CRAY INC
S-3/A, 2000-06-19
ELECTRONIC COMPUTERS
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<PAGE>   1

     As filed with the Securities and Exchange Commission on June 16, 2000

                                                      REGISTRATION NO. 333-30644

================================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                   ----------


                               Amendment No. 3 to
                         Form S-3 Registration Statement
                        Under the Securities Act of 1933


                                   ----------

                                   CRAY INC.
             (Exact name of registrant as specified in its charter)

                                   ----------

WASHINGTON                                                   93-0962605
(State or other jurisdiction                                 (IRS Employer
of incorporation or organization)                            Identification No.)

                             411 First Avenue South
                                    Suite 600
                                Seattle, WA 98104
                           (206) 701-2000 (telephone)
                           (206) 701-2500 (facsimile)
            (Address, including zip code, and telephone and facsimile
          numbers, including area code, of principal executive offices)

                                   ----------

                   Kenneth W. Johnson, Chief Financial Officer
                                   Cray Inc.
                             411 First Avenue South
                                    Suite 600
                                Seattle, WA 98104
                           (206) 701-2000 (telephone)
                           (206) 701-2500 (facsimile)
                (Name, address, including zip code, and telephone
        and facsimile numbers, including area code, of agent for service)

                                    Copy To:
                               Christopher J. Voss
                                 Stoel Rives LLP
                          One Union Square, 36th Floor
                             Seattle, WA 98101-3197
                           (206) 624-0900 (telephone)
                           (206) 386-7500 (facsimile)

        APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC:
      From time to time after this registration statement becomes effective

If the only securities being registered on this Form are to be offered pursuant
to dividend or interest reinvestment plans, please check the following box. [ ]

If any of the securities being registered on this Form are to be offered on a
delayed or continuous basis pursuant to Rule 415 under the Securities Act of
1933, other than securities offered only in connection with a dividend or
interest reinvestment plan, check the following box. [X]

If this Form is filed to register additional securities for an offering pursuant
to Rule 462(b) under the Securities Act, please check the following box and list
the Securities Act registration statement number of the earlier effective
registration statement for the same offering. [ ]

<PAGE>   2

If this Form is a post-effective amendment filed pursuant to Rule 462(c) under
the Securities Act, check the following box and list the Securities Act
registration number of the earlier effective registration statement for the same
offering. [ ]

If delivery of the prospectus is expected to be made pursuant to Rule 434,
please check the following box. [ ]

The Registrant hereby amends this registration statement on such date or dates
as may be necessary to delay its effective date until the Registrant shall file
a further amendment which specifically states that this registration statement
shall thereafter become effective in accordance with section 8(a) of the
Securities Act of 1933 or until the registration statement shall become
effective on such date as the Securities and Exchange Commission, acting
pursuant to said section 8(a), may determine.

<PAGE>   3


PROSPECTUS, Subject to Completion, dated June 16, 2000


                                   CRAY INC.

                        5,536,875 shares of Common Stock


        These shares of Common Stock are being offered and sold from time to
time by certain of our current shareholders.

        The selling shareholders may sell the shares from time to time at fixed
prices, market prices, prices computed with formulas based on market prices, or
at negotiated prices, and may engage a broker or dealer to sell the shares. For
additional information on the selling shareholders' possible methods of sale,
you should refer to the section of this prospectus entitled "Plan of
Distribution" on page 6. We will not receive any proceeds from the sale of the
shares, but will bear the costs relating to the registration of the shares.

        Our Common Stock is traded on the Nasdaq National Market under the
symbol "CRAY." On June 15, 2000, the closing price for our Common Stock was
$4.50 per share.


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


        THE SHARES OFFERED IN THIS PROSPECTUS INVOLVE A HIGH DEGREE OF RISK. YOU
SHOULD CAREFULLY CONSIDER THE "RISK FACTORS" CONTAINED IN OUR QUARTERLY REPORT
ON FORM 10-Q FOR THE QUARTER ENDED MARCH 31, 2000, AND IN OUR FUTURE FILINGS
MADE WITH THE SECURITIES AND EXCHANGE COMMISSION, WHICH ARE INCORPORATED BY
REFERENCE IN THIS PROSPECTUS, IN DETERMINING WHETHER TO PURCHASE SHARES OF OUR
COMMON STOCK.


