MATRIXONE INC
S-8, 2000-04-20
PREPACKAGED SOFTWARE
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<PAGE>

As filed with the Securities and Exchange Commission on April 20, 2000
                                                        Registration No.333-____
================================================================================

                      SECURITIES AND EXCHANGE COMMISSION
                            WASHINGTON, D.C.  20549

                                   FORM S-8

                         REGISTRATION STATEMENT UNDER
                          THE SECURITIES ACT OF 1933

                                MATRIXONE, INC.
            (Exact Name of Registrant as Specified in Its Charter)

             Delaware                            02-0372301
    (State or Other Jurisdiction of   (I.R.S. Employer Identification No.)
    Incorporation or Organization)

                                MatrixOne, Inc.
                              Two Executive Drive
                             Chelmsford, MA 01824
              (Address of Principal Executive Offices) (Zip Code)
                             ____________________

                       2000 Employee Stock Purchase Plan
                                1999 Stock Plan
                      Amended and Restated 1996 Stock Plan
                  Amended and Restated 1987 Stock Option Plan
                           (Full Title of the Plan)
                             ____________________

                               Mark F. O'Connell
                      President & Chief Executive Officer
                                MatrixOne, Inc.
                              Two Executive Drive
                              Chelmsford, MA 01824
                    (Name and Address of Agent For Service)


                                 (978) 322-2000
         (Telephone Number, Including Area Code, of Agent For Service)
                         ______________________________

                                    Copy to:
                           Gordon H. Hayes, Jr., Esq.
                        TESTA, HURWITZ & THIBEAULT, LLP
                                125 High Street
                          Boston, Massachusetts 02110
                                 (617) 248-7000

================================================================================
<PAGE>

                        CALCULATION OF REGISTRATION FEE
================================================================================

<TABLE>
<CAPTION>
                                                                       Proposed
                                                                       Maximum         Proposed Maximum
                                                  Amount to be      Offering Price    Aggregate Offering           Amount of
  Title of Securities to be Registered             Registered         Per Share              Price            Registration Fee (3)
  ------------------------------------             -----------     --------------    -------------------      --------------------
<S>                                               <C>              <C>               <C>                      <C>
2000 Employee Stock Purchase Plan
Common Stock (Par Value $.01 Per Share)             1,350,000 (2)           $22.094     $   29,826,900.00               $ 7,874.30



1999 Stock Plan
Common Stock (Par Value $.01 Per Share)                20,250 (1)           $ 35.00        $   708,750.00               $   187.11
                                                        1,000 (1)           $ 50.20        $    50,200.00               $    13.25
                                                    1,478,750 (2)           $22.094        $32,671,502.50               $ 8,625.28



Amended and Restated 1996 Stock Plan
Common Stock (Par Value $.01 Per Share)                 6,756 (1)           $  0.33        $     2,229.48               $     0.59
                                                   10,109,138 (1)           $  0.44        $ 4,448,020.72               $ 1,174.28
                                                      472,500 (1)           $  0.67        $   316,575.00               $    83.58
                                                    1,665,411 (1)           $  1.11        $ 1,848,606.21               $   488.03
                                                      132,000 (1)           $  3.33        $   439,560.00               $   116.04
                                                      112,500 (1)           $  6.67        $   750,375.00               $   198.10
                                                      443,137 (1)           $  8.00        $ 3,545,096.00               $   935.91
                                                      208,200 (1)           $ 13.00        $ 2,706,600.00               $   714.54
                                                      112,800 (1)           $ 21.00        $ 2,368,800.00               $   625.36
                                                        4,000 (1)           $ 68.50        $   274,000.00               $    72.34
                                                      683,558 (2)           $22.094        $15,102,530.45               $ 3,987.07


Amended and Restated 1987 Stock Option
 Plan
Common Stock (Par Value $.01 Per Share)             1,369,170 (1)           $  0.33        $   451,826.10               $   119.28
                                                    1,040,151 (1)           $  0.44        $   457,666.44               $   120.82
                                                   -------------                           --------------               ----------
TOTAL:                                             19,209,321                              $95,969,237.90               $25,335.88
</TABLE>

___________________________________________

(1) Such shares are issuable upon exercise of outstanding options with fixed
    exercise prices.  Pursuant to Rule 457(h), the aggregate offering price and
    the fee have been computed upon the basis of the price at which the options
    may be exercised.  The offering price per share set forth for such shares is
    the exercise price per share at which such options are exercisable.

(2) The price of $22.094 per share, which is the average of the high and low
    prices of the Common Stock of the Registrant reported on the Nasdaq National
    Market on April 17, 2000, is set forth solely for purposes of calculating
    the filing fee pursuant to Rule 457(c) and has been used for those shares
    without a fixed exercise price.

(3) Calculated pursuant to Section 6(b) of the Securities Act of 1933.

                                       2
<PAGE>

                                    PART I


             INFORMATION REQUIRED IN THE SECTION 10(a) PROSPECTUS


Item 1.   Plan Information.


          The documents containing the information specified in this Item 1 will
be sent or given to employees, directors and others as specified by Rule
428(b)(1). In accordance with the rules and regulations of the Securities and
Exchange Commission (the "Commission") and the instructions to Form S-8, such
documents are not being filed with the Commission either as part of this
Registration Statement or as prospectuses or prospectus supplements pursuant to
Rule 424.


