduced orders.
Significant or numerous cancellations, reductions or delays in orders by a
customer or group of customers could materially adversely affect the Company's
business, financial condition and results of operations. Backlog should not be
relied upon as indicative of the Company's revenues for any future period.

EMPLOYEES

    At June 30, 1999, the Company employed a total of 435 persons, including 136
in research and development, 158 in sales, marketing and customer support, 60 in
manufacturing and 81 in general and administration. Nine of the Company's
employees are located in Europe, seven in Japan and the remainder in the U.S.
None of the Company's employees are represented by a labor organization and the
Company believes that its relations with employees are good. Competition for
qualified personnel in the engineering fields is intense and the Company is
aware that much of its future success will depend on its continued ability to
attract and retain qualified personnel. The Company seeks to attract new
employees by offering competitive compensation packages, including salary,
bonus, stock options and employee benefits. There can be no assurance, however,
that the Company will be successful in retaining its key employees or that it
will be able to attract skilled personnel for the development of its business.

RISK FACTORS

    In this report, as well as oral statements made by the Company, that are
prefaced with the words "may," "will," "expect," "anticipate," "continue,"
"estimate," "project," "intend," "designed" and similar expressions, are
intended to identify forward-looking statements regarding events, conditions and
financial trends that may affect the Company's future plans of operations,
business strategy, results of operations and financial position. These
statements are based on the Company's current expectations and estimates as to
prospective events and circumstances about which the Company can give no firm
assurance. Further, any forward-looking statement speaks only as of the date on
which such statement is made, and the Company undertakes no obligation to update
any forward-looking statement to reflect events or circumstances after the date
on which such statement is made. As it is not possible to predict every new
factor that may emerge, forward-looking statements should not be relied upon as
a prediction of actual future financial condition or results. These
forward-looking statements, like any forward-looking statements, involve risks
and uncertainties that could cause actual results to differ materially from
those projected or unanticipated. Such risks and uncertainties include the
factors set forth below.

    DEPENDENCE ON DEFENSE ELECTRONICS BUSINESS; UNCERTAINTY ASSOCIATED WITH
GOVERNMENT CONTRACTS. Sales of the Company's computer systems to the defense
electronics market accounted for approximately 77%, 79%, and 81% of the
Company's revenues in fiscal 1999, 1998, and 1997, respectively. Reductions in
government spending on programs that incorporate the Company's products could
have a material adverse effect on the Company's business, financial condition
and results of operations. Moreover, the Company's government contracts and
subcontracts are subject to special risks, such as: delays in funding; ability
of the government agency to unilaterally terminate the prime contract; reduction
or modification in the event of changes in government policies or as the result
of budgetary constraints or political changes; increased or unexpected costs
under fixed price contracts; and other factors that are not under the control of
the Company. In addition, consolidation among defense industry contractors has
resulted in fewer contractors with increased bargaining power relative to the
Company. No assurance can be given that such increased bargaining power will not
adversely affect the Company's business, financial condition or results of
operations in the future.

    The Company's contracts with the U.S. and foreign governments and their
prime and subcontractors are subject to termination either upon default by the
Company or at the convenience of the government. Termination for convenience
provisions generally entitle the Company to recover costs incurred, settlement
expenses and profit on work completed prior to termination. In addition to the
right of the government to terminate, government contracts are generally
conditioned upon the continuing availability of legislative appropriations.
Funds are usually appropriated for a given program each fiscal year even though
contract performance may take more than one fiscal year. Consequently, at the
outset of a major program, the contract is usually partially funded, and
additional monies normally are incrementally committed to the contract by the
procuring agency from appropriations made for future fiscal years. No assurance
can be given that the Company will realize the revenue expected from performing
under such contracts. Because the Company contracts to supply goods and services
to U.S. and foreign governments it is also subject to other risks, including
contract suspensions, protests by disappointed bidders of contract awards which
can result in the reopening of the bidding process, changes in governmental
policies or regulations or other political


                                       10
<PAGE>   11


factors.

    DEPENDENCE ON KEY CUSTOMERS. The Company is dependent on a small number of
customers for a large portion of its revenues. In fiscal 1999, Raytheon Systems
Company, Lockheed Martin, and GE Medical accounted for 22%, 16%, and 12%,
respectively, of the Company's revenues. In fiscal 1998, Raytheon Systems
Company, GE Medical, and Northrup Grumman Corporation accounted for 20%, 10%,
and 10%, respectively, of the Company's revenues. In fiscal 1997, Lockheed
Martin and Hughes Aircraft accounted for 22% and 10%, respectively, of the
Company's revenues. The Company's largest customer in the medical imaging
market, GE Medical, accounted for 85%, 76%, and 72% of the Company's aggregate
sales to the medical imaging market in fiscal 1999, 1998, and 1997,
respectively. Customers in the defense electronics market generally purchase the
Company's products in connection with government programs that have a limited
duration, leading to fluctuating sales to any particular customer in the defense
electronics market from year to year. By contrast, many customers in the medical
imaging market historically have purchased the Company's products over a number
of years for use in successive generations of medical imaging devices, although
there can be no assurance that such past behavior will continue in the future. A
significant diminution in the sales to or loss of any of the Company's major
customers would have a material adverse effect on the Company's business,
financial condition and results of operations. In addition, the Company's
revenues are largely dependent upon the ability of its customers to develop and
sell products that incorporate the Company's products. No assurance can be given
that the Company's customers will not experience financial or other difficulties
that could adversely affect their operations and, in turn, the results of
operations of the Company.

    FLUCTUATIONS IN OPERATING RESULTS. The Company has experienced fluctuations
in its results of operations in large part due to the sale by the Company of its
computer systems in relatively large dollar amounts to a relatively small number
of customers. Operating results also have fluctuated due to competitive pricing
programs and volume discounts, the loss of customers, market acceptance of the
Company's products, product obsolescence and general economic conditions. In
addition, the Company, from time to time, has entered into contracts to engineer
a specific solution based on modifications to the Company's standard products (a
"development contract"). The Company's gross margins from development contract
revenues are typically lower than the Company's gross margins from standard
product revenues. The Company intends to continue to enter into development
contracts and anticipates that the gross margins associated with development
contract revenues will continue to be lower than its gross margins on standard
product revenues. The Company expects research and development expenses to
continue to increase as the Company continues to develop products to serve its
markets, all of which are subject to rapidly changing technology, frequent
product performance improvements and evolving industry standards. The ability to
deliver superior technological performance on a timely and cost effective basis
is a critical factor in securing design wins for future generations of defense
electronics and medical imaging systems. Significant research and development
spending by the Company does not ensure that the Company's computer systems will
be designed into a customer's system. Because future production orders are
usually contingent upon securing a design win, the Company's operating results
may fluctuate due to either obtaining or failing to obtain design wins for
significant customer systems.

    The Company's quarterly results may be subject to fluctuations resulting
from the foregoing factors, as well as a number of other factors, including the
timing of significant orders, delays in completion of internal product
development projects, delays in shipping the Company's computer systems and
software programs, delays in acceptance testing by customers, a change in the
mix of products sold to the defense electronics and medical imaging markets,
production delays due to quality problems with outsourced components, shortages
of components, the timing of product line transitions and declines in quarterly
revenues from old generations of products following announcement of replacement
products containing more advanced technology. Another factor contributing to
fluctuations in quarterly results is the fixed nature of the Company's
expenditures on personnel, facilities and marketing programs. The Company's
expense levels for personnel, facilities and marketing programs are based, in
significant part, on the Company's expectations of future revenues on a
quarterly basis. If actual quarterly revenues are below management's
expectations, results of operations likely will be adversely affected. As a
result of the foregoing factors, the Company's operating results, from time to
time, may be below the expectations of public market analysts and investors,
which could have a material adverse effect on the price of the Company's Common
Stock.

    DEPENDENCE ON SUPPLIERS. Several components used in the Company's products
are currently obtained from sole source suppliers. Mercury is dependent on LSI
Logic Corporation for four custom designed ASICs, on Analog Devices for its
SHARC processors, on International Business Machines Corporation for ball grid
array packaging, on Motorola for some of its PowerPC processors and on Intel for
its i860 processors. IBM may terminate its contract with the Company without
cause upon thirty days notice and may cease offering products to the Company
upon


                                       11
<PAGE>   12


sixty days notice. Analog Devices may discontinue or modify any product upon 180
days notice and LSI Logic may discontinue any product upon 180 days notice. If
LSI Logic, Analog Devices, IBM, Motorola or Intel were to limit or reduce the
sale of such components to the Company, or if these or other suppliers to the
Company were to experience financial difficulties or other problems which
prevented them from supplying the Company with the necessary components, such
events could have a material adverse effect on the Company's business, financial
condition and results of operations. These sole source suppliers are subject to
quality and performance issues, materials shortages, excess demand, reduction in
capacity and other factors that may disrupt the flow of goods to the Company or
its customers and thereby adversely affect the Company's business and customer
relationships. The Company has no guaranteed supply arrangements with its
suppliers and there can be no assurance that its suppliers will continue to meet
the Company's requirements. If the Company's supply arrangements are
interrupted, there can be no assurance that the Company would be able to find
another supplier on a timely or satisfactory basis. Any shortage or interruption
in the supply of any of the components used in the Company's products, or the
inability of the Company to procure these components from alternate sources on
acceptable terms could have a material adverse effect on the Company's business,
financial condition and results of operations. There can be no assurance that
severe shortages of components will not occur in the future. Such shortages
could increase the cost or delay the shipment of the Company's products, which
could have a material adverse effect on the Company's business, financial
condition and results of operations. Significant increases in the prices of
these components would also materially adversely affect the Company's financial
performance since the Company may not be able to adjust product pricing to
reflect the increase in component costs. The Company could incur set-up costs
and delays in manufacturing should it become necessary to replace any key
vendors due to work stoppages, shipping delays, financial difficulties or other
factors and, under certain circumstances, these costs and delays could have a
material adverse effect on the Company's business, financial condition and
results of operations.

    DEPENDENCE UPON KEY PERSONNEL AND SKILLED EMPLOYEES. The Company is largely
dependent upon the skills and efforts of its senior management, particularly
James R. Bertelli, its President and Chief Executive Officer, as well as its
managerial, sales and technical employees. None of the senior management or
other key employees of the Company is subject to any employment contract or
noncompetition agreement. The Company maintains key-man life insurance on Mr.
Bertelli and certain other senior managers. The loss of services of any of its
executives or other key personnel could have a material adverse effect on the
Company's business, financial condition and results of operations. The Company's
future success will depend to a significant extent on its ability to attract,
train, motivate and retain highly skilled technical professionals, particularly
project managers, engineers and other senior technical personnel. The Company
believes that there is a shortage of, and significant competition for, technical
development professionals with the skills and experience necessary to perform
the services offered by the Company. The Company's ability to maintain and renew
existing engagements and obtain new business depends, in large part, on its
ability to hire and retain technical personnel with the skills that keep pace
with continuing changes in industry standards, technologies and client
preferences. The inability to hire additional qualified personnel could impair
the Company's ability to satisfy its growing client base, requiring an increase
in the level of responsibility for both existing and new personnel. There can be
no assurance that the Company will be successful in retaining current or future
employees.

    DEPENDENCE ON MEDICAL IMAGING MARKET; POTENTIAL ADVERSE EFFECT OF HEALTH
CARE REFORM. Sales of the Company's computer systems to the medical imaging
market accounted for approximately 14%, 13%, and 11% of the Company's revenues
in fiscal 1999, 1998, and 1997, respectively. These customers are original
equipment manufacturers ("OEMs") of medical imaging devices and, as a result,
any change in the demand for such devices which renders any of the Company's
products unnecessary or obsolete, or any change in the technology in such
devices, could have a material adverse effect on the Company's business,
financial condition and results of operations. Such OEM customers, the end-users
of their products and the health care industry generally are subject to
extensive federal, state and local regulation in the U.S. as well as in other
countries. Changes in applicable health care laws and regulations or new
interpretations of existing laws and regulations could have a material adverse
effect on such customers or end-users. There can be no assurance that future
health care or budgetary legislation or other changes in the administration or
interpretation of governmental health care programs both in the U.S. and abroad
will not have a material adverse effect on the Company's business, financial
condition or results of operations.

    RISK OF ENTRY INTO NEW MARKETS. The Company's expansion strategy includes
developing new products and entering new markets. The Company's ability to
compete in new markets will depend upon a number of factors including, without
limitation, the Company's ability to create demand for its products in such
markets, its ability to manage its growth effectively, the quality of its
products, its ability to respond to changes in its customers' businesses by
updating existing products and introducing, in a timely fashion, products which
meet the needs of its


                                       12
<PAGE>   13


customers and the ability of the Company to respond rapidly to technological
change. The failure of the Company to do any of the foregoing could result in a
material adverse effect on its business, financial condition and results of
operations. In addition, the Company may face competition in these new markets
from various companies which may have substantially greater research and
development resources, marketing and financial resources, manufacturing
capability and customer support organizations than those of the Company.

        RISKS ASSOCIATED WITH INTERNATIONAL OPERATIONS. The Company markets and
sells its products in certain international markets, and the Company has
established offices in the United Kingdom, Japan and France. Foreign revenue is
based on the country in which the legal subsidiary is domiciled. Foreign
revenue and long-lived assets represent less than 10% of the Company's total
revenue and long-lived assets for the fiscal years ended June 30, 1999, 1998,
and 1997, respectively. If revenues generated by foreign activities are not
adequate to offset the expense of establishing and maintaining these foreign
subsidiaries and activities, the Company's business, financial condition and
results of operations could be materially adversely affected. In addition,
there are certain risks inherent in transacting business internationally, such
as changes in applicable laws and regulatory requirements, export and import
restrictions, export controls relating to technology, tariffs and other trade
barriers, less favorable intellectual property laws, difficulties in staffing
and managing foreign operations, longer payment cycles, problems in collecting
accounts receivable, political instability, fluctuations in currency exchange
rates, expatriation controls and potential adverse tax consequences, any of
which could adversely impact the success of the Company's international
activities. In the recent past, the financial markets in Asia have experienced
significant turmoil. There can be no assurance that such turmoil in the Asian
financial markets will not negatively affect the sales by the Company to that
region. A portion of the Company's revenues from sales to foreign entities,
including foreign governments, is in the form of foreign currencies. There can
be no assurance that one or more of such factors will not have a material
adverse effect on the Company's future international activities and,
consequently, on the Company's business, financial condition or results of
operations.

    TECHNOLOGICAL CHANGES; RISK OF DESIGN-IN PROCESS. The Company's future
success will depend in part on its ability to enhance its current products and
to develop new products on a timely and cost-effective basis in order to respond
to technological developments and changing customer needs. The defense
electronics market, in particular, demands constant technological improvements
as a means of gaining military advantage. Military planners historically have
funded significantly more design projects than actual deployments of new
equipment, and those systems which are deployed tend to contain the components
of the subcontractors selected to participate in the design process. In order to
participate in the design of new defense electronics systems, the Company must
be able to demonstrate its ability to deliver superior technological performance
on a timely and cost-effective basis. There can be no assurance that the Company
will be able to secure an adequate number of defense electronics design wins in
the future, that the equipment in which the Company's products are intended to
function eventually will be deployed in the field, or that the Company's
products will be included in such equipment if it eventually is deployed.

    Customers in the medical imaging market also seek technological improvements
through product enhancements and new generations of products. The Company
believes that medical imaging machines in which the Company's computers are
installed have a long product life cycle. Medical equipment OEMs historically
have selected certain suppliers whose products have been included in the OEMs'
machines for a significant portion of the products' life cycle. There can be no
assurance that the Company will be selected to participate in the future design
of any medical imaging equipment, or that, if selected, the Company will
generate any revenues for such design work. Failure to participate in future
designs of medical imaging equipment could have a material adverse effect on the
Company's business, financial condition and results of operations.