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

NEITHER THE SECURITIES AND EXCHANGE COMMISSION NOR ANY STATE SECURITIES
COMMISSION HAS APPROVED OR DISAPPROVED THE SHARES, OR DETERMINED IF THIS
PROSPECTUS IS TRUTHFUL OR COMPLETE. ANY REPRESENTATION TO THE CONTRARY IS A
CRIMINAL OFFENSE.

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

                   The date of this Prospectus is _____, 2000.

<PAGE>   4
                                TABLE OF CONTENTS


<TABLE>
<CAPTION>
        Section                                                    Page
        -------                                                    ----
<S>                                                                <C>
        Our Business ......................................          3
        Selling Shareholders ..............................          3
        Plan of Distribution ..............................          8
        Experts ...........................................         10
        Limitation of Liability and Indemnification .......         10
        Information Incorporated by Reference .............         11
        Available Information .............................         12
</TABLE>



        You should rely only on information contained or incorporated by
reference in this prospectus. See "Information Incorporated by Reference" on
page 11. Neither Cray nor the selling shareholders have authorized any other
person to provide you with information different from that contained in this
prospectus.

        The shares of Common Stock are not being offered in any jurisdiction
where the offering is not permitted.



                                       -2-

<PAGE>   5

                                  OUR BUSINESS


        Cray Inc., formerly known as Tera Computer Company, designs, builds and
sells high-performance computer systems, sometimes referred to as
"supercomputers." Our executive offices are located at Merrill Place, Suite 600,
411 First Avenue South, Seattle, WA 98104-2860, and our telephone number is
(206) 701-2000.

                              SELLING SHAREHOLDERS


        On February 2, 2000, we issued an aggregate of 5,226,875 shares of our
common stock to 28 investors in a private placement (the "February Placement")
that is described more fully in our Current Report on Form 8-K for the event of
February 2, 2000, as filed with the Securities and Exchange Commission on
February 15, 2000. Except as noted below, each investor acquired the number of
shares of our common stock set forth opposite their respective names under the
heading "Shares Being Offered" on the selling shareholder table below in the
February Placement.


        At various times during 1999, we issued warrants to purchase shares of
our common stock to another ten of the selling shareholders listed on the table
below, including Kirlin Securities, Inc., a registered broker-dealer, in
consideration for financial advisory and related services.


        The following table sets forth certain information as of May 8, 2000
regarding the selling shareholders' ownership of our common stock and as
adjusted to reflect the selling shareholders' ownership of our common stock if
all shares covered by this prospectus are sold. The shares covered by this
prospectus include:


        -      shares of common stock issued to certain of the selling
               shareholders in the February Placement;

        -      shares of common stock issuable upon exercise of warrants issued
               to certain of the selling shareholders as payment for financial
               advisory services in January 1999;

        -      shares of common stock issuable upon exercise of warrants issued
               to certain of the selling shareholders as payment for financial
               advisory services in March 1999; and

        -      shares of common stock issuable upon exercise of a warrant issued
               to certain of the selling shareholders for financial advisory
               services in connection with a private placement of our
               securities.


        The selling shareholders' percentage of ownership after this offering is
based on 33,409,206 shares of common stock that were outstanding as of MAY 8,




                                      -3-
<PAGE>   6


2000, and assumes no exercise of any outstanding options or warrants after MAY
8, 2000.




<TABLE>
<CAPTION>
                                                                                     Ownership After Offering
                                                   Shares           Shares             if All Shares Offered
                                               Owned Prior to        Being                Hereby Are Sold
Selling Shareholder                               Offering          Offered          Shares           Percent
-------------------                            --------------      ---------        ---------        ---------
<S>                                            <C>                 <C>              <C>              <C>
Banca del Gottardo (1)                            2,721,402        2,391,875          329,527               (1)

Castle Creek Technology
Partners LLC# (2)                                   773,422          280,000          493,422              1.5%

William David Corbett                                25,000           25,000                0                0

Cranshire Capital, L.P. (3)                         280,000          280,000                0                0

Angel Cruz#                                               0           57,000                0                0

DM Management, LLC (4)                              130,000          130,000                0                0

EDJ Limited (5)                                      50,000           50,000                0                0

Jack E. Erlanger#                                    25,000           25,000                0                0

Nathan Goldstein#                                         0            6,000                0                0