Item 2.   Registrant Information and Employee Plan Annual Information.


          The documents containing the information specified in this Item 2 will
be sent or given to employees, directors or others as specified by Rule
428(b)(1). In accordance with the rules and regulations of the Commission and
the instructions to Form S-8, such documents are not being filed with the
Commission either as part of this Registration Statement or as prospectuses or
prospectus supplements pursuant to Rule 424.


                                    PART II


              INFORMATION REQUIRED IN THE REGISTRATION STATEMENT


Item 3.   Incorporation of Documents by Reference.


          The following documents filed by MatrixOne, Inc. (the "Company" or the
"Registrant") with the Commission pursuant to the Securities Act of 1933, as
amended (the "Securities Act") and the Securities Exchange Act of 1934, as
amended (the "Exchange Act") are incorporated by reference in this Registration
Statement:


          (a)  The Registrant's Prospectus dated February 29, 2000, contained in
               the Registrant's Registration Statement No. 333-92731 on Form S-
               1, as amended (the "S-1 Registration Statement") filed pursuant
               to the Securities Act.


          (b)  The section entitled "Description of Registrant's Securities to
               be Registered" contained in the Registrant's Registration
               Statement on Form 8-A, filed with the Commission pursuant to
               Section 12(g) of the Exchange Act on February 2, 2000.


          All documents subsequently filed with the Commission by the Registrant
pursuant to Sections 13(a), 13(c), 14 and 15(d) of the Exchange Act, prior to
the filing of a post-effective amendment which indicates that all securities
offered herein have been sold or which deregisters all securities then remaining
unsold, shall be deemed to be incorporated by reference in this Registration
Statement and to be a part hereof from the date of filing of such documents.


Item 4.   Description of Securities.


          Not applicable.

                                       3
<PAGE>

Item 5.   Interest of Named Experts and Counsel.


          Not applicable.


Item 6.   Indemnification of Directors and Officers.


          The Delaware General Corporation Law and the Company's Certificate of
Incorporation and By-laws, as amended, provide for indemnification of the
Company's directors and officers for liabilities and expenses that they may
incur in such capacities.


          The Company's Certificate of Incorporation provides that, to the
maximum extent permitted by the General Corporation Law of the State of
Delaware, no director of the Company shall be personally liable to the Company
or to any of its stockholders for monetary damages arising out of such
director's breach of fiduciary duty.


          In addition, the Company's By-laws provide that the Company shall
indemnify any person who was or is a party or is threatened to be made a party
to any threatened, pending or completed action, suit or proceeding, whether
civil, criminal, administrative or investigative by reason of the fact that such
person is or was a director, trustee, partner, officer, employee or agent of the
Company, or is or was serving at the request of the Company as a director,
officer, employee or agent of another corporation, partnership, joint venture,
trust or other enterprise or non-profit entity, against all liability, losses,
expenses (including attorneys' fees), judgments, fines and amounts paid in
settlement by such person in connection with such action, suit or proceeding.
The Company shall only provide indemnification if such person acted in good
faith and in a manner reasonably believed to be in or not opposed to the best
interests of the Company, and, with respect to any criminal action or
proceedings, if such person had no reasonable cause to believe his conduct was
unlawful.


          The Underwriting Agreement by and between the Company and Goldman
Sachs & Co., Dain Rauscher Wessels Incorporated, U.S. Bancorp Piper Jaffray Inc.
and Soundview Technology Group Inc., as representatives of the Underwriters
named in Schedule A thereto, provides that the underwriters are obligated, under
certain circumstances, to indemnify directors, officers and controlling persons
of the Company against certain liabilities, including liabilities under the
Securities Act of 1933, as amended (the "Securities Act").


          In addition, the Company maintains directors and officers liability
insurance for the benefit of its directors and certain of its officers.


Item 7.   Exemption from Registration Claimed.


          Not applicable.


Item 8.   Exhibits.


Exhibit No.    Description of Exhibit
- -----------    ----------------------


4.1            Specimen certificate for shares of the Registrant's Common Stock
               (filed as Exhibit 4.1 to the Registration Statement on Form S-1
               (SEC File No. 333-92731) and incorporated herein by reference).

4.2            Second Amended and Restated Certificate of Incorporation of the
               Registrant.

4.3            Amended and Restated By-Laws of the Registrant.

4.4            1999 Stock Plan.

                                       4
<PAGE>

4.5       Amended and Restated 1996 Stock Plan (filed as Exhibit 10.2 to the
          Registration Statement on Form S-1 (SEC File No. 333-92731) and
          incorporated herein by reference).

4.6       Amended and Restated 1987 Stock Option Plan (filed as Exhibit 10.1 to
          the Registration Statement on Form S-1 (SEC File No. 333-92731) and
          incorporated herein by reference).

4.7       2000 Employee Stock Purchase Plan.