    The design-in process is typically lengthy and expensive, and there can be
no assurance that the Company will be able to continue to meet the product
specifications of its customers in a timely and adequate manner. In addition,
any failure by the Company to anticipate or respond adequately to changes in
technology and customer preferences, or any significant delay in product
developments or introductions, could have a material adverse effect on the
Company's business, financial condition and results of operations. Because of
the complexity of its products, the Company has experienced delays from time to
time in completing products on a timely basis. If the Company is unable to
design, develop or introduce competitive new products on a timely basis, its
future operating results would be adversely affected. There can be no assurance
that the Company will be successful in developing new products or enhancing its
existing products on a timely or cost-effective basis, or that such new products
or product enhancements will achieve market acceptance.

    COMPETITION. The markets for the Company's products are highly competitive
and are characterized by rapidly


                                       13
<PAGE>   14


changing technology, frequent product performance improvements and evolving
industry standards. See "Item 1. Business - Competition."

    LIMITED PROTECTION OF PROPRIETARY RIGHTS; POTENTIAL INFRINGEMENT OF THIRD
PARTY RIGHTS. There can be no assurance that the Company's means of protecting
its proprietary rights in the U.S. or abroad will be adequate, or that others
will not develop technologies similar or superior to the Company's technology or
design around the proprietary rights owned by the Company. In addition, there
can be no assurance that others will not assert claims of infringement in the
future or that, if made, such claims will not be successful. See "Item 1.
Business - Intellectual Property and Proprietary Rights."

    POTENTIAL ACQUISITIONS. In the normal course of its business, the Company
evaluates potential acquisitions of businesses, products and technologies that
could complement or expand the Company's business. In the event the Company were
to identify an appropriate acquisition candidate, there is no assurance that the
Company would be able to successfully negotiate the terms of any such
acquisition, finance such acquisition and integrate such acquired business,
products or technologies into the Company's existing business and operations.
Furthermore, the integration of an acquired business could cause a diversion of
management time and resources. In addition, there can be no assurance that any
acquisition of new technology will lead to the successful development of new
products, or that any such new products, if developed, will achieve market
acceptance or prove to be profitable. There can be no assurance that a given
acquisition, when consummated, would not materially adversely affect the
Company's business, financial condition or results of operations. If the Company
proceeds with one or more significant acquisitions in which the consideration
consists of cash, a substantial portion of the Company's available cash could be
used to consummate the acquisitions. If the Company consummates one or more
significant acquisitions in which the consideration consists of stock, or is
financed with the net proceeds of the issuance of stock, stockholders of the
Company could suffer a significant dilution of their interests in the Company.

    YEAR 2000 COMPLIANCE. The Company uses a significant number of computer
software programs and operating systems in its internal operations, including
applications used in manufacturing, product development, financial business
systems and various administrative functions. To the extent that these software
applications contain source code that is unable to appropriately interpret the
upcoming calendar year "2000," some level of modification or even possibly
replacement of such source code or applications will be necessary. The Company
is still in the preliminary stages of analyzing its software applications and,
to the extent they are not fully "Year 2000" compliant, there can be no
assurance that the costs necessary to update software, or potential systems
interruptions, would not have a material adverse effect on the Company's
business, financial condition or results of operations. See "- Year 2000
Compliance."

ITEM 2.  PROPERTIES

    The Company's headquarters consist of two buildings approximating 187,000
square feet of space in Chelmsford, Massachusetts. These two buildings were
purchased by the Company during fiscal 1999. The Company also maintains offices
near Los Angeles and San Jose, California, and in Lowell, Massachusetts, Dallas,
Texas, Chanhassen, Minnesota, Madison, Wisconsin, Port St Lucie, Florida,
Bellevue, Washington and Vienna, Virginia and has international offices in the
United Kingdom, France and Japan.

ITEM 3.  LEGAL PROCEEDINGS

    To the Company's knowledge, there are no pending legal proceedings, which
are, material to the Company or its business to which it is a party or to which
any of its properties is subject.

ITEM 4. SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS

    No matters were submitted to a vote of stockholders during the fourth
quarter of the fiscal year ended June 30, 1999.


                                       14
<PAGE>   15


                                     PART II

ITEM 5. MARKET FOR REGISTRANT'S COMMON EQUITY AND RELATED STOCKHOLDERS' MATTERS

    The information contained under the heading "Market Information" on page 27
of the Company's Annual Report to Stockholders for the fiscal year ended June
30, 1999 is incorporated herein by reference and is filed herewith as Exhibit
13.1.

ITEM 6.  SELECTED CONSOLIDATED FINANCIAL DATA

     The information contained under the heading "Selected Financial Data" on
page 17 of the Company's Annual Report to Stockholders for the fiscal year ended
June 30, 1999 is incorporated herein by reference and is filed herewith as
Exhibit 13.1.

ITEM 7.  MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS
         OF OPERATIONS

    The information contained under the heading "Management's Discussion and
Analysis of Financial Condition and Results of Operations" on pages 18 through
26 of the Company's Annual Report to Stockholders for the fiscal year ended June
30, 1999 is incorporated herein by reference and is filed herewith as Exhibit
13.1. This information should be read in conjunction with the related
consolidated financial statements incorporated by reference under Item 8.

ITEM 7(A)  QUANTITATIVE AND QUALITATIVE DISCLOSURE ABOUT MARKET RISK

    The information contained under the heading "Quantitative and Qualitative
Disclosure About Market Risk" on page 26 of the Company's Annual Report to
Stockholders for the fiscal year ended June 30, 1999 is incorporated herein by
reference and is filed herewith as Exhibit 13.1

ITEM 8.  FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA

    The information contained in the consolidated financial statements,
notes to consolidated financial statements, report of independent accountants
and supplementary information (unaudited) on pages 28 through 47 of the
Company's Annual Report to Stockholders for the fiscal year ended June 30, 1999
is incorporated herein by reference and is filed herewith as Exhibit 13.1.

ITEM 9.  CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING AND
         FINANCIAL DISCLOSURE

    None.

                                    PART III

ITEM 10.  DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT

    The information required by this item is incorporated herein by reference to
the Company's Proxy Statement.

ITEM 11.  EXECUTIVE COMPENSATION

    The information required by this item is incorporated herein by reference to
the Company's Proxy Statement.

ITEM 12.  SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

    The information required by this item is incorporated herein by reference to
the Company's Proxy Statement.

ITEM 13.  CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS

       The Company had loaned James R. Bertelli, President of the Company, an
aggregate of $200,000, of which $150,000 accrued interest at an annual rate of
9.75% and $50,000 accrued interest at an annual rate of 10.5%. In addition, the
Company had loaned Albert Belle Isle, a Director of the Company, an aggregate of
$125,000, of which $100,000 accrued interest at an annual interest rate of 8%
and $25,000 accrued interest at 9.25%. The notes evidencing such obligations of
Mr. Bertelli and Dr. Belle Isle were paid in full in October, 1998.


                                       15
<PAGE>   16


                                     PART IV

ITEM 14. EXHIBITS, FINANCIAL STATEMENT SCHEDULES, AND REPORTS ON FORM 8-K

(a)  FINANCIAL STATEMENTS, SCHEDULES AND EXHIBITS

    The financial statements, schedule, and exhibits listed below are included
in or incorporated by reference as part of this report:

1.  Financial statements:

    Report of Independent Accountants
    Consolidated Balance Sheets as of June 30, 1999 and 1998
    Consolidated Statements of Operations for the years ended June 30, 1999,
      1998, and 1997
    Consolidated Statements of Stockholders' Equity for the years ended June 30,
      1999, 1998, and 1997
    Consolidated Statements of Cash Flows for the years ended June 30, 1999,
      1998, and 1997
    Notes to Consolidated Financial Statements

2.  Financial Statement Schedule:


II.  Valuation and Qualifying Accounts

                         MERCURY COMPUTER SYSTEMS, INC.
                 SCHEDULE II - VALUATION AND QUALIFYING ACCOUNTS
                FOR THE YEARS ENDED JUNE 30, 1999, 1998, AND 1997
                                 (IN THOUSANDS)

                BALANCE AT                                     BALANCE
                BEGINNING       CHARGES TO                     AT END
                OF PERIOD       EXPENSES       DEDUCTIONS      OF PERIOD
                ---------       --------       ----------      ---------
     Allowance for Doubtful Accounts

     1999         $218            $249             91            $376
     1998          119              99            $--             218
     1997           80              40            $ 1             119

                BALANCE AT                                     BALANCE
                BEGINNING       CHARGES TO                     AT END
                OF PERIOD       EXPENSES       DEDUCTIONS      OF PERIOD
                ---------       --------       ----------      ---------
     Inventory Reserve

     1999        $1,857          $2,786          $1,604         $3,039
     1998         1,723           1,583           1,449          1,857
     1997         1,246             504              27          1,723

    Charges to expenses for inventory are due to program cancellations,
engineering change orders and obsolescence. Deductions are recorded when the
inventory is written off. The Company wrote off $1,604,000 and $1,449,000 during
the years ended June 30, 1999 and 1998, respectively, in inventory relating
primarily to engineering change orders and obsolescence.

                      REPORT OF INDEPENDENT ACCOUNTANTS ON
                          FINANCIAL STATEMENT SCHEDULE



To the Board of Directors
of Mercury Computer Systems, Inc.

Our audits of the consolidated financial statements referred to in our report
dated July 29, 1999, except for the information in the first and second
paragraph of Note L as to which date is August 27, 1999 and September 1, 1999,
respectively, in the Annual Report to Shareholders of Mercury Computer Systems,
Inc. (which report and consolidated financial statements are incorporated by
reference in this Annual Report on Form 10-K) also included an audit of the
financial statement schedule listed in item 14 (a)(2) of this Form 10-K. In our
opinion, the financial statement schedule presents fairly, in all material
respects, the information set forth therein when read in conjunction with the
related consolidated financial statements.


PricewaterhouseCoopers LLP


Boston, Massachusetts
July 29, 1999

3.  Exhibits:

     Exhibits required by Item 601 of Regulation S-K are listed in the Exhibit
Index on page 18, which is incorporated herein by reference.

(b)  Reports on Form 8-K

    None.


                                       16
<PAGE>   17


                                   SIGNATURES

    Pursuant to the requirements of Section 13 or 15(d) of the Securities
Exchange Act of 1934, the registrant has duly caused this report to be signed on
its behalf by the undersigned, thereunto duly authorized, in Chelmsford,
Massachusetts, on September 14, 1999.

                                          MERCURY COMPUTER SYSTEMS, INC.

                                          By: /s/ G. MEAD WYMAN
                                          --------------------------------------
                                          G. MEAD WYMAN
                                          SENIOR VICE PRESIDENT, CHIEF FINANCIAL
                                          OFFICER AND TREASURER

    Pursuant to the requirements of the Securities Exchange Act of 1934, this
report has been signed below by the following persons on behalf of the
registrant and in the capacities and on the dates indicated.


    SIGNATURE                       TITLE(S)                    DATE

/s/ JAMES R. BERTELLI     President, Chief Executive Officer  September 14, 1999
- ------------------------  and Director (principal executive
JAMES R. BERTELLI         officer)

/s/ G. MEAD WYMAN         Senior Vice President, Chief        September 14, 1999
- ------------------------  Financial Officer and Treasurer
G. MEAD WYMAN             (principal financial and
                          accounting officer)

/s/ GORDON B. BATY        Director                            September 14, 1999
- ------------------------
GORDON B. BATY

/s/ R. SCHORR BERMAN      Director                            September 14, 1999
- ------------------------
R. SCHORR BERMAN

/s/ ALBERT P. BELLE ISLE  Director                            September 14, 1999
- ------------------------
ALBERT P. BELLE ISLE

/s/ SHERMAN N. MULLIN     Director                            September 14, 1999
- ------------------------
SHERMAN N. MULLIN

/s/ MELVIN SALLEN         Director                            September 14, 1999
- ------------------------
MELVIN SALLEN


                                       17
<PAGE>   18


                                  EXHIBIT INDEX

ITEM NO.   DESCRIPTION OF EXHIBIT

3.1        Restated Articles of Organization. (incorporated herein by reference
            to Exhibit 3.1 of the Company's Registration Statement on Form S-1
            (File No. 333-41139))
3.2        Bylaws. (incorporated herein by reference to Exhibit 3.2 of the
            Company's Registration Statement on Form S-1 (File No. 333-41139))
3.3        Articles of Amendment to Articles of Organization. (incorporated
            herein by reference to Exhibit 3.3 of the Company's Registration
            Statement on Form S-1 (File No. 333-41139))
4.1        Form of Stock Certificate. (incorporated herein by reference to
            Exhibit 4.1 of the Company's Registration Statement on Form S-1
            (File No. 333-41139))
10.1       1982 Stock Option Plan, as amended. (incorporated herein by reference
            to Exhibit 10.1 of the Company's Registration Statement on Form S-1
            (File No. 333-41139))
10.2       1991 Stock Option Plan, as amended. (incorporated herein by reference
            to Exhibit 10.2 of the Company's Registration Statement on Form S-1
            (File No. 333-41139))
10.3       1993 Stock Option Plan for Non-Employee Directors. (incorporated
            herein by reference to Exhibit 10.3 of the Company's Registration
            Statement on Form S-1 (File No. 333-41139))
10.4       1997 Stock Option Plan. (incorporated herein by reference to Exhibit
            10.4 of the Company's Registration Statement on Form S-1 (File No.
            333-41139))
10.5       1997 Stock Purchase Plan. (incorporated herein by reference to
            Exhibit 10.5 of the Company's Registration Statement on Form S-1
            (File No. 333-41139))
10.6       Purchase and Sale Agreement, dated November 8, 1996 between Corcoran
            Chelmsford & Associates and Northland Development Corporation.
            (incorporated herein by reference to Exhibit 10.7 of the Company's
            Registration Statement on Form S-1 (File No. 333-41139))
10.7#      Term Purchase Agreement, dated July 25, 1995 between the Company and
            Analog Devices, Inc. (incorporated herein by reference to Exhibit
            10.8 of the Company's Registration Statement on Form S-1 (File No.
            333-41139))
10.8#      Risk Reproduction Agreement, dated March 20, 1996, between the
            Company and LSI Logic Corporation. (incorporated herein by reference
            to Exhibit 10.9 of the Company's Registration Statement on Form S-1
            (File No. 333-41139))
10.9#      Purchase Offer Agreement for OEM Manufacturer, dated February 16,
            1995, between the Company & IBM Microelectronics Division.
            (incorporated herein by reference to Exhibit 10.10 of the Company's
            Registration Statement on Form S-1 (File No. 333-41139))
10.10      Quitclaim Deed, dated October 1, 1997, executed by Corcoran
            Chelmsford & Associates Limited Partnership. (incorporated herein by
            reference to Exhibit 10.15 of the Company's Registration Statement
            on Form S-1 (File No. 333-41139))
10.11*     1998 Stock Option Plan
13.1*      Pages 17 through 47 of the 1999 Annual Report to Stockholders of
           Mercury Computer Systems, Inc., a copy of which is furnished for the
           information of the Securities and Exchange Commission. Portions of
           the Annual Report not incorporated herein by reference are not deemed
           "filed" with the Commission.
21.1*      Subsidiaries of the Registrant
23.1*      Consent of PricewaterhouseCoopers L.L.P.
27.1*      Financial Data Schedule.

*  Filed with this Form 10-K.   #  Confidential treatment granted.