Harpel Family Partnership (6)                        76,450           29,840           46,610                *

Harpel International, L.P. (6)                       37,978           16,140           21,838                *

Harpel Partners, L.P. (6)                           345,109          107,820          237,239                *

Harpel Select Growth, L.P. (6)                      152,132           46,200          105,932                *

Headwater Holdings, LLC# (7)                        200,000          200,000                0                0

William Hott                                         40,000           40,000                0                0

JMG Capital Partners, L.P. (8)                      100,000          100,000                0                0

JMG Triton Offshore Fund Ltd. (9)                   100,000          100,000                0                0
</TABLE>




                                      -4-
<PAGE>   7


<TABLE>
<CAPTION>
                                                                                     Ownership After Offering
                                                   Shares           Shares             if All Shares Offered
                                               Owned Prior to        Being                Hereby Are Sold
Selling Shareholder                               Offering          Offered          Shares           Percent
-------------------                            --------------      ---------        ---------        ---------
<S>                                            <C>                 <C>              <C>              <C>
Anthony J. Kirincic#                                      0            6,000                0                0

Kirlin Securities, Inc.+ (10)                             0           20,000                0                0

David O. Lidner#                                          0            6,000                0                0

Ivan Lieberburg                                      25,000           25,000                0                0

Christopher A. Marlett
Living Trust#                                        30,000           30,000                0                0

MDB Capital Group, LLC + (11)                        20,000           20,000                0                0

Montrose Investments Ltd.# (12)                     800,000          400,000          400,000              1.2%

Nob Hill Capital
Associates, L.P. (13)                                15,000           15,000                0                0

Nob Hill Capital Partners, L.P. (13)                 85,000           85,000                0                0

Thomas Parigian#                                          0           64,000                0                0

Timothy R. Pask                                      30,000           30,000                0                0

Thomas Poletti                                            0            5,000                0                0

Photiney Poliak#                                          0            5,000                0                0

Denise Reilly#                                            0           31,000                0                0

Raymond Scott                                        50,000           50,000                0                0

Gary J. Shemano aka The
Shemano Group Investment
Account# (14)                                       100,000          100,000                0                0

David Stefansky#                                     50,000           50,000                0                0

Strong River Investments (15)                       811,864          600,000          211,864                *
</TABLE>



                                      -5-
<PAGE>   8


<TABLE>
<CAPTION>
                                                                                     Ownership After Offering
                                                   Shares           Shares             if All Shares Offered
                                               Owned Prior to        Being                Hereby Are Sold
Selling Shareholder                               Offering          Offered          Shares           Percent
-------------------                            --------------      ---------        ---------        ---------
<S>                                            <C>                 <C>              <C>              <C>
Trans-Union Group, Inc. (16)                         20,000           20,000                0                0

Viviana Partners, L.P. (17)                          50,000           50,000                0                0

Von Graffenried AG
Privatbank (18)                                      60,000           60,000                0                0
</TABLE>


----------

+    Registered broker-dealer

#    Affiliate of registered broker-dealer

*    Less than 1%

(1)     Banca del Gottardo has represented to us that it has purchased our
        common stock for its own account and on behalf of its private banking
        and other clients, that it possesses neither investment nor voting power
        with respect to these securities, and that neither Banca del Gottardo
        nor any client or group of affiliated clients owns more than one percent
        of our outstanding shares of common stock.

(2)     Castle Creek Partners LLC is the investment manager for Castle Creek
        Technology Partners LLC, and consequently may be deemed to have voting
        control and investment discretion over the securities held by Castle
        Creek Technology Partners LLC. Castle Creek Partners LLC disclaims
        beneficial ownership of all securities owned by Castle Creek Technology
        Partners LLC. Daniel Asher and John Ziegelman, managing members of
        Castle Creek Partners LLC, may be deemed as a result thereof to be the
        beneficial owners of the securities held by Castle Creek Technology
        Partners LLC. Messrs. Asher and Ziegelman disclaim such beneficial
        ownership.

(3)     Voting and/or investment power held by Downsview Capital, Inc. (Mitchell
        P. Kopin is sole shareholder, officer and director).

(4)     Voting and/or investment power held by Robert L. Miller and Marc S.
        Drier

(5)     Voting and/or investment power held by Jeffrey H. Porter.

(6)     Voting and/or investment power held by James W. Harpel.