5.1       Opinion of Testa, Hurwitz & Thibeault, LLP.

23.1      Consent of Arthur Andersen LLP.

23.2      Consent of Testa, Hurwitz & Thibeault, LLP (included in Exhibit 5.1).

24.1      Power of Attorney (included as part of the signature page to this
          Registration Statement).


Item 9.   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 the registration statement (or the
               most recent post-effective amendment thereof) which, individually
               or in the aggregate, represent a fundamental change in the
               information set forth in the registration statement.
               Notwithstanding the foregoing, any increase or decrease in volume
               of securities offered (if the total dollar value of securities
               offered would not exceed that which was registered) and any
               deviation from the low or high end of the estimated maximum
               offering range may be reflected in the form of prospectus filed
               with the Commission pursuant to Rule 424(b) if, in the aggregate,
               the changes in volume and price represent no more than a 20
               percent change in the maximum aggregate offering price set forth
               in the "Calculation of Registration Fee" table in the effective
               registration statement;


               (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 registration statement is on Form S-3, Form S-8 or
          Form F-3, and 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 15(d) of the Securities Exchange Act of 1934
          that are incorporated by reference in the Registration Statement.


          (2)  That, for the purpose of determining any liability under the
          Securities Act of 1933, each such 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;

                                       5
<PAGE>

          (3)  To remove from registration by means of a post-effective
          amendment any of the securities being registered which 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 report pursuant to Section 13(a) or
          Section 15(d) of the Securities Exchange Act of 1934 (and, where
          applicable, each filing of an employee benefit plan's annual report
          pursuant to 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 of 1933 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 Securities and Exchange Commission such indemnification
          is against public policy as expressed in the 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 Act and will be
          governed by the final adjudication of such issue.

                                       6
<PAGE>

                                  SIGNATURES


     Pursuant to the requirements of the Securities Act of 1933, the Registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-8 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of Chelmsford, Commonwealth of Massachusetts, on this
20th day of April, 2000.


                                        MATRIXONE, INC.


                                        By:  /s/ Mark F. O'Connell
                                           -----------------------
                                           Mark F. O'Connell
                                           President and Chief Executive Officer



                        POWER OF ATTORNEY AND SIGNATURES


     The undersigned officers and directors of MatrixOne, Inc., hereby
constitute and appoint Mark F. O'Connell and Maurice L. Castonguay, and each of
them singly, our true and lawful attorneys-in-fact, with full power to them and
each of them singly, to sign for us in our names in the capacities indicated
below, any amendments to this Registration Statement on Form S-8 (including
post-effective amendments), and to file the same, with all exhibits thereto and
other documents in connection therewith, with the Securities and Exchange
Commission, and generally to do all things in our names and on our behalf in our
capacities as officers and directors to enable MatrixOne, Inc., to comply with
the provisions of the Securities Act of 1933, as amended, hereby ratifying and
confirming our signatures as they may be signed by our said attorneys, or any of
them, to said Registration Statement and all amendments thereto.


     Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed below by the following persons in the
capacities and on the dates indicated.

<TABLE>
<CAPTION>
        Signature                          Title(s)                                          Date
        ---------                          --------                                          ----
<S>                                        <C>                                               <C>
/s/ Mark F. O'Connell                      President, Chief Executive Officer                April 20, 2000
- ---------------------------
Mark F. O'Connell                          and Director (Principal Executive Officer)

/s/ Maurice L. Castonguay                  Chief Financial Officer, Vice President           April 20, 2000
- ---------------------------
Maurice L. Castonguay                      of Finance and Administration and
                                           Treasurer (Principal Financial and
                                           Accounting Officer)

/s/ Ellen Carnahan                         Director                                          April 20, 2000
- ---------------------------
Ellen Carnahan

/s/ Daniel J. Holland                      Director                                          April 20, 2000
- ---------------------------
Daniel J. Holland

/s/ James F. Morgan                        Director                                          April 20, 2000
- ---------------------------
James F. Morgan

/s/ Charles R. Stuckey, Jr.                Director                                          April 20, 2000
- ---------------------------
Charles R. Stuckey, Jr.
</TABLE>

                                       7
<PAGE>

                                 EXHIBIT INDEX


Exhibit No.    Description of Exhibit
- -----------    ----------------------

4.1            Specimen certificate for shares of the Registrant's Common Stock
               (filed as Exhibit 4.1 to the Registration Statement on Form S-1
               (SEC File No. 333-92731) and incorporated herein by reference).

4.2            Second Amended and Restated Certificate of Incorporation of the
               Registrant.

4.3            Amended and Restated By-Laws of the Registrant.

4.4            1999 Stock Plan.

4.5            Amended and Restated 1996 Stock Plan (filed as Exhibit 10.2 to
               the Registration Statement on Form S-1 (SEC File No. 333-92731)
               and incorporated herein by reference).

4.6            Amended and Restated 1987 Stock Option Plan (filed as Exhibit
               10.1 to the Registration Statement on Form S-1 (SEC File No. 333-
               92731) and incorporated herein by reference).

4.7            2000 Employee Stock Purchase Plan.