                                       18

<PAGE>   1


                                                                    EXHIBIT 10.1

                         MERCURY COMPUTER SYSTEMS, INC.
                             1998 STOCK OPTION PLAN
                           FOR NON-EMPLOYEE DIRECTORS

        1.      PURPOSE
        The purpose of this Mercury Computer Systems, Inc. 1998 Stock Option
Plan for Non-Employee Directors (the "Plan") is to attract and retain the
services of experienced and knowledgeable independent directors who are not
employees (sometimes referred to herein collectively as "Participants") of
Mercury Computer Systems, Inc. ("Mercury") for the benefit of Mercury and its
stockholders and to provide additional incentive for such Participants to
continue to work in the best interests of Mercury and its stockholders through
continuing ownership of its common stock.

        2.      SHARES SUBJECT TO THE PLAN
        The total number of shares of common stock, par value $.01 per share
("Shares"), of Mercury for which options may be granted under the Plan shall not
exceed 50,000 in the aggregate, subject to adjustment in accordance with Section
9 hereof.

        3.      ELIGIBILITY; GRANT OF OPTION
        On September 30 of each of 1998, 1999, 2000, 2001 and 2002, each person
who is then a member of the Board of Directors of Mercury (the "Board") and who
is not then an employee of Mercury or any subsidiary shall be granted an option
to acquire the Formula Number of Shares under the Plan. Any options granted
prior to stockholder approval of this Plan shall become effective as of their
date of grant only upon stockholder approval of this Plan in accordance with
Section 13 hereof. The options shall be non-qualified options not intended to
meet the requirements of Section 422 of the Internal Revenue Code of 1986, as
amended (the "Code").

        The Formula Number shall be that number equal to one percent (1%) of the
net income of Mercury for the most recent fiscal year ending prior to the grant
date as shown on Mercury's audited financial statements divided by the fair
market value of a share of Mercury common stock, as determined under Section 5
hereof, on the first day of such most recent fiscal year,


                                       19
<PAGE>   2


divided by the number of the non-employee Directors of Mercury granted options
hereunder on such grant date. No fractional shares shall be issued.

        4.      OPTION AGREEMENT
        Each option granted under the Plan shall be evidenced by an option
agreement (the "Agreement") duly executed on behalf of Mercury and by the
director to whom such option is granted, which Agreements shall comply with and
be subject to the terms and conditions of the Plan.

        5.      OPTION EXERCISE PRICE
        Subject to the provisions of Section 9 hereof, the option exercise price
for an option granted under the Plan shall be the fair market value of the
Shares of the common stock of Mercury covered by the option on the date of grant
of the option. For the purposes hereof, the fair market value of the Shares of
the common stock of Mercury shall be determined as follows. If such shares are
then listed on any national securities exchange, the fair market value shall be
the mean between the high and low sales prices, if any, on the largest such
exchange on the date of the grant of the option or, if none, shall be determined
by taking a weighted average of the means between the highest and lowest sales
prices on the nearest date before and the nearest date after the date of grant
in accordance with Treasury Regulations Section 25.2512-2. If the shares are not
then listed on any such exchange, the fair market value of such shares shall be
the mean between the high and low sales prices, if any, as reported in the
National Association of Securities Dealers Automated Quotation System National
Market System ("NASDAQ/NMS") for the date of the grant of the option, or, if
none, shall be determined by taking a weighted average of the means between the
highest and lowest sales on the nearest date before and the nearest date after
the date of grant in accordance with Treasury Regulations Section 25.2512-2. If
the shares are not then either listed on any such exchange or quoted in
NASDAQ/NMS, the fair market value shall be the mean between the average of the
"Bid" and the average of the "Ask" prices, if any, as reported in the National
Daily Quotation Service for the date of the grant of the option, or, if none,
shall be determined by taking a weighted average of the means between the
highest and lowest sales prices on the nearest date before and the nearest date
after the date of grant in accordance with Treasury Regulations Section
25.2512-2. If the fair market value cannot be determined under the preceding
three sentences, it shall be determined by the Company's independent auditors.


                                       20
<PAGE>   3


6.      TIME AND MANNER OF EXERCISE OF OPTION
        (a) Options granted under the Plan shall, subject to the provisions of
Section 7, be exercisable as provided in this Section 6(a). The options granted
under this Plan shall vest 1/3 on each of the first, second, and third
anniversaries of the date of grant. Following the third anniversary of the date
of grant, all options granted pursuant to a particular grant shall be
exercisable in full.

        (b) To the extent that the right to exercise an option has accrued and
is in effect, the option may be exercised in full at one time or in part from
time to time by giving written notice, signed by the person or persons
exercising the option, to Mercury, stating the number of Shares with respect to
which the option is being exercised, accompanied by payment in full for such
Shares, which payment must be in cash or certified check payable to the order of
the Company; provided, however, that there shall be no such exercise at any one
as to fewer than Two Hundred Fifty (250) Shares or all of the remaining Shares
then purchasable by the person or persons exercising the option, if fewer than
Two Hundred Fifty (250) Shares. Upon such exercise, delivery of a certificate
for paid-up non- assessable Shares shall be made at the principal Massachusetts
office of Mercury to the person or persons exercising the option at such time,
during ordinary business hours, not more than thirty (30) days from the date of
receipt of the notice by Mercury, as shall be designated in such notice, or at
such time, place and manner as may be agreed upon by Mercury and the person or
persons exercising the option.

        7.      TERM OF OPTIONS
        (a) Each option shall expire ten (10) years from the date of the
granting thereof, but shall be subject to earlier termination as herein
provided.

        (b) In the event of the death of an optionee, the option granted to such
optionee may be exercised, to the extent the optionee was entitled to do so on
the date of such

        (c) optionee's death, by the estate of such optionee or by any person or
persons who acquired the right to exercise such

        (d) option by bequest or inheritance or otherwise by reason of the death
of such optionee. Such option may be exercised at any time within one (1) year
after the date of death of such optionee, at which time the option shall
terminate, or prior to the date on which the option otherwise expires by its
terms, whichever is earlier.


                                       21
<PAGE>   4


        (c) In the event that an optionee ceases to be a director of Mercury,
the option granted to such optionee may be exercised by him, but only to the
extent that under Section 6 hereof the right to exercise the option has accrued
and is in effect. Such option may be exercised at any time within one (1) month
after the date such optionee ceases to be a director of Mercury, at which time
the option shall terminate, but in any event prior to the date on which the
option expires by its terms, whichever is earlier, unless termination as a
director (a) was by Mercury for cause, in which case the option shall terminate
immediately at the time the optionee ceases to be a director of Mercury, (b) was
because the optionee has become disabled (within the meaning of Section 22(e)(3)
of the Code), or (c) was by reason of the death of the optionee. In the case of
death, see Section 7(b) of the Plan. In the case of disability, the option may
be exercised, to the extent then exercisable under Section 6 hereof, at any time
within one (1) year after the date of termination of the optionee's directorship
with Mercury, at which time the option shall terminate, but in any event prior
to the date on which the option otherwise expires by its terms, whichever is
earlier.

        8. OPTIONS NOT TRANSFERABLE
        The right of any optionee to exercise an option granted to him under the
Plan shall not be assignable or transferable by such optionee otherwise than by
will or the laws of descent and distribution, or pursuant to a qualified
domestic relations order as defined by the Code or Title I of the Employee
Retirement Income Security Act, or the rules thereunder. Any option granted
under the Plan shall be exercisable during the lifetime of such optionee only by
him. Any option granted under the Plan shall be null and void and without effect
upon the bankruptcy of the optionee, or upon any attempted assignment or
transfer, except as herein provided, including without limitation any purported
assignment, whether voluntary or by operation of law, pledge, hypothecation or
other disposition, attachment, trustee process or similar process, whether legal
or equitable, upon such option.

        9. ADJUSTMENTS UPON CHANGES IN CAPITALIZATION
        In the event that the outstanding Shares of the common stock of Mercury
are changed into or exchanged for a different number or kind of shares or other
securities of Mercury or of another corporation by reason of any reorganization,
merger, consolidation, recapitalization, reclassification, stock split-up,
combination of shares or dividends payable in capital stock, appropriate
adjustment shall be made in the number and kind of shares as to which
outstanding options, or portions thereof then unexercised, shall be exercisable,
to the end that the


                                       22
<PAGE>   5


proportionate interest of the optionee shall be maintained as before the
occurrence of such event, and such adjustment in outstanding options shall be
made without change in the total price applicable to the unexercised portion of
such options and with a corresponding adjustment in the option price per share.

        10. RESTRICTIONS ON ISSUE OF SHARES
        Notwithstanding the provisions of Section 6 hereof, Mercury may delay
the issuance of Shares covered by the exercise of any option and the delivery of
a certificate for such Shares until one of the following conditions shall be
satisfied:

                (i) the Shares with respect to which an option has been
exercised are at the time of the issue of such Shares effectively registered
under applicable Federal and state securities acts now in force or hereafter
amended; or

                (ii) counsel for Mercury shall have given an opinion, which
opinion shall not be unreasonably conditioned or withheld, that such Shares are
exempt from registration under applicable Federal and state securities acts now
in force or hereafter amended.

        It is intended that all exercises of options shall be effective.
Accordingly, Mercury shall use its best efforts to bring about compliance with
the above conditions within a reasonable time, except that Mercury shall be
under no obligation to cause a registration statement or a post-effective
amendment to any registration statement to be prepared at its expense solely for
the purpose of covering the issue of Shares in respect of which any option may
be exercised, except as otherwise agreed to by Mercury in writing.

11.     RIGHTS OF HOLDER ON PURCHASE FOR INVESTMENT; SUBSEQUENT REGISTRATION
        Unless the Shares to be issued upon exercise of an option granted under
the Plan have been effectively registered under the Securities Act of 1933, as
now in force or hereafter amended, Mercury shall be under no obligation to issue
any Shares covered by any option unless the person who exercises such option, in
whole or in part, shall give a written representation and undertaking to Mercury
which is satisfactory in form and scope to counsel to Mercury and upon which, in
the opinion of such counsel, Mercury may reasonably rely, that he is acquiring
the Shares issued to him pursuant to such exercise of the option for his own
account as an investment and


                                       23
<PAGE>   6


not with a view to, or for sale in connection with, the distribution of any such
Shares, and that he will make no transfer of the same except in compliance with
any rules and regulations in force at the time of such transfer under the
Securities Act of 1933, or any other applicable law, and that if Shares are
issued without such registration a legend to this effect may be endorsed upon
the securities so issued. In the event that Mercury shall, nevertheless, deem it
necessary or desirable to register under the Securities Act of 1933 or other
applicable statutes any Shares with respect to which an option shall have been
exercised, or to qualify any such Shares for exemption from the Securities Act
of 1933 or other applicable statutes, then Mercury shall take such action at its
own expense and may require from each optionee such information in writing for
use in any registration statement, prospectus, preliminary prospectus or
offering circular as is reasonably necessary for such purpose and may require
reasonable indemnity to Mercury and its officers and directors from such holder
against all losses, claims, damages and liabilities arising from such use of the
information so furnished and caused by any untrue statement of any material fact
therein or caused by the omission to state a material fact required to be stated
therein or necessary to make the statements therein not misleading in light of
the circumstances under which they were made.

        12.     LOANS PROHIBITED
Mercury shall not, directly or indirectly, lend money to an optionee or to any
person or persons entitled to exercise an option by reason of the death of an
optionee for the purpose of assisting him or them in the acquisition of Shares
covered by an option granted under the Plan.

        13.     APPROVAL OF STOCKHOLDERS
        The Plan shall be subject to approval by the vote of stockholders
holding at least a majority of the voting stock of Mercury voting in person or
by proxy at a duly held stockholders' meeting, or by written consent of all of
the stockholders, and shall take effect immediately as of its date of adoption
upon such approval.

        14.     EXPENSES OF THE PLAN
        All costs and expenses of the adoption and administration of the Plan
shall be borne by Mercury, and none of such expenses shall be charged to any
optionee.

        15.     TERMINATION AND AMENDMENT OF PLAN
        Unless sooner terminated as herein provided, the Plan shall terminate
ten (10) years from the date upon which the Plan was duly approved by the
stockholders. The Board may at any time terminate the Plan or make such
modification or amendment thereof as it deems advisable, provided however that,
except as provided in Section 9


                                       24
<PAGE>   7


hereof, no modification or amendment to the provisions of the Plan may be made
more than once every six (6) months other than to comport with changes in the
Code, the Employee Retirement Income Security Act, or the rules thereunder, if
the effect of such amendment or modification would be to change (i) the
requirements for eligibility under the Plan, (ii) the timing of the grants of
options to be granted under the Plan or the exercise price or vesting schedule
thereof, or (iii) the number of Shares subject to options to be granted under
the Plan either in the aggregate or to one director. Any amendment to the
provisions of the Plan which (i) materially increases the number of Shares which
may be subject to options granted under the Plan, (ii) materially increases the
benefits accruing to Participants under the Plan, or (iii) materially modifies
the requirement for eligibility to participate in the Plan, shall be subject to
approval by the stockholders of Mercury obtained in the manner stated in Section
13 hereof. Termination or any modification or amendment of the Plan shall not,
without the consent of an optionee, affect his rights under an option previously
granted to him.

        16.     LIMITATION OF RIGHTS IN THE OPTION SHARES
        An optionee shall not be deemed for any purpose to be a stockholder of
Mercury with respect to any of the options except to the extent that the option
shall have been exercised with respect thereto and, in addition, a certificate
shall have been issued theretofore and delivered to the optionee.

        17.     NOTICES
        Any communication or notice required or permitted to be given under the
Plan shall be in writing, and mailed by registered or certified mail or
delivered by hand, if to Mercury, to its principal place of business, attention:
President, and, if to an optionee, to the address as appearing on the records of
Mercury.

        18.     COMPLIANCE WITH RULE 16b-3
        It is the intention of Mercury that the Plan comply in all respects with
Rule 16b-3 promulgated under Section 16(b) of the Securities Exchange Act of
1934 (the "Act") and that Participants remain disinterested persons for purposes
of administering other employee benefit plans of Mercury and having transactions
under such other plans be exempt from Section 16(b) of the Act. Therefore, if
any Plan provision is found not to be in compliance with Rule 16b-3 or if any
Plan provisions would disqualify Participants from remaining disinterested
persons, that provisions shall be deemed null and void, and in all events the
Plan shall be construed in favor of its meeting the requirements of Rule 16b-3.


                                       25

<PAGE>   1
                                                                EXHIBIT 13.1

                                             MERCURY COMPUTER SYSTEMS, INC.   17




SELECTED FINANCIAL DATA


The following table summarizes certain historical consolidated financial data,
which should be read in conjunction with the Company's financial statements and
related notes included elsewhere herein (in thousands except per share data):

<TABLE>
<CAPTION>

YEAR ENDED JUNE 30,                                 1999        1998        1997        1996        1995

STATEMENT OF OPERATIONS DATA:
<S>                                               <C>          <C>         <C>         <C>         <C>
Revenues                                          $106,571     $85,544     $64,574     $58,300     $54,323
Cost of revenues                                    34,237      30,084      22,034      24,688      21,221
                                                  --------     -------     -------     -------     -------
    Gross profit                                    72,334      55,460      42,540      33,612      33,102
                                                  --------     -------     -------     -------     -------
Operating expenses:
    Selling, general and administrative             33,002      27,879      22,631      16,927      15,798
    Research and development                        20,709      14,476      12,837       9,776       8,586
                                                  --------     -------     -------     -------     -------
    Total operating expenses                        53,711      42,355      35,468      26,703      24,384
                                                  --------     -------     -------     -------     -------
Income from operations                              18,623      13,105       7,072       6,909       8,718
                                                  --------     -------     -------     -------     -------
Interest income, net                                 1,285       1,084         560         548         240
Other income (expense), net                            185         (30)        (88)        (77)         22
                                                  --------     -------     -------     -------     -------
Income before income taxes                          20,093      14,159       7,544       7,380       8,980
Provision for income taxes                           6,631       5,428       2,933       2,952       2,636
                                                  --------     -------     -------     -------     -------
Net income                                        $ 13,462     $ 8,731     $ 4,611     $ 4,428     $ 6,344
                                                  ========     =======     =======     =======     =======
Net income per common share:
    Basic                                         $   1.32     $  1.21     $  0.90     $  0.88     $  1.27
    Diluted                                       $   1.25     $  0.94     $  0.58     $  0.55     $  0.80
Weighted average number of common and
    common equivalent shares outstanding(1):
    Basic                                           10,168       7,235       5,141       5,050       4,992
    Diluted                                         10,800       9,270       7,897       7,983       7,977

June 30,                                              1999        1998        1997        1996        1995

BALANCE SHEET DATA:
Working capital                                   $ 42,312     $32,794     $27,547     $23,554     $20,156
Total assets                                        97,511      73,569      44,848      33,264      33,543
Convertible preferred stock(2)                          --          --       1,200       1,200       1,200
Total stockholders' equity                          77,440      61,040      33,322      28,529      24,003
</TABLE>

(1) See Note B of Notes to Consolidated Financial Statements for an explanation
of the determination of the weighted average common and common equivalent shares
used to compute basic and diluted net income per common share.
(2) Upon completion of the Company's initial public offering on January 29,
1998, the Company's series A convertible preferred stock was converted into
2,556,792 shares of common stock.