(7)     Voting and/or investment power held by Jeff Goshay.

(8)     Voting and/or investment power held by Jonathan M. Glaser, Member
        Manager.

(9)     Voting and/or investment power held by Roger Richter.

(10)    Voting and/or investment power held by Anthony Kirincic.

(11)    Voting and/or investment power held by Chris Marlett, Dyana Marlett,
        Anthony DiGandomenico and James D. Bowyer. MDB Capital Group is an NASD
        registered broker/dealer. The above-named individuals are NASD
        registered persons.

(12)    Voting and/or investment power held by Harlan B. Korenvacs, Kenneth M.
        Hirsh, Laurence H. Lebowitz, William E. Rose, Richard L. Booth, David C.
        Haley and Jamiel A. Akhtar.

(13)    Voting and/or investment power held by Stephen R. Mittel.



                                      -6-
<PAGE>   9

(14)    Voting and/or investment power held by Gary Shemano, aka Shemano Group
        Investment Account.

(15)    Voting and/or investment power held by Tom Waugh, Managing Director,
        Cavallo Capital Corp.

(16)    Voting and/or investment power held by Robert Yin Chin Lee and Robert
        Hsiang Lin Wu.

(17)    Voting and/or investment power held by Stuart Zimmerman.


(18)    Voting and/or investment power held by Peter L. Heller and Fritz Rudolf.


        The shares of common stock listed as owned by Banca del Gottardo after
this offering, together with 1,241,111 shares issuable upon exercise of
warrants, have been registered for offer and sale by Banca del Gottardo in
Registration Statements on Form S-3, Registration Nos. 333-76223 and 333-83521.
Banca del Gottardo has represented to us that it has purchased our common stock
for its own account and on behalf of its private banking and other clients, that
it possesses neither investment nor voting power with respect to these
securities, and that neither Banca del Gottardo nor any client or group of
affiliated clients owns more than one percent of our outstanding shares of
common stock.

        The shares of common stock listed as owned by Castle Creek Technology
Partners LLC, DM Management, LLC, Harpel Family Partnership, Harpel
International, L.P., Harpel Partners, L.P., Harpel Select Growth, L.P., Montrose
Investments Ltd. and Strong River Investments after this offering have been
registered for offer and sale by these selling shareholders in a Registration
Statement on Form S-3, Registration No. 333-83521.

        Except as set forth below, none of the selling shareholders has held any
positions or office or had any other material relationship with us or any of our
affiliates within the past three years:

        -      On February 2, 2000, Castle Creek Technology Partners LLC filed a
               Schedule 13 G/A, indicating that it had beneficial ownership of
               1,552,744 shares, or 6.2%, of our outstanding common stock. On
               March 20, 2000, Castle Creek Technology Partners LLC filed an
               additional Schedule 13G/A indicating that it no longer owned 5%
               or more of our outstanding common stock.

        In recognition of the fact that the selling shareholders may wish to be
legally permitted to sell their shares when they deem appropriate, we have
agreed with the selling shareholders to file with the Securities and Exchange
Commission ("SEC"), under the Securities Act of 1933 (the "Securities Act"), a
registration statement on Form S-3, of which this prospectus forms a part, with
respect to the resale of the shares, and have agreed to prepare and file such
amendments and supplements to the registration statement as may be necessary to
keep the registration statement effective until the shares are no longer
required to be registered for sale by the selling shareholders.



                                      -7-
<PAGE>   10

                              PLAN OF DISTRIBUTION

        Cray is registering the shares covered by this prospectus for the
selling shareholders. As used in this prospectus, "selling shareholders"
includes the pledgees, donees, transferees or others who may later hold the
selling shareholders' interest. Cray will pay the costs and fees of registering
the shares, but the selling shareholders will pay any brokerage commissions,
discounts or other expenses relating to the sale of the shares. Cray and the
selling shareholders each have agreed to indemnify the other against certain
liabilities, including liabilities arising under the Securities Act, that relate
to statements or omissions in the registration statement of which this
prospectus forms a part.