5.1            Opinion of Testa, Hurwitz & Thibeault, LLP.

23.1           Consent of Arthur Andersen LLP.

23.2           Consent of Testa, Hurwitz & Thibeault, LLP (included in Exhibit
               5.1).

24.1           Power of Attorney (included as part of the signature page to this
               Registration Statement).

<PAGE>

                                                                     Exhibit 4.2
                                                                     -----------


           SECOND AMENDED AND RESTATED CERTIFICATE OF INCORPORATION

                                      OF

                                MATRIXONE, INC.

              (Incorporated July 19, 1983 as Adra Systems, Inc.)

                                  * * * * * *


     I, Mark F. O'Connell, President and Chief Executive Officer of MatrixOne,
Inc. (the "Corporation"), a corporation organized and existing under and by
virtue of the General Corporation Law of the State of Delaware, do hereby
certify that the Certificate of Incorporation of MatrixOne, Inc., as amended,
originally incorporated under the name Adra Systems, Inc., has been further
amended, and restated as amended, in accordance with the provisions of Sections
242 and 245 of the General Corporation Law of the State of Delaware, and, as
amended and restated, is set forth in its entirety as follows:

     FIRST.  The name of the Corporation is MatrixOne, Inc.

     SECOND.  The address of the registered office of the Corporation in the
State of Delaware is 1209 Orange Street, Wilmington, County of New Castle,
Delaware 19801. The name of its registered agent at such address is The
Corporation Trust Company.

     THIRD.  The nature of the business or purposes to be conducted or promoted
is to engage in any lawful act or activity for which corporations may be
organized under the General Corporation Law of the State of Delaware.

     FOURTH.  The total number of shares of all classes of capital stock which
the Corporation shall have authority to issue is 105,000,000 shares, consisting
of 100,000,000 shares of Common Stock with a par value of $.01 per share (the
"Common Stock") and 5,000,000 shares of Preferred Stock with a par value of $.01
per share (the "Preferred Stock").

     A description of the respective classes of stock and a statement of the
designations, powers, preferences and rights, and the qualifications,
limitations and restrictions of the Preferred Stock and Common Stock are as
follows:

     A.   COMMON STOCK
          ------------

     1.   General.  All shares of Common Stock will be identical and will
          -------
entitle the holders thereof to the same rights, powers and privileges. The
rights, powers and privileges of
<PAGE>

                                      -2-

the holders of the Common Stock are subject to and qualified by the rights of
holders of the Preferred Stock.

     2.   Dividends.  Dividends may be declared and paid on the Common Stock
          ---------
from funds lawfully available therefor as and when determined by the Board of
Directors and subject to any preferential dividend rights of any then
outstanding Preferred Stock.

     3.   Dissolution, Liquidation or Winding Up. In the event of any
          --------------------------------------
dissolution, liquidation or winding up of the affairs of the Corporation,
whether voluntary or involuntary, each issued and outstanding share of Common
Stock shall entitle the holder thereof to receive an equal portion of the net
assets of the Corporation available for distribution to the holders of Common
Stock, subject to any preferential rights of any then outstanding Preferred
Stock.

     4.   Voting Rights.  Except as otherwise required by law or this Second
          -------------
Amended and Restated Certificate of Incorporation, each holder of Common Stock
shall have one vote in respect of each share of stock held of record by such
holder on the books of the Corporation for the election of directors and on all
matters submitted to a vote of stockholders of the Corporation. Except as
otherwise required by law or provided herein, holders of Common Stock shall vote
together with holders of the Preferred Stock as a single class, subject to any
special or preferential voting rights of any then outstanding Preferred Stock.
There shall be no cumulative voting.

     B.   PREFERRED STOCK
          ---------------

     The Preferred Stock may be issued in one or more series at such time or
times and for such consideration or considerations as the Board of Directors of
the Corporation may determine. Each series shall be so designated as to
distinguish the shares thereof from the shares of all other series and classes.
Except as otherwise provided in this Second Amended and Restated Certificate of
Incorporation, different series of Preferred Stock shall not be construed to
constitute different classes of shares for the purpose of voting by classes.

     The Board of Directors is expressly authorized to provide for the issuance
of all or any shares of the undesignated Preferred Stock in one or more series,
each with such designations, preferences, voting powers (or special,
preferential or no voting powers), relative, participating, optional or other
special rights and privileges and such qualifications, limitations or
restrictions thereof as shall be stated in the resolution or resolutions adopted
by the Board of Directors to create such series, and a certificate of said
resolution or resolutions (a "Certificate of Designation") shall be filed in
accordance with the General Corporation Law of the State of Delaware. The
authority of the Board of Directors with respect to each such series shall
include, without limitation of the foregoing, the right to provide that the
shares of each such series may be: (i) subject to redemption at such time or
times and at such price or prices; (ii) entitled to receive dividends (which may
be cumulative or non-cumulative) at such rates, on such conditions, and at such
times, and payable in preference to, or in such relation to, the dividends
payable on any other class or classes or any other series; (iii) entitled to
such rights upon the dissolution of, or upon any distribution of the assets of,
the Corporation; (iv) convertible into, or exchangeable for, shares of any other
class or classes of stock, or of any other series of the same
<PAGE>

                                      -3-

or any other class or classes of stock of the Corporation at such price or
prices or at such rates of exchange and with such adjustments, if any; (v)
entitled to the benefit of such limitations, if any, on the issuance of
additional shares of such series or shares of any other series of Preferred
Stock; or (vi) entitled to such other preferences, powers, qualifications,
rights and privileges, all as the Board of Directors may deem advisable and as
are not inconsistent with law and the provisions of this Second Amended and
Restated Certificate of Incorporation.