<PAGE>   2


18   MERCURY COMPUTER SYSTEMS, INC.


MANAGEMENT'S DISCUSSION AND ANALYSIS OF
FINANCIAL CONDITION AND RESULTS OF OPERATIONS


In this report, as well as oral statements made by the Company, that are
prefaced with the words "may," "will," "expect," "anticipate," "continue,"
"estimate," "project," "intend," "designed" and similar expressions, are
intended to identify forward-looking statements regarding events, conditions and
financial trends that may affect the Company's future plans of operations,
business strategy, results of operations and financial position. These
statements are based on the Company's current expectations and estimates as to
prospective events and circumstances about which the Company can give no firm
assurance. Further, any forward-looking statement speaks only as of the date on
which such statement is made, and the Company undertakes no obligation to update
any forward-looking statement to reflect events or circumstances after the date
on which such statement is made. As it is not possible to predict every new
factor that may emerge, forward-looking statements should not be relied upon as
a prediction of actual future financial condition or results. These
forward-looking statements, like any forward-looking statements, involve risks
and uncertainties that could cause actual results to differ materially from
those projected or unanticipated. Such risks and uncertainties include certain
factors identified in the following discussion as well as the risk factors
reported in the Company's Form 10-K.


OVERVIEW
Mercury designs, manufactures and markets high performance, real-time digital
signal processing computer systems that transform sensor-generated data into
information which can be displayed as images for human interpretation or
subjected to additional computer analysis. These multicomputer systems are
heterogeneous and scalable, allowing them to accommodate several microprocessor
types and to scale from a few to hundreds of microprocessors within a single
system.
         During the past several years, the majority of the Company's revenues
has been generated from sales of its products to the defense electronics market,
generally for use in intelligence gathering electronic warfare systems. The
Company's activities in this area have focused on the proof of concept,
development and deployment of advanced military applications in radar, sonar and
airborne surveillance. Medical diagnostic imaging is the other primary market
currently served by the Company. Mercury's computer systems are embedded in
Magnetic Resonance Imaging ("MRI") and Computed Tomography ("CT") machines. The
remaining revenues are derived from computer systems used in such commercial
applications as baggage scanning, seismic analysis and automatic testing
equipment, and from sales of the Company's shared storage products,
SANergy(R) software and related products and services.
         Mercury uses a direct sales force to sell its computer systems to the
defense electronics markets in the U.S., Japan, the United Kingdom and France.
Defense electronics sales to other countries are achieved through distributors.
The Company also uses a direct sales force to sell its computer systems to the
U.S. and international medical imaging markets. The Company uses various
distribution channels for sales of shared storage products to the broadcast and
post-production industry. The Company sells its products to OEMs, value added
re-sellers and end-users. Over the past three fiscal years, the Company has
expanded its sales force to support growing revenues and has made significant
expenditures to recruit additional technical and professional staff, to invest
in information technology and to improve the Company's financial, administrative
and management infrastructure.


<PAGE>   3


                                             MERCURY COMPUTER SYSTEMS, INC.   19



         Revenues include both hardware and software products, development
contracts, services such as maintenance, training, engineering consulting and
system integration of Mercury software with third-party hardware. Revenues from
maintenance, training, engineering consulting services and system integration
historically have not constituted a material portion of total revenues. Revenue
from product sales is recorded upon completion of delivery obligations provided
customer acceptance is reasonably assured and collectability is deemed probable.
The Company accrues for anticipated warranty costs upon shipment. Service
revenue is recognized ratably over applicable contract periods or as the
services are performed. Revenue from contracts involving significant product
modification or customization that are eligible for the percentage-of-completion
accounting method are recognized on an efforts-expended basis. Changes to total
estimated costs and anticipated losses, if any, are recognized in the period in
which determined.
         Cost of revenues includes the cost of materials, component assembly,
internal labor and related overhead. Cost of revenues also can include
engineering and other technical labor and related overhead incurred in
development and engineering consulting contracts.
         Gross profit as a percentage of revenues ("gross margin") varies from
period to period depending upon numerous variables including the mix of revenues
from hardware, software, development and engineering consulting contracts; the
mix of revenues among the markets served by the Company; the cost of raw
materials; the cost of outsourced services and labor; operational efficiencies;
actual production volume compared to planned volume; and the mix of applications
for which the Company's computer systems are sold. Historically, the Company's
gross margins on service revenues have been lower than on product revenues. In
addition, the Company's gross margins from development contract revenues are
typically lower than the Company's gross margins from standard product revenues.
The Company intends to continue to enter into development contracts and
anticipates that the gross margins associated with development contract revenues
will continue to be lower than its gross margins on standard product revenues.
         Mercury has made significant investments in research and development in
an effort to maintain its technology leadership in digital signal processing and
to create new software products for the shared storage market. Mercury invested
$12.8 million, $14.5 million and $20.7 million in fiscal years 1997, 1998 and
1999, respectively, in development activities associated with the Company's key
technology competencies as well as in activities that are targeted at developing
new technologies and products. The Company expects research and development
expenses to continue to increase as the Company continues to develop products to
serve its markets, all of which are subject to rapidly changing technology,
frequent product performance improvements and evolving industry standards. The
ability to deliver superior technological performance on a timely and
cost-effective basis is a critical factor in securing design wins for future
generations of defense electronics and medical imaging systems. Significant
research and development spending by the Company does not ensure that the
Company's computer systems will be designed into a customer's system. Because
future production orders are usually contingent upon securing a design win, the
Company's operating results may fluctuate due to either obtaining or failing to
obtain design wins for significant customer systems.


<PAGE>   4

20   MERCURY COMPUTER SYSTEMS, INC.


RESULTS OF OPERATIONS
The following table sets forth, for the periods indicated, certain financial
data as a percentage of total revenues.



YEAR ENDED JUNE 30,                            1999       1998       1997

Revenues                                      100.0%     100.0%     100.0%
Cost of revenues                               32.1       35.2       34.1
                                              -----      -----      -----
Gross profit                                   67.9       64.8       65.9
Operating expenses:
    Selling, general and administrative        31.0       32.6       35.0
    Research and development                   19.4       16.9       19.9
                                              -----      -----      -----
    Total operating expenses                   50.4       49.5       54.9
                                              -----      -----      -----
Income from operations                         17.5       15.3       11.0
Other income, net                               1.4        1.3        0.7
                                              -----      -----      -----
Income before income taxes                     18.9       16.6       11.7
Provision for income taxes                      6.3        6.4        4.6
                                              -----      -----      -----
Net income                                     12.6%      10.2%       7.1%
                                              =====      =====      =====

FISCAL 1998 VS. FISCAL 1999

REVENUES
Total revenues increased 25% from $85.5 million during the year ended June 30,
1998 to $106.6 million during the year ended June 30, 1999. Revenues from
defense electronics, medical imaging and other commercial markets increased, as
described below.
         Defense electronics revenues increased 23% from $67.2 million or 79% of
total revenues during the year ended June 30, 1998 to $82.6 million or 77% of
total revenues during the year ended June 30, 1999. The increase in revenues was
due primarily to increased unit demand for defense electronics products.
         Medical imaging revenues increased 36% from $11.2 million or 13% of
total revenues during the year ended June 30, 1998 to $15.3 million or 14% of
total revenues during the year ended June 30, 1999. The increase in revenues was
due primarily to the expansion of the business into new applications.
         Other revenues increased 22% from $7.1 million or 8% of total revenues
during the year ended June 30, 1998 to $8.7 million or 8% of total revenues
during the year ended June 30, 1999. The increase in other revenues was due to
the shared storage business unit revenues increasing by 152% while the other
commercial businesses remained relatively flat year over year.

COST OF REVENUES
Cost of revenues increased 14% from $30.1 million during the year ended June 30,
1998 to $34.2 million during the year ended June 30, 1999. Cost of revenues as a
percentage of total revenues decreased from 35% during the year ended June 30,
1998 to 32% during the year ended June 30, 1999. The decrease in costs as a
percentage of total revenues was primarily due to a decline in component costs
and tighter control over manufacturing spending.

<PAGE>   5


                                             MERCURY COMPUTER SYSTEMS, INC.   21



SELLING, GENERAL AND ADMINISTRATIVE
Selling, general and administrative expenses increased 18% from $27.9 million
during the year ended June 30, 1998 to $33.0 million during the year ended June
30, 1999. Selling, general and administrative expenses as a percentage of total
revenues were 33% during the year ended June 30, 1998 and 31% during the year
ended June 30, 1999. The increase in expense dollars reflects the hiring of
additional sales and administrative personnel, increased commissions and
marketing communication related to increased revenues, as well as the ongoing
development of the Company's financial, administrative and management
infrastructure to support the Company's growth.

RESEARCH AND DEVELOPMENT
Research and development expenses, excluding capitalized software expenditures,
increased 43% from $14.5 million during the year ended June 30, 1998 to $20.7
million during the year ended June 30, 1999. Research and development expenses
as a percentage of total revenues were 17% during the year ended June 30, 1998
and 19% during the year ended June 30, 1999. The increase in research and
development expenses was due primarily to the hiring of additional software and
hardware engineers to develop and enhance the features and functionality of the
Company's products in response to increased demand for next generation products.
Engineering expenses currently are running higher than management's target
levels as the Company is working on some major development programs to deliver
important new technology to its customers. Management believes that higher
engineering spending will continue through fiscal 2000.
         The Company's future success and ability to make the appropriate
engineering investments will depend to a significant extent on its ability to
attract, train, motivate and retain highly skilled technical professionals,
particularly project managers, engineers and other senior technical personnel.
The Company believes that there is a shortage of, and significant competition
for, technical development professionals with the skills and experience
necessary to perform the services offered by the Company. The Company's ability
to maintain and renew existing engagements and obtain new business depends, in
large part, on its ability to hire and retain technical personnel with the
skills that keep pace with continuing changes in industry standards,
technologies and client preferences. The inability to hire additional qualified
personnel could impair the Company's ability to satisfy its growing client base,
requiring an increase in the level of responsibility for both existing and new
personnel. There can be no assurance that the Company will be successful in
retaining current or future employees and therefore able to continue to make the
investments in engineering at the projected higher expenditure levels.
Furthermore, the Company's inability to retain or hire technical personnel may
require contracting or outsourcing engineering activities. This factor could
result in higher than planned engineering expenses and therefore, a possible
fluctuation in the Company's operating results.

INCOME FROM OPERATIONS
Income from operations increased 42% from $13.1 million during the year ended
June 30, 1998 to $18.6 million during the year ended June 30, 1999. Included in
income from operations during the year ended June 30, 1999 were $2.2 million in
hardware and software revenues and $4.0 million in direct expenses related to
the shared storage business. The expenses include direct expenses from marketing
and engineering activities, primarily related to compensation, trade shows,
prototype development and direct costs related to the sale of the product.
Included in income from operations during the year ended June 30, 1998 were
$885,000 in hardware and software revenues and $4.3 million in direct expenses
related to the shared storage business. Revenues from the shared storage
business increased substantially year over year due primarily to the expanding
distribution


<PAGE>   6

22   MERCURY COMPUTER SYSTEMS, INC.


base and the availability of fiber channel interconnect technology. Refer to
separate discussion below in the liquidity and capital resource section of this
management discussion and analysis regarding the alternative ways to fund the
continuing development of the shared storage business unit.

INTEREST INCOME, NET
The Company earned $1.1 million in interest income, net, during the year ended
June 30, 1998 and $1.3 million during the year ended June 30, 1999. This
increase reflects higher average cash balances primarily as a result of proceeds
received from the Company's initial public offering in mid fiscal 1998.
Offsetting the effect of higher average cash balances were lower yields achieved
on the Company's cash. These lower yields were the result of a shift in
investment strategy from taxable money market instruments to non-taxable
securities.


PROVISION FOR INCOME TAXES
The Company's provision for income taxes was $5.4 million during the year ended
June 30, 1998 and $6.6 million during the year ended June 30, 1999. The
Company's effective tax rate was 38% during the year ended June 30, 1998 and 33%
during the year ended June 30, 1999. During fiscal 1999, the tax rate was
reduced primarily due to a one-time state investment tax credit ("ITC") benefit
resulting from the purchase of two facilities during the year, increase in
research and development credits, and a shift in investment strategy from
taxable to non-taxable securities.

FISCAL 1997 VS. FISCAL 1998

REVENUES
Total revenues increased 32% from $64.6 million during the year ended June 30,
1997 to $85.5 million during the year ended June 30, 1998. Revenues from defense
electronics, medical imaging and other commercial markets increased, as
described below.
         Defense electronics revenues increased 29% from $52.3 million or 81% of
total revenues during the year ended June 30, 1997 to $67.2 million or 79% of
total revenues during the year ended June 30, 1998. The increase in revenues was
due primarily to increased unit demand for defense electronics products.
         Medical imaging revenues increased 62% from $6.9 million or 11% of
total revenues during the year ended June 30, 1997 to $11.2 million or 13% of
total revenues during the year ended June 30, 1998. The increase in revenues was
due primarily to increased unit demand for medical imaging products.
         Other revenues increased 31% from $5.4 million or 8% of total revenues
during the year ended June 30, 1997 to $7.1 million or 8% of total revenues
during the year ended June 30, 1998. This increase in other revenues was due
primarily to an increase in unit demand from new and existing commercial
customers, partially offset by a decrease in revenues from the shared storage
business.

COST OF REVENUES
Cost of revenues increased 37% from $22.0 million during the year ended June 30,
1997 to $30.1 million during the year ended June 30, 1998. Cost of revenues as a
percentage of total revenues increased from 34% during the year ended June 30,
1997 to 35% during the year ended June 30, 1998. This increase in costs relative
to revenue was due to a price reduction put in place during 1998 and increased
manufacturing operating costs. These increases were offset, partially, by a
decline in material costs.

<PAGE>   7


                                             MERCURY COMPUTER SYSTEMS, INC.   23


SELLING, GENERAL AND ADMINISTRATIVE
Selling, general and administrative expenses increased 23% from $22.6 million
during the year ended June 30, 1997 to $27.9 million during the year ended June
30, 1998. Selling, general and administrative expenses as a percentage of total
revenues were 35% during the year ended June 30, 1997 and 33% during the year
ended June 30, 1998. The increase, in expense dollars, reflects the hiring of
additional sales and administrative personnel, increased commissions and the
development of the Company's financial, administrative and management
infrastructure to support the Company's growth.