        The selling shareholders may sell the shares in the over-the-counter
market or otherwise, at market prices prevailing at the time of sale, at prices
related to prevailing market prices, or at negotiated prices. In addition, the
selling shareholders may sell some or all of their shares through:

        -      a block trade in which a broker-dealer may resell a portion of
               the block, as principal, in order to facilitate the transaction;

        -      purchases by a broker-dealer, as principal, and resale by the
               broker-dealer for its account;

        -      transactions directly with a market maker;

        -      in privately registered transactions not involving a broker; or

        -      ordinary brokerage transactions and transactions in which a
               broker solicits purchases.

        When selling the shares, the selling shareholders may enter into hedging
transactions. For example, the selling shareholders may:

        -      enter into transactions involving short sales of the shares by
               broker-dealers;

        -      sell shares short themselves and redeliver such shares to close
               out their short positions;

        -      enter into option or other types of transactions that require the
               selling shareholder to deliver shares to a broker-dealer, who
               will then resell or transfer the shares under this prospectus; or



                                      -8-
<PAGE>   11

        -      loan or pledge the shares to a broker-dealer, who may sell the
               loaned shares or, in the event of default, sell the pledged
               shares.

        We have been advised that an affiliate of Castle Creek Technology
Partners LLC has a short position in our common stock. Castle Creek Technology
Partners LLC has confirmed to us that none of the shares covered by the
registration statement of which this prospectus forms a part will be used to
cover any portion of this short position.

        Regulation M under the Securities Exchange Act of 1934 provides that
during the period that any person is engaged in the distribution, as so defined
in Regulation M, of our common stock, such person generally may not purchase
shares of our common stock. The selling shareholders are subject to applicable
provisions of the Securities Act of 1933 and the Securities Exchange Act of 1934
and the rules and regulations thereunder, including, without limitation,
Regulation M, which provisions may limit the timing of purchases and sales of
shares of our common stock by the selling shareholders. The foregoing may affect
the marketability of our common stock.


        The selling shareholders may negotiate and pay broker-dealers
commissions, discounts or concessions for their services. Broker-dealers engaged
by the selling shareholders may allow other broker-dealers to participate in
resales. MDB Capital Group, LLC, is an "underwriter," within the meaning of
Section 2(a)(11) of the Securities Act, with respect to the shares being offered
by it hereunder; the other selling shareholders, and any broker-dealers involved
in the sale or resale of the shares, may qualify as "underwriters" within the
meaning of Section 2(a)(11) of the Securities Act. In addition, the
broker-dealers' commissions, discounts or concessions may qualify as
underwriters' compensation under the Securities Act. If the selling shareholders
qualify as "underwriters," they will be subject to the prospectus delivery
requirements of Section 5(b)(2) of the Securities Act.

        Each selling shareholder that is identified on the selling shareholder
table beginning on page 4 as an affiliate of a registered broker-dealer (i)
purchased the shares of our common stock included in the registration statement
of which this prospectus forms a part in the ordinary course of business and
(ii) at the time of purchase, had no agreements or understandings, directly or
indirectly, with any person to distribute the securities.


        In addition to selling their shares under this prospectus, the selling
shareholders may:

        -      agree to indemnify any broker-dealer or agent against certain
               liabilities related to the selling of the shares, including
               liabilities arising under the Securities Act;



                                      -9-
<PAGE>   12

        -      transfer their shares in other ways not involving market makers
               or established trading markets, including directly by gift,
               distribution, or other transfer; or

        -      sell their shares under Rule 144 of the Securities Act rather
               than under this prospectus, if the transaction meets the
               requirements of Rule 144.


        Upon notification by a selling shareholder that any material arrangement
has been entered into with a broker-dealer for the sale of the shares through a
block trade, special offering, exchange distribution or secondary distribution
or a purchase by a broker or dealer, we will file a supplement to this
prospectus, if required, pursuant to Rule 424(b) under the Securities Act,
disclosing the material terms of the transaction. In addition, we will file a
supplement to this prospectus if a selling shareholder notifies us that a donee
or pledgees intends to sell more than 500 shares.