     FIFTH.  The Corporation is to have perpetual existence.

     SIXTH.  The following provisions are included for the management of the
business and the conduct of the affairs of the Corporation, and for further
definition, limitation and regulation of the powers of the Corporation and of
its Board of Directors and stockholders:

     1.   The business and affairs of the Corporation shall be managed by or
under the direction of the Board of Directors of the Corporation.

     2.   The Board of Directors of the Corporation is expressly authorized to
adopt, amend or repeal the By-laws of the Corporation, subject to any limitation
thereof contained in the By-laws. The stockholders shall also have the power to
adopt, amend or repeal the By-laws of the Corporation; provided, however, that,
                                                       --------  -------
in addition to any vote of the holders of any class or series of stock of the
Corporation required by law or by this Second Amended and Restated Certificate
of Incorporation, the affirmative vote of the holders of at least sixty-six and
two-thirds percent (66 2/3%) of the voting power of all of the then outstanding
shares of the capital stock of the Corporation entitled to vote generally in the
election of directors, voting together as a single class, shall be required to
adopt, amend or repeal any provision of the By-laws of the Corporation.

     3.   Stockholders of the Corporation may not take any action by written
consent in lieu of a meeting.

     4.   Special meetings of stockholders may be called at any time only by the
President, the Chairman of the Board of Directors (if any) or a majority of the
Board of Directors. Business transacted at any special meeting of stockholders
shall be limited to matters relating to the purpose or purposes stated in the
notice of meeting.

     5.   The books of the Corporation may be kept at such place within or
without the State of Delaware as the By-laws of the Corporation may provide or
as may be designated from time to time by the Board of Directors of the
Corporation.

     SEVENTH.

     1.   Number of Directors.  The number of directors which shall constitute
          -------------------
the whole Board of Directors shall be determined by resolution of a majority of
the Board of Directors, but in no event shall the number of directors be less
than three. The number of directors may be decreased at any time and from time
to time by a majority of the directors then in office, but only to eliminate
vacancies existing by reason of the death, resignation, removal or expiration of
<PAGE>

                                      -4-

the term of one or more directors. The directors shall be elected at the annual
meeting of stockholders by such stockholders as have the right to vote on such
election. Directors need not be stockholders of the Corporation.

     2.   Classes of Directors.  The Board of Directors shall be and is divided
          --------------------
into three classes: Class I, Class II and Class III. No one class shall have
more than one director more than any other class.

     3.   Election of Directors.  Elections of directors need not be by written
          ---------------------
ballot except as and to the extent provided in the By-laws of the Corporation.

     4.   Terms of Office.  Each director shall serve for a term ending on the
          ---------------
date of the third annual meeting following the annual meeting at which such
director was elected; provided, however, that each initial director in Class I
shall serve for a term ending on the date of the annual meeting next following
the end of the Corporation's fiscal year ending July 1, 2000; each initial
director in Class II shall serve for a term ending on the date of the annual
meeting next following the end of the Corporation's fiscal year ending June 30,
2001; and each initial director in Class III shall serve for a term ending on
the date of the annual meeting next following the end of the Corporation's
fiscal year ending June 29, 2002.

     5.   Allocation of Directors Among Classes in the Event of Increases or
          ------------------------------------------------------------------
Decreases in the Number of Directors.  In the event of any increase or decrease
- ------------------------------------
in the authorized number of directors, (i) each director then serving as such
shall nevertheless continue as director of the class of which he or she is a
member until the expiration of such director's current term or his or her prior
death, removal or resignation and (ii) the newly created or eliminated
directorships resulting from such increase or decrease shall be apportioned by
the Board of Directors among the three classes of directors so as to ensure that
no one class has more than one director more than any other class. To the extent
possible, consistent with the foregoing rule, any newly created directorships
shall be added to those classes whose terms of office are to expire at the
earliest dates following such allocation, unless otherwise provided for from
time to time by resolution adopted by a majority of the directors then in
office, though less than a quorum. No decrease in the number of directors
constituting the whole Board of Directors shall shorten the term of an incumbent
Director.

     6.   Tenure.  Notwithstanding any provisions to the contrary contained
          ------
herein, each director shall hold office until his or her successor is elected
and qualified, or until his or her earlier death, resignation or removal.

     7.   Vacancies.  Unless and until filled by the stockholders, any vacancy
          ---------
in the Board of Directors, however occurring, including a vacancy resulting from
an enlargement of the Board of Directors, may be filled only by vote of a
majority of the directors then in office, even if less than a quorum, or by a
sole remaining director. A director elected to fill a vacancy shall be elected
for the unexpired term of his or her predecessor in office, if applicable, and a
director chosen to fill a position resulting from an increase in the number of
directors shall hold office until the next election of the class for which such
director shall have been chosen and until his or her successor is elected and
qualified, or until his or her earlier death, resignation or removal.
<PAGE>

                                      -5-

     8.   Quorum.  A majority of the total number of the whole Board of
          ------
Directors shall constitute a quorum at all meetings of the Board of Directors.
In the event one or more of the directors shall be disqualified to vote at any
meeting, then the required quorum shall be reduced by one for each such director
so disqualified; provided, however, that in no case shall less than one-third
(1/3) of the number so fixed constitute a quorum. In the absence of a quorum at
any such meeting, a majority of the directors present may adjourn the meeting
from time to time without further notice other than announcement at the meeting,
until a quorum shall be present.