RESEARCH AND DEVELOPMENT
Research and development expenses, excluding capitalized software
expenditures, increased 13% from $12.8 million during the year ended June 30,
1997 to $14.5 million during the year ended June 30, 1998. Research and
development expenses as a percentage of total revenues were 20% during the year
ended June 30, 1997 and 17% during the year ended June 30, 1998. The increase in
research and development expenses reflects increased investments in the
Company's core technological competencies, as well as in new medical, shared
storage and other technologies and products.

INCOME FROM OPERATIONS
Income from operations increased 85% from $7.1 million during the year ended
June 30, 1997 to $13.1 million during the year ended June 30, 1998. Included in
income from operations during the year ended June 30, 1998 were $885,000 in
hardware and software revenues and $4.3 million in direct expenses related to
the shared storage business. The expenses include direct expenses from marketing
and engineering activities, primarily related to compensation, trade shows,
prototype development and direct costs related to the sale of the product.
Included in income from operations during the year ended June 30, 1997 were $2.1
million in hardware and software revenues and $3.8 million in direct expenses
related to the shared storage business. Revenues from the shared storage
business declined year over year due primarily to the inclusion in 1997 revenue
of one large non-recurring order.

INTEREST INCOME, NET
The Company earned $560,000 in interest income, net, during the year ended June
30, 1997 and $1.1 million during the year ended June 30, 1998. This increase
reflects an increase in the Company's average cash balances primarily as a
result of cash received from the Company's initial public offering in mid fiscal
1998. Offsetting the effect of higher average cash balances were lower yields
achieved on the Company's cash. These lower yields were the result of a shift in
investment strategy from taxable money market instruments to non-taxable
securities.

PROVISION FOR INCOME TAXES
The Company's provision for income taxes was $2.9 million during the year ended
June 30, 1997 and $5.4 million during the year ended June 30, 1998. The
Company's effective tax rate was 39% during the year ended June 30, 1997 and 38%
during the year ended June 30, 1998.

LIQUIDITY AND CAPITAL RESOURCES
As of June 30, 1999 the Company had cash and marketable securities of
approximately $25.4 million. During the year ended June 30, 1999 the Company
generated $9.1 million in cash from operations compared to $7.1 million
generated during the year ended June 30, 1998. The increase in cash generated
from operations is attributable primarily to the Company's improved
profitability and an

<PAGE>   8

24   MERCURY COMPUTER SYSTEMS, INC.


increase in liabilities. These positive factors were partially offset by an
increase in accounts receivable and inventory balances. The Company's days
sales, based on revenues of each calendar quarter, increased from 66 days at the
end of 1998 to 88 days at the end of 1999. This increase in days sales was due
to a disproportionate amount of revenue being recorded at the end of the
accounting period. This disproportion occurred during the fourth quarter of
fiscal 1999 and was caused by intermittent failure in a major supplier's
component part. The situation was ultimately resolved but delayed shipments
until the last few weeks of the quarter. Consequently, the Accounts Receivable
balance at the end of the fiscal year was inflated.
         The Company used $12.7 million in investing activities during the year
ended June 30, 1999 compared to $35.4 million during the year ended June 30,
1998. The reduction in investing activities year-over-year was primarily due to
the increased net sale of marketable securities amounting to $36.2 million,
partially offset by $15.1 million associated with the purchase of the Company's
corporate headquarters and completed construction of an adjacent building.
         The Company generated $1.4 million in cash from financing activities
during the year ended June 30, 1999 compared to $19.1 million during the year
ended June 30, 1998. This significant reduction year over year was primarily due
to the fact that during fiscal 1998, the Company completed its initial public
offering, which resulted in net proceeds amounting to $18.6 million. In
addition, $303,000 was paid under a capital lease obligation during fiscal 1999
and none was paid during fiscal 1998. These reductions were partially offset by
the implementation during fiscal 1999 of the employee stock purchase plan
("ESPP"). During fiscal 1999, 28,224 additional shares of common stock were
issued through the ESPP for a total value of $469,000. In addition, 309,162
stock options were exercised during fiscal 1999 compared to 204,468 stock
options exercised during fiscal 1998. Proceeds received from stock option
exercises were $708,000 greater in fiscal 1999 than in fiscal 1998.
         On August 27, 1999, the Company signed a commitment letter with a
commercial financing company to issue two 7.30%, senior secured financing notes
("the Notes"), due September 2014. The total principal value of the Notes amount
to $14,500,000. The Company's corporate headquarters and an adjacent building,
with a combined cost basis of $17,670,000, secure the Notes.
         Management believes that the Company's available cash, cash generated
from operations, and cash received from the financing arrangement described
above will be sufficient to provide for the Company's working capital and
capital expenditure requirements for the foreseeable future. If the Company
acquires one or more businesses or products, the Company's capital requirements
could increase substantially. In the event of such an acquisition or in the
event that unanticipated circumstances arise which significantly increase the
Company's capital requirements, there can be no assurance that necessary
additional capital will be available on terms acceptable to the Company, if at
all.

SHARED STORAGE BUSINESS UNIT
On March 1st, 1999, the Company issued a Confidential Information Memorandum
seeking alternative ways to fund the continuing development of the Shared
Storage business unit. This business unit was created to exploit some of
Mercury's innovative software developments. It has evolved into software for use
in applications and market segments that, while exciting and potentially
offering large returns, is outside of Mercury's core businesses and strengths.
There can be no assurances that the Company will obtain such funding.

CORPORATE DEVELOPMENT
On September 1, 1999, Mercury formed a new joint venture company ("AgileVision")
with Sarnoff Corporation, the developer of color television and a pioneer in the
creation of digital television ("DTV"). Combining the intellectual property of
both companies,


<PAGE>   9


                                             MERCURY COMPUTER SYSTEMS, INC.   25


this new venture is expected to provide the broadcast and cable
industries with products and solutions that will significantly increase the
flexibility of a digital television broadcast infrastructure. The new company
will provide products and services that allow an economical entry point to DTV
services, with the option of expanding performance and features to meet the
high-bandwidth digital signal processing demands of the evolving DTV market. The
Company is initially required to contribute $2.5 million in cash in addition to
technology to the joint venture.


YEAR 2000 COMPLIANCE
The Company is aware of the potential for industry wide business disruption
which could be caused by computer systems, software products and embedded
micro-processing chips which may be coded to accept only two-digit entries in
the date code field and may not be able to distinguish 20th century dates from
21st century dates. The Company believes it has a prudent plan in place to
address these issues within our Company and our supply chain.

         STATE OF READINESS. The Company is engaged in a process of evaluating
the Year 2000 readiness of hardware and software products sold by the Company
("Products"), information technology systems used in its operations ("IT
Systems"), and its non-IT Systems such as building security, voice mail and
other systems. The Company anticipates that the project will cover the following
phases: (i) identification of all Products, IT Systems, and non-IT Systems; (ii)
assessment of repair or replacement requirements; (iii) repair or replacement;
(iv) testing; (v) implementation; and (vi) creation of contingency plans in the
event of Year 2000 failures.
         PRODUCTS. The Company has completed a review of the source code for all
versions of its Products sold after January 1, 1997 and based on such review,
the Company believes that such Products are "Year 2000 Compliant," meaning that
when used properly and in conformity with the product information provided by
the Company, the product furnished by the Company will accurately store,
display, process, provide, and/or receive data from, into, and between 1999 and
2000, including leap year calculations, provided that all technology used in
combination with the Company product properly exchanges date data with the
Company product. In general, software provided by the Company does not require
the user to input date fields and depends instead on date information supplied
by host operating systems not manufactured by the Company. Therefore, the
assessment of whether a complete system or device in which a Product is embedded
will operate correctly for an end-user depends in large part on the Year 2000
Compliance of the system's other components, most of which are supplied by
parties other than the Company. For this reason, end-users must consult with the
manufacturers of host operating systems and test such systems in their entirety
for Year 2000 Compliance. The Company has determined that it is not feasible to
test versions of its Products sold prior to January 1, 1997. However, based on
similarities in source code between prior and current Product versions, the
Company believes that versions of its Products sold prior to January 1, 1997 are
Year 2000 Compliant.
         IT AND NON-IT SYSTEMS. The Company has compiled a comprehensive list of
the Company's IT and non-IT systems. Based on the Company's internal assessment,
the Company believes that most of these systems are Year 2000 Compliant. The
source code underlying the Company's financial and accounting software has been
reprogrammed and tested using the Company's internal technical resources. The
Company has determined to its satisfaction that its financial and accounting
systems are Year 2000 Compliant. The Company has identified three IT Systems
which are not Year 2000 Compliant and the Company expects to purchase, install
and test upgrades for such non-compliant systems by the end of October, 1999.
The Company is dependent in part upon Microsoft software products to ensure
completion of this task in a timely fashion.


<PAGE>   10


26   MERCURY COMPUTER SYSTEMS, INC.


         THIRD PARTIES. The Company relies, both domestically and
internationally, upon various vendors, governmental agencies, utility companies,
telecommunications service companies, delivery service companies and other
service providers who are outside of Mercury's control. The Company has
completed a questionnaire-based assessment of its primary vendors to assess
their ability to continue to provide goods and services to the Company from,
into and between 1999 and 2000. While the Company has received assurances from
vendors regarding their Year 2000 Compliance status, the Company may never be
able to know with certainty whether its vendors are compliant. Failure of
critical vendors to achieve Year 2000 Compliance could result in delayed
deliveries of products and services to the Company. If such delays are
extensive, they could have a material adverse effect on the Company's business.
         COSTS. Most of the Company's effort toward Year 2000 readiness is
funded as ongoing operating expense. The Company is in the process of
determining the total cost of Year 2000 relevant upgrading. Expenditures
directly related to the Year 2000 readiness program, consisting of dedicated
staff and consulting services, are estimated to be less than $1,000,000.
         RISKS. The failure to correct a material Year 2000 problem could
result in an interruption in, or a failure of, certain normal business
activities. Such failures could materially and adversely affect the Company's
results of operations, liquidity and financial condition. Due to the general
uncertainty inherent with the Year 2000 issue, resulting in large part from the
uncertainty of the Year 2000 readiness of third-parties outside of the Company's
control, the Company is unable to determine at this time whether the
consequences of a Year 2000 failure will have a material impact on the Company's
results of operations, liquidity, or financial position. The Year 2000
Compliance project is expected to reduce, but not eliminate, the Company's level
of uncertainty about the Year 2000 issue and in particular, about the Year 2000
Compliance and readiness of its critical vendors. The Company believes that,
with the completion of the Year 2000 Compliance project as scheduled, the
possibility of significant interruptions to normal operations should be reduced.
         CONTINGENCY PLAN. The Company is developing a contingency plan for its
information technology infrastructure as well as non-IT elements. The Company
expects that this plan will include provisions for additional customer and
facility support. The contingency plan may also include obtaining component
parts in December, 1999 rather than January, 2000 in the event vendors encounter
Year 2000 problems. The Company expects that its contingency plan will be
developed in greater detail if and when specific issues are identified.


RECENT ACCOUNTING PRONOUNCEMENTS
See Note B to the Company's Consolidated Financial Statements for a description
of the impact on the Company of recent accounting pronouncements.

QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

INTEREST RATE RISK MANAGEMENT
Due to its short-term duration, the fair value of the Company's cash and
investment portfolio at June 30, 1999 approximated carrying value. Interest rate
risk is estimated as the potential decrease in fair value resulting from a
hypothetical 10% increase in interest rates for issues contained in the
investment portfolio. The resulting hypothetical fair value was not materially
different from the year-end carrying value.


<PAGE>   11


                                             MERCURY COMPUTER SYSTEMS, INC.   27


MARKET INFORMATION


The Company's Common Stock is traded in the over-the-counter market and is
quoted on the Nasdaq National Market under the symbol MRCY. The following table
sets forth, for the periods indicated since the Company's initial public
offering on January 29, 1998, the high and low transactions per share during
such periods. Such over-the-counter market quotations reflect inter-dealer
prices without retail markup, markdown or commission.

                                                       HIGH            LOW
1998  Third quarter (from January 29, 1998)           19 1/8          9 3/8
      Fourth quarter                                  19             12 1/4

1999  First quarter                                   17 3/8          9 3/4
      Second quarter                                  28 5/8         12 1/2
      Third quarter                                   28 1/4         17 1/8
      Fourth quarter                                  33 3/8         15 1/16

As of August 31, 1999 the Company had approximately 4,000 shareholders including
record and nominee holders.
         The Company has never declared or paid cash dividends on shares of its
Common Stock and does not expect to declare or pay cash dividends on its Common
Stock in the foreseeable future. The Company currently intends to retain any
earnings for future growth.


<PAGE>   12



28   MERCURY COMPUTER SYSTEMS, INC.


CONSOLIDATED BALANCE SHEETS


(IN THOUSANDS, EXCEPT SHARE DATA) JUNE 30,                    1999        1998
ASSETS
Current assets:
    Cash and cash equivalents                               $ 3,676     $ 6,054
    Marketable securities                                    12,762      10,077
    Trade accounts receivable, net of allowance for
      doubtful accounts of $376 and $218 at June 30,
      1999 and 1998, respectively                            28,915      17,143
    Inventory                                                12,431       9,125
    Deferred income taxes, net                                2,617       1,669
    Prepaid expenses and other current assets                 1,392       1,255
                                                            -------     -------
      Total current assets                                   61,793      45,323
    Marketable securities                                     8,978      18,889
    Property and equipment, net                              25,325       8,466
    Deferred income taxes, net                                  668         429
    Other assets                                                747         462
                                                            -------     -------
      Total assets                                          $97,511     $73,569
                                                            =======     =======

LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
    Accounts payable                                        $ 5,580     $ 3,368
    Accrued expenses                                          3,694       2,804
    Accrued compensation                                      4,292       3,316
    Capital lease - short term                                  434          --
    Billings in excess of revenues and customer
      advances                                                3,169       1,017
    Income taxes payable                                      2,312       2,024
                                                            -------     -------
      Total current liabilities                              19,481      12,529
Commitments and contingencies (Note F)                           --          --
Capital lease - long term                                       590          --

STOCKHOLDERS' EQUITY
Common stock, $.01 par value; 25,000,000 shares
     authorized; 10,310,877 and 9,973,491 shares
     issued and outstanding at June 30, 1999 and
     1998, respectively                                         103         100
    Additional paid-in capital                               28,515      25,961
    Retained earnings                                        48,945      35,483
    Accumulated other comprehensive income                     (123)       (179)
    Subscriptions and related parties notes receivable         --          (325)
                                                            -------     -------
      Total stockholders' equity                             77,440      61,040
                                                            -------     -------
      Total liabilities and stockholders' equity            $97,511     $73,569
                                                            =======     =======

The accompanying notes are an integral part of the consolidated financial
statements.



<PAGE>   13


                                             MERCURY COMPUTER SYSTEMS, INC.   29



CONSOLIDATED STATEMENTS OF OPERATIONS


(IN THOUSANDS, EXCEPT PER SHARE
DATA) YEAR ENDED JUNE 30,                          1999        1998       1997

Revenues                                         $106,571    $85,544    $64,574
Cost of revenues                                   34,237     30,084     22,034
                                                 --------    -------    -------
    Gross profit                                   72,334     55,460     42,540
                                                 --------    -------    -------
Operating expenses:
    Selling, general and administrative            33,002     27,879     22,631
    Research and development                       20,709     14,476     12,837
                                                 --------    -------    -------
      Total operating expenses                     53,711     42,355     35,468
                                                 --------    -------    -------
Income from operations                             18,623     13,105      7,072
                                                 --------    -------    -------
Interest income, net                                1,285      1,084        560
Other income (expense), net                           185        (30)       (88)
                                                 --------    -------    -------
Income before income tax provision                 20,093     14,159      7,544
Income tax provision                                6,631      5,428      2,933
                                                 --------    -------    -------
Net income                                       $ 13,462    $ 8,731    $ 4,611
                                                 ========    =======    =======
Net income per common share:
    Basic                                        $   1.32    $  1.21    $  0.90
                                                 ========    =======    =======
    Diluted                                      $   1.25    $  0.94    $  0.58
                                                 ========    =======    =======
Weighted average number of common and common
  equivalent shares outstanding:
    Basic                                          10,168      7,235      5,141
                                                 ========    =======    =======
    Diluted                                        10,800      9,270      7,897
                                                 ========    =======    =======









The accompanying notes are an integral part of the consolidated financial
statements.