                                     EXPERTS

     The balance sheets of Cray Inc., formerly known as Tera Computer Company,
as of December 31, 1998 and 1999 and the related statements of operations,
stockholders' equity and cash flows for each of the three years in the period
ended December 31, 1999, incorporated by reference into this prospectus, have
been audited by Deloitte & Touche LLP, independent auditors, as stated in their
report with respect thereto, which report includes an explanatory paragraph
concerning our ability to continue as a going-concern. The statements of assets
acquired and liabilities assumed of the Cray Research business unit of Silicon
Graphics, Inc. as of March 31, 2000, and the related statements of revenue and
direct operating expenses for the years ended June 30, 1998 and 1999 and the
nine month period ended March 31, 2000, included in the Form 8-K/A of Cray Inc.,
filed on June 16, 2000 and incorporated by reference into this prospectus, have
been audited by Deloitte & Touche LLP, independent auditors, as stated in their
report with respect thereto, which report includes an explanatory
paragraph describing the expense allocations by Silicon Graphics, Inc. These
financial statements has been incorporated herein by reference in reliance upon
the reports of such firm given upon their authority as experts in accounting and
auditing.

                   LIMITATION OF LIABILITY AND INDEMNIFICATION

        Our Restated Articles of Incorporation provide that, to the fullest
extent permitted by the Washington Business Corporation Act, our directors will
not be liable for monetary damages to Cray or its shareholders, excluding,
however, liability for acts or omissions involving intentional misconduct or
knowing violations of law, illegal distributions or transactions from which the
director receives benefits to which the director is not legally entitled. Our
Restated Bylaws provide that Cray will indemnify its directors and, by action of
the Board of Directors, may indemnify its officers, employees and other agents
to the fullest extent permitted by applicable law, except for any legal
proceeding that is initiated by such directors, officers, employees or agents
without authorization of the Board of Directors.

        Insofar as indemnification for liabilities arising under the Securities
Act may be permitted to directors, officers and controlling persons of Cray
pursuant to the foregoing provisions, or



                                      -10-
<PAGE>   13

otherwise, we have been advised that, in the opinion of the SEC, such
indemnification is against public policy as expressed in the Securities Act and
is, therefore, unenforceable.

                      INFORMATION INCORPORATED BY REFERENCE

        The SEC allows us to "incorporate by reference" our publicly-filed
reports into this prospectus, which means that information included in those
reports is considered part of this prospectus. Information that we file with the
SEC subsequent to the date of this prospectus will automatically update and
supersede the information contained in this prospectus. We incorporate by
reference the documents listed below and any future filings made with the SEC
under Sections 13(a), 13(c), 14 or 15(d) of the Securities Exchange Act of 1934
until the selling shareholders have sold all the shares.

        The following documents filed with the SEC are incorporated by reference
in this prospectus:

        1.     Our Annual Report on Form 10-K for the year ended December 31,
               1999;


        2.     Our Current Report on Form 8-K for the event of April 2, 2000, as
               filed with the SEC on April 17, 2000 and Amendment No. 1 thereto
               on Form 8-K/A, as filed with the SEC on June 16, 2000;


        3.     Our Current Report on Form 8-K for the event of April 3, 2000, as
               filed with the SEC on April 5, 2000;

        4.     Our Current Report on Form 8-K for the event of March 1, 2000, as
               filed with the SEC on March 3, 2000;

        5.     Our Current Report on Form 8-K for the event of February 2, 2000,
               as filed with the SEC on February 15, 2000;

        6.     Our Definitive Proxy Statement, as filed with the SEC on April
               13, 2000;


        7.     Our Quarterly Report on Form 10-Q for the quarter ended March 31,
               2000; and

        8.     The description of our common stock set forth in our Registration
               Statement on Form SB-2 (Registration No. 33-95460-LA), including
               any amendment or report filed for the purpose of updating such
               description, as incorporated by reference in




                                      -11-
<PAGE>   14

               our Registration Statement on Form 8-A (Registration No.
               0-26820), including the amendment thereto on Form 8-A/A.


        We will furnish without charge to you, on written or oral request, a
copy of any or all of the documents incorporated by reference, other than
exhibits to such documents. You should direct any requests for documents to
Investor Relations, Cray Inc., 411 First Avenue South, Suite 600, Seattle,
Washington 98104, Telephone (206) 701-2000.


        The information relating to Cray contained in this prospectus is not
comprehensive and should be read together with the information contained in the
incorporated documents.

                              AVAILABLE INFORMATION

        This prospectus is part of a Registration Statement on Form S-3 that we
filed with the SEC. Certain information in the Registration Statement has been
omitted from this prospectus in accordance with SEC rules.