     9.   Action at Meeting.  At any meeting of the Board of Directors at which
          -----------------
a quorum is present, the vote of a majority of those present shall be sufficient
to take any action, unless a different vote is specified by law or the
Corporation's By-laws.

     10.  Removal.  Any one or more or all of the directors may be removed with
          -------
cause only by the holders of at least sixty-six and two-thirds percent (66 2/3%)
of the shares then entitled to vote at an election of directors. Directors may
not be removed without cause.

     11.  Stockholder Nominations and Introduction of Business, Etc.  Advance
          ----------------------------------------------------------
notice of stockholder nominations for election of directors and other business
to be brought by stockholders before a meeting of stockholders shall be given in
the manner provided in the By-laws of the Corporation.

     12.  Rights of Preferred Stock.  The provisions of this Article are subject
          -------------------------
to the rights of the holders of any series of Preferred Stock from time to time
outstanding.

     EIGHTH.  No director (including any advisory director) of the Corporation
shall be personally liable to the Corporation or its stockholders for monetary
damages for breach of fiduciary duty as a director notwithstanding any provision
of law imposing such liability; provided, however, that, to the extent provided
by applicable law, this provision shall not eliminate the liability of a
director (i) for any breach of the director's duty of loyalty to the Corporation
or its stockholders, (ii) for acts or omissions not in good faith or which
involve intentional misconduct or a knowing violation of law, (iii) under
Section 174 of the General Corporation Law of the State of Delaware, or (iv) for
any transaction from which the director derived an improper personal benefit. No
amendment to or repeal of this provision shall apply to or have any effect on
the liability or alleged liability of any director for or with respect to any
acts or omissions of such director occurring prior to such amendment or repeal.

     NINTH.  The Board of Directors of the Corporation, when evaluating any
offer of another party (a) to make a tender or exchange offer for any equity
security of the Corporation or (b) to effect a business combination, shall, in
connection with the exercise of its judgment in determining what is in the best
interests of the Corporation as whole, be authorized to give due consideration
to any such factors as the Board of Directors determines to be relevant,
including, without limitation:

     (i)  the interests of the Corporation's stockholders, including the
   possibility that these interests might be best served by the continued
   independence of the Corporation;
<PAGE>

                                      -6-

     (ii)  whether the proposed transaction might violate federal or state laws;

     (iii) not only the consideration being offered in the proposed transaction,
   in relation to the then current market price for the outstanding capital
   stock of the Corporation, but also to the market price for the capital stock
   of the Corporation over a period of years, the estimated price that might be
   achieved in a negotiated sale of the Corporation as a whole or in part or
   through orderly liquidation, the premiums over market price for the
   securities of other corporations in similar transactions, current political,
   economic and other factors bearing on securities prices and the Corporation's
   financial condition and future prospects; and

     (iv)  the social, legal and economic effects upon employees, suppliers,
   customers, creditors and others having similar relationships with the
   Corporation, upon the communities in which the Corporation conducts its
   business and upon the economy of the state, region and nation.

In connection with any such evaluation, the Board of Directors is authorized to
conduct such investigations and engage in such legal proceedings as the Board of
Directors may determine.

     TENTH.  The Corporation reserves the right to amend or repeal any provision
contained in this Second Amended and Restated Certificate of Incorporation in
the manner prescribed by the laws of the State of Delaware and all rights
conferred upon stockholders are granted subject to this reservation, provided,
                                                                     --------
however, that in addition to any vote of the holders of any class or series of
- -------
stock of the Corporation required by law, this Second Amended and Restated
Certificate of Incorporation or a Certificate of Designation with respect to a
series of Preferred Stock, the affirmative vote of the holders of shares of
voting stock of the Corporation representing at least sixty-six and two-thirds
percent (66 2/3%) of the voting power of all of the then outstanding shares of
the capital stock of the Corporation entitled to vote generally in the election
of directors, voting together as a single class, shall be required to (i) reduce
or eliminate the number of authorized shares of Common Stock or the number of
authorized shares of Preferred Stock set forth in Article FOURTH or (ii) amend
or repeal, or adopt any provision inconsistent with, Parts A and B of Article
FOURTH and Articles FIFTH, SIXTH, SEVENTH, EIGHTH, NINTH and this Article TENTH
of this Second Amended and Restated Certificate of Incorporation.

                 [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]
<PAGE>

                                      -7-

     IN WITNESS WHEREOF, the undersigned has hereunto signed his name and
affirms that the statements made in this Second Amended and Restated Certificate
of Incorporation are true under the penalties of perjury this 6th day of March,
2000.