<PAGE>   14


30   MERCURY COMPUTER SYSTEMS, INC.



CONSOLIDATED STATEMENTS OF CHANGES IN STOCKHOLDERS' EQUITY


<TABLE>
<CAPTION>

                                        Series A                                      Accumulated           Subscriptions
FOR THE YEARS ENDED                   Convertible                                           Other             and Related   Total
June 30, 1999, 1998                 Preferred Stock    Common Stock    Add'l                Compre-  Compre-      Parties   Stock-
AND 1997                            ---------------   --------------  Paid-In  Retained    hensive   hensive        Notes   holder's
(IN THOUSANDS)                      Shares  Amount    Shares  Amount  Capital  Earnings     Income   Income    Receivable   Equity

<S>                                 <C>     <C>       <C>      <C>    <C>       <C>         <C>      <C>         <C>        <C>
Balance, June 30, 1996               852    $1,200     5,083   $ 51   $ 5,434   $22,141     $   3                $(300)     $28,529
Issuance of notes receivable to
  related parties                                                                                                  (25)         (25)
Exercise of common stock options                          86      1       137                                                   138
Issuance of common stock                                  33              132                                                   132
Comprehensive income:
  Net income                                                                      4,611              $ 4,611                  4,611
  Foreign currency translation                                                                (63)       (63)                   (63)
                                                                                                     -------
  Comprehensive income                                                                               $ 4,548
                                     ---    ------    ------   ----   -------   -------     -----    =======     -----      -------
Balance, June 30, 1997               852     1,200     5,202     52     5,703    26,752       (60)                (325)      33,322
Exercise of common stock options                         204      2       506                                                   508
Issuance of common stock pursuant
  to initial public offering, net
  of issuance costs of $952                            2,000     20    18,558                                                18,578
Conversion of series A convertible
  preferred stock into common stock (852)   (1,200)    2,557     26     1,174

Exercise of common stock warrants                         10               20                                                    20
Comprehensive income:
  Net income                                                                      8,731                8,731                  8,731
  Foreign currency translation                                                               (119)      (119)                  (119)
                                                                                                     -------
  Comprehensive income                                                                               $ 8,612
                                     ---    ------    ------   ----   -------   -------     -----    =======     -----      -------
Balance June 30, 1998                 --        --     9,973    100    25,961    35,483      (179)                (325)      61,040
Exercise of common stock options                         309      3     1,213                                                 1,216
Issuance of common stock in
  conjunction with employee stock
  purchase plan                                           29              469                                                   469
Tax benefit from disqualified
  dispositions                                                            826                                                   826
Employee based stock compensation                                          46                                                    46
Payment of notes by related parties                                                                                325          325
Comprehensive income:
  Net income                                                                     13,462               13,462                 13,462
  Unrealized loss on securities                                                               (30)       (30)                   (30)
  Foreign currency translation                                                                 86         86                     86
                                                                                                     -------
  Comprehensive income                                                                               $13,518
                                     ---    ------    ------   ----   -------   -------     -----    =======     -----      -------
Balance June 30, 1999                 --        --    10,311   $103   $28,515   $48,945     $(123)                  --      $77,440
                                     ===    ======    ======   ====   =======   =======     =====                =====      =======
</TABLE>

The accompanying notes are an integral part of the consolidated financial
statements.


<PAGE>   15


                                             MERCURY COMPUTER SYSTEMS, INC.   31



CONSOLIDATED STATEMENTS OF CASH FLOWS
<TABLE>
<CAPTION>


(IN THOUSANDS) YEAR ENDED JUNE 30,                                       1999           1998           1997
Cash flows from operating activities:
<S>                                                                    <C>             <C>            <C>
  Net income                                                           $ 13,462        $ 8,731        $ 4,611
  Adjustments to reconcile net income to net cash provided by
   operating activities:
    Depreciation and amortization of property and equipment               3,916          2,829          2,855
    Amortization of capitalized software development costs                  602            490            438
    Provision for inventory write-downs                                   2,786          1,583            504
    Provision for doubtful accounts                                         249             99             40
    Deferred income taxes                                                (1,187)        (1,133)          (596)
    Tax benefit from disqualified dispositions                              826             --             --
    Other non-cash items                                                     46             --             87
  Changes in assets and liabilities:
    Trade accounts receivable                                           (11,871)        (4,596)        (2,710)
    Trade notes receivable                                                   --             --            296
    Contracts in progress                                                    --          1,096         (1,096)
    Inventory                                                            (6,048)        (2,398)        (1,662)
    Prepaid expenses and other current assets                              (108)          (560)          (246)
    Other assets                                                            (98)           (69)          (101)
    Accounts payable                                                      2,216            570          1,081
    Accrued expenses and compensation                                     1,874          1,908          1,846
    Billings in excess of revenues and customer advances                  2,151         (1,847)         2,472
    Income taxes payable                                                    284            411          1,403
                                                                       --------        -------        -------
Net cash provided by operating activities                                 9,100          7,114          9,222
                                                                       --------        -------        -------
Cash flows from investing activities:
  Purchase of marketable securities                                    (114,574)       (73,571)            --
  Sale of marketable securities                                         121,768         44,605             --
  Purchases of property and equipment                                   (19,440)        (6,336)        (3,457)
  Capitalized software development costs                                   (810)          (111)          (550)
  Notes receivable from related parties                                     325             --            (25)
                                                                       --------        -------        -------
Net cash used in investing activities                                   (12,731)       (35,413)        (4,032)
                                                                       --------        -------        -------
Cash flows from financing activities:
  Proceeds from employee stock purchase program                             469             --             --
  Proceeds from exercise of stock options                                 1,216            508             --
  Proceeds from issuance of common stock                                     --         18,578            270
  Proceeds from exercise of stock warrants                                   --             20             --
  Principal payments under capital lease obligations                       (303)            --             --
                                                                       --------        -------        -------
Net cash provided by financing activities                                 1,382         19,106            270
                                                                       --------        -------        -------
Net increase in cash and cash equivalents                                (2,249)        (9,193)         5,460
Effect of exchange rate changes on cash and cash equivalents               (129)            54             29
Cash and cash equivalents at beginning of year                            6,054         15,193          9,704
                                                                       --------        -------        -------
Cash and cash equivalents at end of period                             $  3,676        $ 6,054        $15,193
                                                                       ========        =======        =======
Cash paid during the period for:
  Interest                                                             $     51        $    --        $    22
  Income taxes                                                            7,155          6,166          2,133
Non-cash transactions:
  Equipment acquired under capital leases                              $  1,327        $    --        $    --
  Series A convertible preferred stock converted to
   common stock                                                              --          1,200             --
</TABLE>


The accompanying notes are an integral part of the consolidated financial
statements.


<PAGE>   16


32   MERCURY COMPUTER SYSTEMS, INC.


NOTES TO CONSOLIDATED FINANCIAL STATEMENTS


(TABLES IN THOUSANDS EXCEPT FOR SHARE AND PER SHARE DATA)

A. DESCRIPTION OF BUSINESS:
Mercury Computer Systems, Inc. (the "Company") designs, manufactures and markets
high performance real-time digital signal processing computer systems which
transform sensor-generated data into information which can be displayed as
images for human interpretation or subjected to additional computer analysis.
These multicomputer systems are heterogeneous and scalable, allowing them to
accommodate several different microprocessor types and to scale from a few to
hundreds of microprocessors within a single system. The two primary markets for
the Company's products are defense electronics and medical diagnostic imaging.
Both of these markets have computing needs which benefit from the unique system
architecture developed by the Company.

B. SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES:

BASIS OF PRESENTATION
The consolidated financial statements include the accounts of the Company and
its wholly-owned subsidiaries. All significant intercompany transactions and
balances have been eliminated.

USE OF ESTIMATES
The preparation of financial statements in conformity with generally accepted
accounting principles requires management to make estimates and assumptions that
affect the reported amounts of assets and liabilities and disclosure of
contingent assets and liabilities at the dates of the financial statements and
the reported amounts of revenues and expenses during the reporting periods.
Actual results could differ from those estimates.

REVENUE RECOGNITION
Revenue from product sales is recorded upon completion of delivery obligations
provided customer acceptance is reasonably assured and collectability is deemed
probable. The Company accrues for anticipated warranty costs upon shipment.
Service revenue is recognized ratably over applicable contract periods or as the
services are performed. Revenue from contracts involving significant product
modification or customization that are eligible for the percentage-of-completion
accounting method are recognized on an efforts-expended basis. Changes to total
estimated costs and anticipated losses, if any, are recognized in the period in
which determined. There was no revenue recognized for year ended June 30, 1999
under the percentage-of-completion method while $3,835,000 and $2,102,000 of
revenue was recognized under the percentage-of-completion method for the fiscal
years ended June 30, 1998 and 1997, respectively. There were no retainages at
June 30, 1999, 1998 or 1997.

BILLINGS IN EXCESS OF REVENUES AND CUSTOMER ADVANCES
Billings in excess of revenues and customer advances include amounts billed on
uncompleted contracts and amounts billed on annual maintenance contracts.

CASH AND CASH EQUIVALENTS
Cash equivalents, consisting of money market funds and U.S. government and U.S.
government agency issues with original maturities of 90 days or less, are
carried at fair value.


<PAGE>   17

                                             MERCURY COMPUTER SYSTEMS, INC.   33



MARKETABLE SECURITIES
The Company classifies investments in marketable securities as either trading,
available-for-sale or held-to-maturity at the time of purchase and periodically
re-evaluates such classification. There were no securities classified as trading
or held-to-maturity as of June 30, 1999 and 1998. Securities are classified as
held-to-maturity when the Company has the positive intent and ability to hold
the securities to maturity. Held-to-maturity securities are stated at cost with
corresponding premiums or discounts amortized over the life of the investment to
interest income. Securities classified as available-for-sale are reported at
fair market value. Unrealized gains or losses on available-for-sale securities
are included, net of tax, in shareholders' equity until disposition. Realized
gains and losses and declines in value judged to be other than temporary on
available-for-sale securities are included in other income. The cost of
securities sold is based on the specific identification method.
         The fair market value of cash equivalents and short-term and long-term
investments in marketable securities represents the quoted market prices at the
balance sheet dates. The short-term marketable securities have original
maturities greater than 90 days and remaining maturities less than one year.
Long-term marketable securities have remaining maturities greater than one year.
Long-term marketable securities have maturities of one to three years. At June
30, 1999 and 1998, marketable securities were classified as follows:

                                                            1999          1998
                                                      Available-    Available-
                                                        For-Sale      For-Sale

Short-term marketable securities:
Municipal/tax free bonds & money market instruments      $12,762       $10,077
Long-term marketable securities:
Municipal/tax free bonds                                 $ 8,978       $18,889


CONCENTRATION OF CREDIT RISK
Financial instruments which potentially expose the Company to concentrations of
credit risk consist principally of cash, marketable securities and trade
accounts receivable. The Company places its cash and cash equivalents with
financial institutions which management believes are of high credit quality. At
June 30, 1999 and 1998, the Company had approximately $2,904,000 and $5,552,000,
respectively, on deposit or invested with its primary financial and lending
institution.
         Customers comprising 10% or more of the Company's receivables for the
periods shown below are as follows:

YEAR ENDED JUNE 30,                                         1999          1998

Customer A                                                  --            32%
Customer B                                                  27%           15%
Customer C                                                  17%           13%
Customer D                                                  11%           --

INVENTORY
Inventory is stated at the lower of cost, determined on the first-in, first-out
(FIFO) basis, or market.


<PAGE>   18


34   MERCURY COMPUTER SYSTEMS, INC.



PROPERTY AND EQUIPMENT
Property and equipment are recorded at cost. Equipment under capital lease is
recorded at the present value of the minimum lease payments required during the
lease period. Depreciation is based on the following estimated useful lives of
the assets using the straight-line method:


Computer equipment                                                       3 years
Machinery and equipment                                                  5 years
Furniture and fixtures                                                   5 years
Buildings                                                          15 - 30 years
Building improvements                                                   10 years
Leasehold improvements                                      Shorter of the lease
                                                           term or economic life

Expenditures for additions, renewals and betterments of property and equipment
are capitalized. Expenditures for repairs and maintenance are charged to expense
as incurred. As assets are retired or sold, the related cost and accumulated
depreciation are removed from the accounts and any resulting gain or loss is
included in the results of operations.

CAPITALIZED SOFTWARE DEVELOPMENT COSTS
The Company capitalizes software development costs incurred after a product's
technological feasibility has been established and before it is available for
general release to customers. Amortization of capitalized software costs is
computed on an individual product basis and is the greater of a) the ratio that
current gross revenues for a product bear to the total of current and
anticipated future gross revenues for that product or b) the straight-line
method over the estimated economic life of the product. Currently, the Company
uses an estimated economic life of 24 months or less for all capitalized
software costs.

RESEARCH AND DEVELOPMENT COSTS
All research and development costs are expensed as incurred except for
capitalized software development costs.

INCOME TAXES
The Company recognizes deferred tax assets and liabilities for the expected
future tax consequences of events that have been included in the Company's
consolidated financial statements. Under this method, deferred tax liabilities
and assets are determined based on the difference between the financial
statement and tax basis of assets and liabilities using currently enacted tax
rates for the year in which the differences are expected to reverse. The Company
records a valuation allowance against net deferred tax assets if, based upon the
available evidence, it is more likely than not that some or all of the deferred
tax assets will not be realized.

NET INCOME PER COMMON SHARE
The Company previously adopted SFAS No. 128, "Earnings per Share" (Statement
128). Statement 128 specifies the calculation and presentation of basic and
diluted net income per share. Basic net income per common share is calculated by
dividing net income by the weighted average number of common shares outstanding
during the period. Diluted net income per common share is calculated by dividing
net income by the sum of the weighted average number of common shares plus
additional common shares that would have been outstanding if potential dilutive
common shares had been issued for granted stock options.


<PAGE>   19

                                             MERCURY COMPUTER SYSTEMS, INC.   35


FOREIGN CURRENCY
The accounts of foreign subsidiaries are translated using exchange rates in
effect at period-end for assets and liabilities and at average exchange rates
during the period for results of operations. The local currency for all foreign
subsidiaries is the functional currency. The related translation adjustments are
reported in accumulated other comprehensive income in stockholders' equity.
Gains (losses) resulting from foreign currency transactions are included in
other income (expense) and are immaterial for all periods presented.

RECLASSIFICATION
Certain reclassifications have been made to the prior years' financial
statements to conform to the current year's presentation.