        We file annual, quarterly and special reports and other information with
the SEC. You may read and copy the Registration Statement and any other document
that we file at the SEC's public reference rooms located at Room 1024, Judiciary
Plaza, 450 Fifth Street N.W., Washington, D.C. 20549; 7 World Trade Center,
Suite 1300, New York, New York 10048; and Citicorp Center, 500 West Madison
Street, Suite 1400, Chicago, Illinois 60661. Please call the SEC at
1-800-SEC-0330 for further information on the public reference rooms. Our SEC
filings are also available to you free of charge at the SEC's web site at
http://www.sec.gov.

        Statements contained in this prospectus as to the contents of any
contract or other document referred to are not necessarily complete. You should
refer to the copy of such contract or other document filed as an exhibit to the
Registration Statement.



                                      -12-
<PAGE>   15

                                     PART II

                   INFORMATION NOT REQUIRED IN THE PROSPECTUS

Item 14.    Other Expenses of Issuance and Distribution.

        All expenses in connection with the issuance and distribution of the
securities being registered will be paid by the Company. The following is an
itemized statement of these expenses (all amounts are estimated except for the
SEC and Nasdaq listing fees):

<TABLE>
<S>                                                             <C>
        SEC Registration fee .............................      $ 9,449

        Nasdaq listing fee ...............................      $17,500

        Legal fees .......................................      $ 8,000

        Accountant's Fees ................................      $ 3,000

        Miscellaneous ....................................      $    51
                                                                -------

        Total ............................................      $38,000
                                                                =======
</TABLE>


Item 15.    Indemnification of Officers and Directors.

        Article XII of the Company's Restated Articles of Incorporation and
Section 11 of the Company's Restated Bylaws require indemnification of
directors, officers, employees and agents of the Company to the fullest extent
permitted by the Washington Business Corporation Act (the "Act"). Sections
23B.08.500 through 23B.08.600 of the Act authorize a court to award, or a
corporation's board of directors to grant, indemnification to directors and
officers on terms sufficiently broad to permit indemnification under certain
circumstances for liabilities arising under the Securities Act.

        Section 23B.08.320 of the Act authorizes a corporation to limit a
director's liability to the corporation or its shareholders for monetary damages
for acts or omissions as a director, except in certain circumstances involving
intentional misconduct, self-dealing or illegal corporate loans or
distributions, or any transaction from which the director personally receives a
benefit in money, property or services to which the director is not legally
entitled. Article XI of the Company's Restated Articles of Incorporation
contains provisions implementing, to the fullest



                                      II-1
<PAGE>   16

extent permitted by Washington law, such limitations on a director's liability
to the Company and its shareholders.


Item 16.       Exhibits.

<TABLE>
<S>            <C>
        3.1    Restated Articles of Incorporation of the Company (1)

        3.2    Restated Bylaws of the Company (1)

        5      Opinion on Legality (2)

        10.1   Form of Registration Rights Agreement, dated January 21, 2000
               between the Company and certain selling shareholders (and
               schedule of similar agreements) (3)

        10.2   Form of Purchase Agreement, dated January 21, 2000, between the
               Company and certain selling shareholders (and schedule of similar
               agreements) (3)

        10.3   Form of Warrant, between the Company and DM Management, LLC (4)

        10.4   Form of Warrant, between the Company and certain selling
               shareholders (and schedule of similar warrants) (2)

        23     Consent of Deloitte & Touche LLP

        24     Power of Attorney (2)
</TABLE>

----------

(1)     Incorporated by reference to the Company's Current Report on Form 8-K
        for the event of May 21, 1999, filed with the Commission on July 21,
        1999.

(2)     Incorporated by reference to the Company's Registration Statement on
        Form S-3, Registration No. 333-30644, filed with the Commission on
        February 17, 2000.

(3)     Incorporated by reference to the Company's Current Report on Form 8-K
        for the event of February 2, 2000, filed with the Commission on February
        15, 2000.

(4)     Incorporated by reference to Exhibit 10.2 on the Company's Current
        Report on Form 8-K for the event of June 21, 1999, filed with the
        Commission on June 30, 1999.



                                      II-2
<PAGE>   17

Item 17.    Undertakings.