                                  /s/ Mark F. O'Connell
                                  ---------------------------------------------
                                  Name: Mark F. O'Connell
                                  Title: President and Chief Executive Officer



Attest:



/s/ Gordon H. Hayes, Jr.
- -------------------------------
Name: Gordon H. Hayes, Jr.
Title: Secretary

<PAGE>

                                                                     Exhibit 4.3
                                                                     -----------

                             AMENDED AND RESTATED

                                    BY-LAWS

                                      OF

                                MATRIXONE, INC.

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


                            A Delaware Corporation
<PAGE>

                                    BY-LAWS

                               TABLE OF CONTENTS
<TABLE>
<CAPTION>
                                                                           Page
                                                                           ----
<S>                                                                        <C>
ARTICLE 1 - Stockholders....................................................  1

     Section 1.1    Place of Meetings.......................................  1
     Section 1.2    Annual Meeting..........................................  1
     Section 1.3    Special Meetings........................................  1
     Section 1.4    Notice of Meetings......................................  1
     Section 1.5    Voting List.............................................  1
     Section 1.6    Quorum..................................................  2
     Section 1.7    Adjournments............................................  2
     Section 1.8    Voting and Proxies......................................  2
     Section 1.9    Action at Meeting.......................................  3
     Section 1.10   Introduction of Business at Meeting.....................  3
     Section 1.11   Action without Meeting..................................  5

ARTICLE 2 - Directors........................................................ 6

     Section 2.1    General Powers........................................... 6
     Section 2.2    Number; Election and Qualification....................... 6
     Section 2.3    Classes of Directors..................................... 7
     Section 2.4    Terms in Office.......................................... 7
     Section 2.5    Allocation of Directors Among Classes in the Event
                    of Increases or Decreases in the Number of Directors..... 7
     Section 2.6    Tenure................................................... 7
     Section 2.7    Vacancies................................................ 7
     Section 2.8    Resignation.............................................. 7
     Section 2.9    Regular Meetings......................................... 8
     Section 2.10   Special Meetings......................................... 8
     Section 2.11   Notice of Special Meetings............................... 8
     Section 2.12   Meetings by Telephone Conference Calls................... 8
     Section 2.13   Quorum................................................... 8
     Section 2.14   Action at Meeting........................................ 8
     Section 2.15   Action by Written Consent................................ 8
     Section 2.16   Removal.................................................. 9
     Section 2.17   Committees............................................... 9
     Section 2.18   Compensation of Directors................................ 9
     Section 2.19   Amendments to Article.................................... 9
</TABLE>
<PAGE>

                                     -ii-

<TABLE>
<S>                                                                          <C>
ARTICLE 3 - Officers......................................................... 9

     Section 3.1    Enumeration.............................................. 10
     Section 3.2    Election................................................. 10
     Section 3.3    Qualification............................................ 10
     Section 3.4    Tenure................................................... 10
     Section 3.5    Resignation and Removal.................................. 10
     Section 3.6    Vacancies................................................ 10
     Section 3.7    Chairman of the Board and Vice-Chairman of the Board..... 10
     Section 3.8    President................................................ 11
     Section 3.9    Vice Presidents.......................................... 11
     Section 3.10   Secretary and Assistant Secretaries...................... 11
     Section 3.11   Treasurer and Assistant Treasurers....................... 12
     Section 3.12   Salaries................................................. 12
     Section 3.13   Action with Respect to Securities of Other Corporations.. 12

ARTICLE 4 - Capital Stock....................................................

     Section 4.1    Issuance of Stock........................................ 12
     Section 4.2    Certificates of Stock.................................... 12
     Section 4.3    Transfers................................................ 13
     Section 4.4    Lost, Stolen or Destroyed Certificates................... 13
     Section 4.5    Record Date.............................................. 13

ARTICLE 5 - General Provisions............................................... 14

     Section 5.1    Fiscal Year.............................................. 14
     Section 5.2    Corporate Seal........................................... 14
     Section 5.3    Notices.................................................. 14
     Section 5.4    Waiver of Notice......................................... 14
     Section 5.5    Evidence of Authority.................................... 14
     Section 5.6    Facsimile Signatures..................................... 14
     Section 5.7    Reliance upon Books, Reports and Records................. 14
     Section 5.8    Time Periods............................................. 14
     Section 5.9    Certificate of Incorporation............................. 15
     Section 5.10   Transactions with Interested Parties..................... 15
     Section 5.11   Severability............................................. 15
     Section 5.12   Pronouns................................................. 15

ARTICLE 6 - Amendments....................................................... 15

     Section 6.1    By the Board of Directors................................ 15
     Section 6.2    By the Stockholders...................................... 16

ARTICLE 7 - Indemnification.................................................. 16
</TABLE>
<PAGE>

                                     -iii-

<TABLE>
<S>                                                                          <C>
     Section 7.1    Actions Other Than by or in the Right of the
                    Corporation.............................................. 16
     Section 7.2    Actions by or in the Right of the Corporation............ 16
     Section 7.3    Success on the Merits.................................... 17
     Section 7.4    Authorization............................................ 17
     Section 7.5    Expense Advance.......................................... 17
     Section 7.6    Nonexclusivity........................................... 17
     Section 7.7    Insurance................................................ 17
     Section 7.8    "The Corporation"........................................ 18
     Section 7.9    Other Indemnification.................................... 18
     Section 7.10   Other Definitions........................................ 18
     Section 7.11   Continuation of Indemnification.......................... 18
</TABLE>
<PAGE>

                              AMENDED AND RESTATED

                                    BY-LAWS

                                       OF

                      MATRIXONE, INC. (the "Corporation")


                            ARTICLE 1 - Stockholders
                            ------------------------

          1.1  Place of Meetings.  All meetings of stockholders shall be held at
               -----------------
such place within or without the State of Delaware as may be designated from
time to time by the Chairman of the Board (if any), the board of directors of
the Corporation (the "Board of Directors") or the President or, if not so
designated, at the registered office of the Corporation.