NEW ACCOUNTING PRONOUNCEMENTS
In March 1998, the American Institute of Certified Public Accountants issued SOP
98-1, "Internal Use Software," which provides guidance on the accounting for the
costs of software developed or obtained for internal use. SOP 98-1 is effective
for fiscal years beginning after December 15, 1998. The Company will adopt this
statement's provisions for its fiscal year 2000 which commences on July 1, 1999.
Management does not expect the statement to have a material impact on its
financial position or results of operations.
         In June 1999, the Financial Accounting Standards Board issued SFAS No.
137, "Accounting for Derivative Instruments and Hedging Activities - Deferral of
the Effective Date of FASB Statement No. 133." SFAS No. 137 amends SFAS No. 133,
"Accounting for Derivative Instruments and Hedging Activities" which was issued
in June 1998. SFAS No. 137 defers the effective date of SFAS No. 133 to all
fiscal quarters beginning after June 15, 2000. Accordingly, the Company will
adopt the provisions of SFAS No. 133 for its fiscal year 2001 which commences on
July 1, 2000. SFAS No. 133 requires that all derivative instruments must be
recorded on the balance sheet at their fair value. Changes in the fair value of
derivatives are recorded each period in current earnings or accumulated other
comprehensive income, depending on whether a derivative is designated as part of
a hedge transaction and the type of hedge transaction. Management of the Company
anticipates that, due to its limited use of derivative instruments, the adoption
of SFAS No. 133 will not have a material impact on its financial position or
results of operations.


C. NET INCOME PER COMMON SHARE:
The following table sets forth the computation of basic and diluted net income
per common share:

FOR THE YEARS ENDED JUNE, 30                              1999     1998     1997

Net Income                                             $13,462   $8,731   $4,611
                                                       =======   ======   ======
Shares used in net income per common share-basic        10,168    7,235    5,141
    Effect of dilutive securities:
      Convertible Preferred Stock                           --    1,492    2,557
      Stock options                                        632      542      194
      Warrants                                              --        1        5
                                                       -------   ------   ------
    Dilutive potential common shares                       632    2,035    2,756
                                                       -------   ------   ------
Shares used in net income per common share - diluted    10,800    9,270    7,897
                                                       =======   ======   ======
Net income per common share - basic                    $  1.32   $ 1.21   $ 0.90
                                                       =======   ======   ======


<PAGE>   20


36   MERCURY COMPUTER SYSTEMS, INC.



Net income per common share - diluted                  $  1.25   $ 0.94   $ 0.58
                                                       =======   ======   ======

Options to purchase 111,000 shares of common stock in 1999, 29,000 shares in
1998, and 36,000 in 1997 were outstanding during the years then ended but were
not included in the year-to-date calculation of diluted net income per share
because the options' exercise price was greater than the average market price of
the common shares during those periods.


D. INVENTORY:
Inventory consists of the following:


JUNE 30,                                                    1999       1998

Raw materials                                             $ 3,508     $4,707
Work in process                                             6,841      2,814
Finished goods                                              2,082      1,604
                                                          -------     ------
                                                          $12,431     $9,125
                                                          =======     ======

E. PROPERTY AND EQUIPMENT:
Property and equipment consists of the following:


JUNE 30,                                                    1999       1998

Computer equipment                                        $17,280    $14,027
Buildings                                                  15,819         --
Land                                                        1,852         --
Machinery and equipment                                       404        310
Furniture and fixtures                                      3,365      2,391
Building and leasehold improvements                         1,334      1,159
Construction in progress                                       --      2,737
                                                          -------    -------
                                                           40,054     20,624
Less: accumulated depreciation and amortization           (14,729)   (12,158)
                                                          -------    -------
                                                          $25,325    $ 8,466
                                                          =======    =======

During the fiscal year ended June 30, 1999, the Company purchased its existing
headquarters building and an adjacent newly constructed facility, including land
for $15,058,000. In addition, during the fiscal year ended June 30, 1999,
$1,289,000 of property and equipment was retired of which $1,260,000 was fully
depreciated.


F. COMMITMENTS AND CONTINGENCIES:
FINANCING ARRANGEMENT

During the fiscal years ended June 30, 1997 and 1998, the Company had a credit
agreement with a commercial bank to borrow up to $5,000,000 at an interest rate
equal to the prime rate or, at the election of the Company, two and one-quarter
percentage


<PAGE>   21

                                             MERCURY COMPUTER SYSTEMS, INC.   37


points above the London InterBank Offered Rate, payable monthly. The credit
agreement contained certain covenants, including restrictions on incurrence of
additional indebtedness and liens on its assets, capital expenditures,
disposition of assets, investments and acquisitions, limitations on
distributions, and required the Company to meet certain financial tests
pertaining to current and debt ratios and income before tax provision. There
were no borrowings outstanding at June 30, 1998 or June 30, 1997. During the
fiscal year ended June 30, 1999, the Company terminated this financing
arrangement. Accordingly, there were no borrowings outstanding at June 30, 1999.

LEASE COMMITMENTS

The Company leases certain of its facilities and machinery and equipment under
capital and operating leases expiring in various years through 2003 and
thereafter. The leases contain various renewal options. Rental charges are
subject to escalation for increases in certain operating costs of the lessor.

         Minimum lease payments under operating and capital leases are as
follows:

                                            Operating lease        Capital Lease
YEAR ENDING JUNE 30,                  Real Estate       Equipment      Equipment

2000                                        $408           $363           492
2001                                         191            264           492
2002                                         175             --           137
2003                                          40             --            --
Thereafter                                    --             --            --
                                            ----           ----        ------
Total minimum lease payments                $814           $627        $1,121
                                            ====           ====        ======
Less: amounts representing interest                                        97
                                                                       ------
Present value of minimum lease payments                                 1,024
Less: current portion                                                     434
                                                                       ------
Long term portion                                                      $  590
                                                                       ======

Rental expense during the fiscal years ended June 30, 1999, 1998 and 1997 was
approximately $1,116,000, $1,029,000 and $642,000, respectively.

INTERNAL REVENUE SERVICE AUDIT
On December 12, 1997, the Internal Revenue Service ("IRS") concluded an audit of
the Company's tax returns for the years ended June 30, 1992 through June 30,
1995, and issued a formal report reflecting proposed adjustments with respect to
the years under audit. The proposed IRS adjustments primarily related to the
disallowance of research and experimental tax credits claimed by the Company, as
well as the treatment of certain other items. In June, 1999 the Company agreed
to a final settlement with the IRS amounting to $585,000, including an estimated
interest amount of $220,000. The Company had previously accrued a liability for
this settlement and accordingly, no charge was recorded during the fiscal year
ended June 30, 1999.

<PAGE>   22


38   MERCURY COMPUTER SYSTEMS, INC.



G. STOCKHOLDERS' EQUITY:

COMMON STOCK
On January 29, 1998, 3,500,000 shares of the Company's common stock were sold in
the Company's initial public offering ("IPO") of which 2,000,000 shares were
sold by the Company and 1,500,000 shares were sold by certain stockholders of
the Company. The Company received $18,578,000 in net proceeds from the IPO after
deducting underwriting discounts and commissions of $1,470,000 and $952,000 in
offering expenses.

PREFERRED STOCK

GENERAL
The Company is authorized to issue 1,000,000 shares of preferred stock with a
par value of $.01 per share.

SERIES A CONVERTIBLE PREFERRED STOCK
The series A convertible preferred stock had a liquidation preference of $1.41
per share and voting rights similar to the common stock. Each of the preferred
stockholders had one vote for each share of common stock into which the series A
convertible preferred stock was convertible. On January 29, 1998, the series A
convertible preferred stock was converted into common stock on a three-for-one
basis.


H. STOCK BASED COMPENSATION
At June 30, 1999, the Company had both stock option plans and a stock purchase
plan. In fiscal year 1997, the Company adopted SFAS No. 123, "Accounting for
Stock-Based Compensation." SFAS No. 123 requires that companies either recognize
compensation expense for grants of stock, stock options and other equity
instruments based on fair value or provide pro forma disclosure of net income
and earnings per share in the notes to the financial statements. The Company
adopted the disclosure provisions of SFAS No. 123 in fiscal 1997 and has applied
APB Opinion No. 25 and related interpretations in accounting for all of its
stock option and employee stock purchase plans. Compensation cost is measured as
the excess, if any, of the fair market value of the Company's stock at the date
of grant over the amount an individual must pay to acquire the stock.
Compensation expense recognized for stock based compensation amounted to
$46,000, $0, and $0 for the fiscal year ended June 30, 1999, 1998, and 1997,
respectively.

STOCK OPTION PLANS
The Company has five stock option plans. The 1982, 1991, and 1993 Stock Option
Plans (the "Plans") provide for the granting of options to purchase an aggregate
of not more than 1,950,000 shares of the Company's common stock to employees and
directors. Under these plans, options are granted at not less than the fair
value of the stock on the date of grant as determined by the Board. The terms of
the options are established by the Board on an individual basis. The options
generally vest between three and five years and have a maximum term of ten
years.
         The 1997 Stock Option Plan (the "1997 Plan"), which the Board approved
in June 1997, provides for the granting of options to purchase an aggregate of
not more than 1,325,000 shares of the Company's common stock. The Plan provides
for the grant of non-qualified and incentive stock options to employees.
Incentive stock options are granted at a price set by the Board of Directors not
to be less than 100% of the fair value at the date of the grant. Non-qualified
stock options are granted at not less than 50% of the fair value of the stock on
the date of grant as determined by the Board. The options vest over five years

<PAGE>   23

                                             MERCURY COMPUTER SYSTEMS, INC.   39


and have a maximum term of ten years. With the implementation of the 1997 Plan,
no further stock options were granted under the 1982 and 1991 Stock Option
Plans.
         The 1998 Stock Option Plan (the "1998 Plan"), which the Board approved
in September 1998, provides for the granting of options to purchase an aggregate
of not more than 50,000 shares of the Company's common stock. The Plan provides
for the grant of non-qualified stock options to non-employee directors.
Non-qualified stock options are granted at fair value of the stock at the date
of the grant as determined by the Board of Directors. The options vest over
three years and have a maximum term of ten years. With the implementation of the
1998 Plan, no further stock options were granted under the 1993 Stock Option
Plan.


RE-PRICING STOCK OPTIONS
On July 30, 1996, the Board approved a plan (the "Re-pricing Plan") to re-price
employee stock options under the Plans to restore the long-term employee
retention and performance incentives of the stock options outstanding. In
accordance with the Re-pricing Plan, all stock options with exercise prices
above $4.00 per share and approved by the individual option holder were canceled
and replaced by the same number of options exercisable at $4.00 per share, the
fair value of the Company's common stock as determined by the Board on the date
of the re-pricing. In reaching this determination, the Board considered a broad
range of factors including the illiquid nature of an investment in the Company's
common stock, transactions of the Company's common stock with third parties, the
Company's historical financial performance relative to that of comparable
companies and its future prospects. Fifty percent of those options which were
vested prior to the re-pricing vested immediately under the Re-pricing Plan. All
remaining stock options, previously vested and unvested, had the same term as
the original option grants but with the vesting schedule commencing July 30,
1996.

                                                                        Weighted
                                                            Weighted     Average
                                                             Average  Fair Value
                                                Number of   Exercise  of Options
                                                   Shares      Price     Granted

Outstanding at June 30, 1996                      709,376     $ 4.02
Granted                                           526,292       4.00      $ 1.64
Exercised                                         (85,850)      1.61
Canceled                                         (305,226)      6.15
                                                ---------
Outstanding at June 30, 1997                      844,592       3.41
                                                ---------
Granted                                           471,131       9.41      $ 5.27
Exercised                                        (204,468)      2.48
Canceled                                          (16,693)      7.11
                                                ---------
Outstanding at June 30, 1998                    1,094,562       6.11
                                                ---------
Granted                                           635,705      19.29      $12.07
Exercised                                        (309,162)      3.93
Canceled                                          (38,227)     10.36
                                                ---------
Outstanding at June 30, 1999                    1,382,878      12.54
                                                =========

<PAGE>   24

40   MERCURY COMPUTER SYSTEMS, INC.



Information related to stock options outstanding as of June 30, 1999, is as
follows:
<TABLE>
<CAPTION>

                                              Weighted                                  Exercisable
                                               Average        Weighted  Exercisable        Weighted
                              Number         Remaining         Average    Number of         Average
Range of Exercise Prices  of Options  Contractual Life  Exercise Price      Options  Exercise Price
<S>                        <C>                    <C>           <C>         <C>              <C>
$ 2.00-$ 3.50                 64,500              2.72          $ 2.64       64,300          $ 2.64
$ 4.00                       306,243              7.37            4.00      142,909            4.00
$ 5.00-$ 7.50                 11,900              4.58            7.35       11,500            7.35
$ 8.00                       276,030              8.31            8.00       59,180            8.00
$10.00-$15.25                242,020              9.16           14.23       10,860           12.30
$15.63-$26.38                482,185              9.46           21.15       14,057           17.42
                           ---------                                        -------
$ 2.00-$26.38              1,382,878              8.36           12.54      302,806            5.54
                           =========                                        =======
</TABLE>

There were 377,240 and 473,890 options exercisable at June 30, 1998 and 1997,
respectively, with weighted average exercise prices of $3.57 and $2.89. The fair
value of each option granted during fiscal years ended June 30, 1999, 1998 and
1997, is estimated on the date of grant using the Black-Scholes option-pricing
model utilizing the following weighted-average assumptions: (1) expected
risk-free interest rate of 4.90% in 1999, 6.25% in 1998 and 6.80% in 1997; (2)
expected option life of 6 years in 1999 and 1998 and 8 years in 1997; (3)
expected stock volatility of 63% for June 30, 1999, 50% for June 30, 1998 and
none for June 30, 1997; and (4) expected dividend yield of 0.0%.


EMPLOYEE STOCK PURCHASE PLAN
During 1997, the Company adopted the 1997 Employee Stock Purchase Plan ("ESPP")
and authorized 250,000 shares for future issuance under which rights are granted
to purchase shares of common stock at 85% of the lesser of the market value of
such shares at either the beginning or the end of each six month offering
period. The plan permits employees to purchase common stock through payroll
deductions, which may not exceed 10% of an employee's compensation as defined in
the plan. During the two offerings in fiscal 1999, the Company issued 16,213 and
12,011 shares of common stock to employees who participated in the plan at
prices of $11.90 and $22.95, respectively. Shares available for future purchase
under the ESPP totaled 221,776 at June 30, 1999.
         The weighted-average fair value of purchase rights granted in fiscal
1999 was $6.46. The fair value of the employees' purchase rights was estimated
using the Black-Scholes model with the following assumptions; dividend yield of
0.0%, an expected life of 6 months, expected volatility of 63%, and risk-free
interest rate of 4.90%.

<PAGE>   25


                                             MERCURY COMPUTER SYSTEMS, INC.   41


         Had compensation cost for the Company's stock option grants and stock
issued in conjunction with the ESPP been determined based on the fair value at
the grant dates, as calculated in accordance with SFAS No. 123, the Company's
net income and net income per common share for the fiscal years ended June 30,
1999, 1998 and 1997, would approximate the following pro forma amounts as
compared to the amounts reported:

                                   Net Income per    Net Income per
                                     Common Share      Common Share
                         Net Income        -Basic          -Diluted
As reported:
   1999                    $13,462          $1.32           $1.25
   1998                    $ 8,731          $1.21           $0.94
   1997                    $ 4,611          $0.90           $0.58
Pro forma:
   1999                    $11,950          $1.18           $1.11
   1998                    $ 8,244          $1.14           $0.89
   1997                    $ 4,345          $0.85           $0.55

The effects of applying SFAS No. 123 in this disclosure are not indicative of
future amounts. SFAS No. 123 does not apply to awards prior to 1995 and
additional awards in future years are anticipated.

WARRANTS
At June 30, 1997 a warrant to purchase 10,000 shares of the Company's common
stock was outstanding with an exercise price of $2.00 per share and exercisable
through June 30, 2000. In September 1997 the warrants were exercised.