        (a)    The undersigned registrant hereby undertakes:

               (1)    To file, during any period in which offers or sales are
                      being made, a post-effective amendment to this
                      Registration Statement

                      (i)    To include any prospectus required by Section
                             10(a)(3) of the Securities Act of 1933;

                      (ii)   To reflect in the prospectus any facts or events
                             arising after the effective date of this
                             Registration Statement (or the most recent
                             post-effective amendment thereof) that,
                             individually or in the aggregate, represent a
                             fundamental change in the information set forth in
                             this Registration Statement; and

                      (iii)  To include any material information with respect to
                             the plan of distribution not previously disclosed
                             in the registration statement or any material
                             change to such information in the registration
                             statement;

                      provided, however, that paragraphs (a)(1)(i) and
                      (a)(1)(ii) do not apply if the information required to be
                      included in a post-effective amendment by those paragraphs
                      is contained in periodic reports filed with or furnished
                      to the Commission by the registrant pursuant to Section 13
                      or Section 15(d) of the Exchange Act that are incorporated
                      by reference in the registration statement;

               (2)    That, for the purpose of determining any liability under
                      the Securities Act, each post-effective amendment shall be
                      deemed to be a new registration statement relating to the
                      securities offered therein, and the offering of such
                      securities at that time shall be deemed to be the initial
                      bona fide offering thereof; and

               (3)    To remove from registration by means of a post-effective
                      amendment any of the securities being registered that
                      remain unsold at the termination of the offering.

        (b)    The undersigned registrant hereby undertakes that, for purposes
               of determining any liability under the Securities Act of 1933,
               each filing of the registrant's annual



                                      II-3

<PAGE>   18

               report pursuant to Section 13(a) or Section 15(d) of the
               Securities Exchange Act of 1934 that is incorporated by reference
               in the registration statement shall be deemed to be a new
               registration statement relating to the securities offered
               therein, and the offering of such securities at that time shall
               be deemed to be the initial bona fide offering thereof.

        (c)    Insofar as indemnification for liabilities arising under the
               Securities Act may be permitted to directors, officers and
               controlling persons of the registrant pursuant to the foregoing
               provisions, or otherwise, the registrant has been advised that in
               the opinion of the Commission such indemnification is against
               public policy as expressed in the Securities Act and is,
               therefore, unenforceable. In the event that a claim for
               indemnification against such liabilities (other than the payment
               by the registrant of expenses incurred or paid by a director,
               officer or controlling person of the registrant in the successful
               defense of any action, suit or proceeding) is asserted by such
               director, officer or controlling person in connection with the
               securities being registered, the registrant will, unless in the
               opinion of its counsel the matter has been settled by controlling
               precedent, submit to a court of appropriate jurisdiction the
               question, whether such indemnification by it is against public
               policy as expressed in the Securities Act and will be governed by
               the final adjudication of such issue.



                                      II-4

<PAGE>   19

                                   SIGNATURES


        Pursuant to the requirements of the Securities Act of 1933, as amended,
the registrant certifies that it has reasonable grounds to believe that it meets
all of the requirements for filing on Form S-3 and has duly caused this
Registration Statement to be signed on its behalf by the undersigned, thereunto
duly authorized, in the City of Seattle, State of Washington, on June 15, 2000.


                                             CRAY INC.


                                             By: /s/
                                                --------------------------------
                                                   James E. Rottsolk
                                                   Chief Executive Officer


<PAGE>   20


        Pursuant to the requirements of the Securities Act of 1933, as amended,
this Registration Statement has been signed by the following persons in the
capacities indicated below on the 15th day of June, 2000:


Signature and Title


                 *
-----------------------------------
Terren S. Peizer, Chairman
of the Board of Directors


                 *                                             *
-----------------------------------          -----------------------------------
Burton J. Smith, Director                    Daniel J. Evans, Director



     /s/                                                       *
-----------------------------------          -----------------------------------
James E. Rottsolk                            Kenneth W. Kennedy, Director
Chief Executive Officer and
Director


     /s/                                                       *
-----------------------------------          -----------------------------------
Kenneth W. Johnson                           John W. Titcomb, Jr., Director
Chief Financial Officer


     /s/                                                       *
-----------------------------------          -----------------------------------
Philissa Sargin                              David N. Cutler, Director
Chief Accounting Officer


                 *                                             *
-----------------------------------          -----------------------------------
Stephen C. Kiely, Director                   Dean D. Thornton, Director


     /s/
-----------------------------------
* By: James E. Rottsolk
      Attorney-in-Fact



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