I. INCOME TAXES:
Income tax expense consisted of the following:


YEAR ENDED JUNE 30,                        1999            1998           1997
Federal:
    Current                               $6,377          $5,680         $3,088
    Deferred                                (479)         (1,172)          (592)
                                          ------          ------         ------
                                           5,898           4,508          2,496
State:
    Current                                1,295             925            301
    Deferred                                (708)           (111)            (4)
                                          ------          ------         ------
                                             587             814            297
Foreign - current                            146             106            140
                                          ------          ------         ------
                                          $6,631          $5,428         $2,933
                                          ======          ======         ======

<PAGE>   26

42   MERCURY COMPUTER SYSTEMS, INC.



The following is a reconciliation between the statutory provision for federal
income taxes and the effective income tax expense:

YEAR ENDED JUNE 30,                                        1999    1998    1997

Income taxes at federal statutory rates                    35.0%   35.0%   34.0%
State income tax, net of federal tax benefit and credits    1.9     3.7     3.9
Research and development credits utilized                  (3.8)   (2.2)   (3.5)
Tax-exempt interest income                                 (1.8)     --      --
Other                                                       1.7     1.8     4.5
                                                           ----    ----    ----
                                                           33.0%   38.3%   38.9%
                                                           ====    ====    ====

The components of the net deferred tax asset are as follows:

JUNE 30,                                                   1999        1998

Receivables, allowances and inventory reserves            $1,654      $  810
Accrued vacation                                             368         620
Property and equipment                                       301         429
Capitalized software development costs                      (125)        (42)
State tax credit carryforwards                               491          --
Other temporary differences                                  596         281
                                                          ------      ------
Total deferred tax asset, net                             $3,285      $2,098
                                                          ======      ======

No valuation allowance was deemed necessary for the deferred tax asset. Although
realization is not assured, management believes it is more likely than not that
all of the deferred tax asset will be realized.
         At June 30, 1999, the Company had state research and development and
investment tax credit carryforwards of approximately $502,000 and $254,000
respectively. Research and development credit carryforwards begin to expire in
2014 and investment tax credit carryforwards have no expiration.


<PAGE>   27

                                             MERCURY COMPUTER SYSTEMS, INC.   43



J. EMPLOYEE BENEFIT PLANS:
The Company maintains a qualified profit sharing 401(a) Plan and 401(k) Plan.
The plans cover employees who have attained the age of 21. Employee
contributions to the 401(k) Plan may range from 1% to 15% of compensation with a
discretionary matching Company contribution. The Company will match up to 2% of
compensation. The Company may also make optional contributions to both plans for
any plan year at its discretion.
         Expense recognized by the Company under the 401(a) and 401(k) plans was
approximately $1,000,000, $710,000 and $427,000 during the years ended June 30,
1999, 1998 and 1997, respectively.
         The Company maintains a bonus plan which provides cash awards to
employees, at the discretion of the Board of Directors, based upon operating
results and employee performance. Bonus expense to employees was approximately
$2,753,000, $1,988,000, and $1,245,000 during the years ended June 30, 1999,
1998 and 1997, respectively.


K. OPERATING SEGMENT AND GEOGRAPHIC INFORMATION:
The Company adopted SFAS No. 131 "Disclosures about Segments of an Enterprise
and Related Information" (Statement No. 131), in fiscal 1999. This Statement
supersedes SFAS No. 14 "Financial Reporting for Segments of a Business
Enterprise," but retains the requirement to report information about major
customers. This statement establishes standards for reporting information about
operating segments in annual financial statements and requires selected
information about operating segments in interim financial reports issued to
stockholders. It also establishes standards for related disclosures about
products and services and geographic areas.
         Operating segments are defined as components of an enterprise evaluated
regularly by the Company's senior management in deciding how to allocate
resources and in assessing performance. The Company has seven principal
operating segments: North American defense and commercial, medical imaging,
international defense and commercial, shared storage, digital wireless, research
and development, and other commercial businesses. These operating segments were
determined based upon the nature of the products offer ed to customers, the
market characteristics of each operating segment, and the Company's management
structure. The Company has five reportable segments; North American defense and
commercial segment, medical imaging segment, shared storage segment, other
defense and commercial segment, and research and development segment. The other
defense and commercial segment is comprised of international defense and
commercial, digital wireless, and other commercial businesses unrelated to the
defense, medical imaging or shared storage businesses. These operating segments
are not separately reported, as they do not meet any of Statement No. 131's
quantitative thresholds.

<PAGE>   28

44   MERCURY COMPUTER SYSTEMS, INC.



         The accounting policies of the business segments are the same as those
described in "Note B: Summary of Significant Accounting Policies."
<TABLE>
<CAPTION>

                            North American                           Other
                             Defense and     Medical      Shared   Defense and     Research and
                              Commercial     Imaging      Storage   Commercial     Development
                              Segment(2)     Segment      Segment     Segment        Segment     Corporate    Consolidated
1999
Sales to unaffiliated
<S>                            <C>          <C>          <C>           <C>          <C>           <C>           <C>
    customers                  $79,906      $15,295      $ 2,232       $9,138       $    --       $    --       $ 106,571
Income (loss)
    before taxes(1)             53,174        6,353       (1,775)       2,747       (19,639)      (20,767)         20,093
Depreciation/
    amortization expense           191           70          102           11         1,263         2,881           4,518

1998
Sales to unaffiliated
    customers                  $66,074      $11,232      $   885       $7,353       $    --       $    --       $  85,544
Income (loss)
    before taxes(1)             40,399        4,499       (3,423)       1,542       (12,917)      (15,941)         14,159
Depreciation/
    amortization expense           155           68           52           15           924         2,105           3,319

1997
Sales to unaffiliated
    customers                  $50,921      $ 6,906      $ 2,128       $4,619       $    --       $    --       $  64,574
Income (loss)
    before taxes(1)             30,781        2,303       (1,639)       1,318       (11,566)      (13,653)          7,544
Depreciation/
    amortization expense           154           51           41           22         1,067         1,958           3,293
</TABLE>

(1) Interest income, interest expense and foreign exchange gain/(loss) are
reported in Corporate and not allocated to the principal operating segments.
Only expenses directly related to an operating segment are charged to the
appropriate operating segment. All other expenses for marketing and
administrative support activities that cannot be specifically identified with a
principal operating segment are allocated to Corporate.

(2) The North American defense and commercial segment differs in definition from
the defense market segment described in the Company's management discussion and
analysis ("MD&A"). The defense market segment in the MD&A refers to the
worldwide defense market. The North American defense and commercial segment is
an operating segment as defined by Statement No. 131 and includes the defense
business in North America only with some North American commercial business.

<PAGE>   29


                                             MERCURY COMPUTER SYSTEMS, INC.   45



Foreign revenue is based on the country in which the legal subsidiary is
domiciled. Foreign revenue and long-lived assets represent less than 10% of the
Company's total revenue and long-lived assets for the fiscal years ended June
30, 1999, 1998, and 1997, respectively.
         Customers comprising 10% or more of the Company's revenues for the
periods shown below are as follows:


YEAR ENDED JUNE 30,                         1999     1998     1997

Customer D                                   12%      10%      --
Customer E                                   --       --       10%
Customer F                                   16%      --       22%
Customer B                                   22%      20%      --
Customer A                                   --       10%      --

During the fiscal year ended June 30, 1998, Customer E was acquired by Customer
B. During the fiscal year ended June 30, 1998, revenues to Customer E, on a
stand alone basis, were approximately 5%.


L. SUBSEQUENT EVENTS:
On August 27, 1999, the Company signed a commitment letter with a commercial
financing company to issue two 7.30%, senior secured financing notes ("the
Notes"), due September 2014. The total principal value of the Notes amount to
$14,500,000. The Company's corporate headquarters and an adjacent building with
a combined cost basis of $17,670,000, secure the Notes.
         On September 1, 1999, Mercury formed a new joint venture company
("AgileVision") with Sarnoff Corporation, the developer of color television and
a pioneer in the creation of digital television ("DTV"). Combining the
intellectual property of both companies, this new venture is expected to provide
the broadcast and cable industries with products and solutions that will
significantly increase the flexibility of a digital television infrastructure.
The new company will provide products and services that allow an economical
entry point to DTVservices, with the option of expanding performance and
features to meet the demands of the evolving DTVaudience. The Company is
initially required to contribute $2.5 million in cash in addition to technology
to the joint venture.

<PAGE>   30




46   MERCURY COMPUTER SYSTEMS, INC.



REPORT OF INDEPENDENT ACCOUNTANTS


To the Board of Directors and
Stockholders of Mercury Computer Systems, Inc.:

In our opinion, the accompanying consolidated balance sheets and the related
consolidated statements of operations, of changes in stockholders' equity, and
of cash flows present fairly, in all material respects, the financial position
of Mercury Computer Systems, Inc. and its subsidiaries at June 30, 1999 and
1998, and the results of their operations and their cash flows for each of the
three years in the period ended June 30, 1999 in conformity with generally
accepted accounting principles. These financial statements are the
responsibility of the Company's management; our responsibility is to express an
opinion on these financial statements based on our audits. We conducted our
audits of these statements in accordance with generally accepted auditing
standards, which require that we plan and perform the audit to obtain reasonable
assurance about whether the financial statements are free of material
misstatement. An audit includes examining, on a test basis, evidence supporting
the amounts and disclosures in the financial statements, assessing the
accounting principles used and significant estimates made by management, and
evaluating the overall financial statement presentation. We believe that our
audits provide a reasonable basis for the opinion expressed above.



/s/ PricewaterhouseCoopers LLP

Boston, Massachusetts
July 29, 1999, except for the information
in the first and second paragraph of Note L
as to which the date is August 27, 1999
and September 1, 1999, respectively

<PAGE>   31




                                              MERCURY COMPUTER SYSTEMS,INC.   47


SUPPLEMENTARY INFORMATION (UNAUDITED)


The following sets forth certain unaudited consolidated quarterly statements of
operations data for each of the Company's last eight quarters. In management's
opinion, this quarterly information reflects all adjustments, consisting only of
normal recurring adjustments, necessary for a fair presentation for the periods
presented. Such quarterly results are not necessarily indicative of future
results of operations and should be read in conjunction with the audited
consolidated financial statements of the Company and the notes thereto included
elsewhere herein.


<TABLE>
<CAPTION>

1999                                     1ST QUARTER  2ND QUARTER   3RD QUARTER    4TH QUARTER
<S>                                          <C>          <C>           <C>            <C>
Revenues                                     $24,062      $25,598       $27,225        $29,686
Cost of revenues                               8,460        8,606         8,229          8,942
                                             -------      -------       -------        -------
    Gross profit                              15,602       16,992        18,996         20,744
                                             -------      -------       -------        -------
Operating expenses:
    Selling, general and administrative        7,358        8,304         8,668          8,672
    Research and development                   4,707        4,669         5,373          5,960
                                             -------      -------       -------        -------
    Total operating expenses                  12,065       12,973        14,041         14,632
                                             -------      -------       -------        -------
Income from operations                         3,537        4,019         4,955          6,112
                                             -------      -------       -------        -------
Interest income, net                             369          326           313            277
Other income (expense), net                       45          261           (24)           (97)
                                             -------      -------       -------        -------
Income before taxes                            3,951        4,606         5,244          6,292
Provision for income taxes                     1,422        1,572         1,835          1,802
                                             -------      -------       -------        -------
Net income                                   $ 2,529      $ 3,034       $ 3,409        $ 4,490
                                             =======      =======       =======        =======
Net income per common share:
    Basic                                    $  0.25      $  0.30       $  0.33        $  0.44
                                             =======      =======       =======        =======
    Diluted                                  $  0.24      $  0.28       $  0.31        $  0.41
                                             =======      =======       =======        =======



1998                                     1ST QUARTER  2ND QUARTER   3RD QUARTER    4TH QUARTER
Revenues                                     $19,039      $20,624       $22,364        $23,517
Cost of revenues                               6,661        7,283         7,832          8,308
                                             -------      -------       -------        -------
    Gross profit                              12,378       13,341        14,532         15,209
Operating expenses:
    Selling, general and administrative        6,645        6,846         7,104          7,284
    Research and development                   3,381        3,405         3,749          3,941
                                             -------      -------       -------        -------
    Total operating expenses                  10,026       10,251        10,853         11,225
                                             -------      -------       -------        -------
Income from operations                         2,352        3,090         3,679          3,984
Interest income, net                             231          219           266            368
Other income (expense), net                       83         (125)          (10)            22
                                             -------      -------       -------        -------
Income before taxes                            2,666        3,184         3,935          4,374
Provision for income taxes                     1,060        1,210         1,496          1,662
                                             -------      -------       -------        -------
Net income                                   $ 1,606      $ 1,974       $ 2,439        $ 2,712
                                             =======      =======       =======        =======
Net income per common share:
    Basic                                    $  0.31      $  0.37       $  0.29        $  0.27
                                             =======      =======       =======        =======
    Diluted                                  $  0.20      $  0.24       $  0.24        $  0.25
                                             =======      =======       =======        =======
</TABLE>


<PAGE>   1


                                                                    EXHIBIT 21.1


                         SUBSIDIARIES OF THE REGISTRANT


           NAME                                     JURISDICTION OF ORGANIZATION

Mercury Computer Securities Corporation             Massachusetts
Riverneck Road LLC                                  Delaware
199 Riverneck LLC                                   Delaware
Mercury Computer International Sales Corporation    Delaware
Mercury Computer Systems BV                         The Netherlands
Nihon Mercury Computer Systems KK                   Japan
Mercury Computer Systems SARL                       France
Mercury Systems Ltd                                 United Kingdom
Mercury Computer Systems Export, Incorporated       Barbados


                                       26

<PAGE>   1
                                                             EXHIBIT 23.1





                       CONSENT OF INDEPENDENT ACCOUNTANTS


We hereby consent to the incorporation by reference in the Registration
Statement on Form S-8 (No. 333-53291) of Mercury Computer Systems, Inc. of our
report dated July 29, 1999, except for the information in the first and second
paragraph of Note L as to which date is August 27, 1999 and September 1, 1999,
respectively, relating to the consolidated financial statements, which appears
in the Annual Report to Shareholders, which is incorporated by reference in this
Annual Report on Form 10-K. We also consent to the incorporation by reference of
our report dated July 29, 1999, relating to the financial statement schedule,
which appears in this Form 10-K.

PricewaterhouseCoopers LLP

Boston, Massachusetts
September 24, 1999



<TABLE> <S> <C>

<ARTICLE> 5
<MULTIPLIER> 1
<CURRENCY> U.S. DOLLARS

<S>                             <C>
<PERIOD-TYPE>                   12-MOS
<FISCAL-YEAR-END>                          JUN-30-1999
<PERIOD-START>                             JUL-01-1998
<PERIOD-END>                               JUN-30-1999
<EXCHANGE-RATE>                                      1
<CASH>                                           3,676
<SECURITIES>                                    21,740
<RECEIVABLES>                                   28,915
<ALLOWANCES>                                       376
<INVENTORY>                                     12,431
<CURRENT-ASSETS>                                61,793
<PP&E>                                          40,054
<DEPRECIATION>                                  14,729
<TOTAL-ASSETS>                                  97,511
<CURRENT-LIABILITIES>                           19,481
<BONDS>                                              0
                                0
                                          0
<COMMON>                                           103
<OTHER-SE>                                      77,337
<TOTAL-LIABILITY-AND-EQUITY>                    97,511
<SALES>                                        106,571
<TOTAL-REVENUES>                               106,571
<CGS>                                           34,237
<TOTAL-COSTS>                                   34,237
<OTHER-EXPENSES>                                52,241
<LOSS-PROVISION>                                     0
<INTEREST-EXPENSE>                                   0
<INCOME-PRETAX>                                 20,093
<INCOME-TAX>                                     6,631
<INCOME-CONTINUING>                             13,462
<DISCONTINUED>                                       0
<EXTRAORDINARY>                                      0
<CHANGES>                                            0
<NET-INCOME>                                    13,462
<EPS-BASIC>                                       1.32
<EPS-DILUTED>                                     1.25


</TABLE>


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