          1.2  Annual Meeting.  The annual meeting of stockholders for the
               --------------
election of directors and for the transaction of such other business as may
properly be brought before the meeting shall be held on a date to be fixed by
the Chairman of the Board (if any), the Board of Directors or the President
(which date shall not be a legal holiday in the place where the meeting is to be
held) at the time and place to be fixed by the Chairman of the Board, the Board
of Directors or the President and stated in the notice of the meeting.

          1.3  Special Meetings.  Special meetings of stockholders may be called
               ----------------
at any time only by the Chairman of the Board (if any), a majority of the Board
of Directors or the President and shall be held at such place, on such date and
at such time as shall be fixed by the Board of Directors or the person calling
the meeting.  Business transacted at any special meeting of stockholders shall
be limited to matters relating to the purpose or purposes stated in the notice
of meeting.

          1.4  Notice of Meetings.  Except as otherwise provided by law, written
               ------------------
notice of each meeting of stockholders, whether annual or special, shall be
given not less than ten (10) nor more than sixty (60) days before the date of
the meeting to each stockholder entitled to vote at such meeting.  The notices
of all meetings shall state the place, date and hour of the meeting.  The notice
of a special meeting shall state, in addition, the purpose or purposes for which
the meeting is called.  If mailed, notice is given when deposited in the United
States mail, postage prepaid, directed to the stockholder at his or her address
as it appears on the records of the Corporation.

          1.5  Voting List.  The officer who has charge of the stock ledger of
               -----------
the Corporation shall prepare, at least ten (10) days before every meeting of
stockholders, a complete list of the stockholders entitled to vote at the
meeting, arranged in alphabetical order, and showing the address of each
stockholder and the number of shares registered in the name of each stockholder.
Such list shall be open to the examination of any stockholder, for any purpose
germane to the meeting, during ordinary business hours, for a period of at least
ten (10) days prior to the meeting, either at a place within the metropolitan
area of the city where the meeting is to be held, which place shall be specified
in the notice of the
<PAGE>

                                      -2-

meeting, or if not so specified, at the place where the meeting is to be held.
The list shall also be produced and kept at the time and place of the meeting
during the whole time of the meeting, and may be inspected by any stockholder
who is present. This list shall presumptively determine the identity of the
stockholders entitled to vote at the meeting and the number of shares held by
each of them.

          1.6  Quorum.  Except as otherwise provided by law, the Certificate of
               ------
Incorporation or these Amended and Restated By-Laws, as amended from time to
time (the "By-Laws") the holders of a majority of the shares of the capital
stock of the Corporation issued and outstanding and entitled to vote at the
meeting, present in person or represented by proxy, shall constitute a quorum
for the transaction of business.  Shares held by brokers which such brokers are
prohibited from voting (pursuant to their discretionary authority on behalf of
beneficial owners of such shares who have not submitted a proxy with respect to
such shares) on some or all of the matters before the stockholders, but which
shares would otherwise be entitled to vote at the meeting ("Broker Non-Votes")
shall be counted, for the purpose of determining the presence or absence of a
quorum, both (a) toward the total voting power of the shares of capital stock of
the Corporation and (b) as being represented by proxy.  If a quorum has been
established for the purpose of conducting the meeting, a quorum shall be deemed
to be present for the purpose of all votes to be conducted at such meeting,
provided that where a separate vote by a class or classes, or series thereof, is
required, a majority of the voting power of the shares of such class or classes,
or series, present in person or represented by proxy shall constitute a quorum
entitled to take action with respect to that vote on that matter.  If a quorum
shall fail to attend any meeting, the chairman of the meeting or the holders of
a majority of the voting power of the shares of stock entitled to vote who are
present, in person or by proxy, may adjourn the meeting to another place, date,
or time.

          1.7  Adjournments.  Any meeting of stockholders may be adjourned to
               ------------
any other time and to any other place at which a meeting of stockholders may be
held under these By-Laws by the stockholders present or represented at the
meeting and entitled to vote, although less than a quorum, or, if no stockholder
is present, by any officer entitled to preside at or to act as Secretary of such
meeting.  It shall not be necessary to notify any stockholder of any adjournment
of less than 30 days if the time and place of the adjourned meeting are
announced at the meeting at which adjournment is taken, unless after the
adjournment a new record date is fixed for the adjourned meeting.  At the
adjourned meeting, the Corporation may transact any business that might have
been transacted at the original meeting.

          1.8  Voting and Proxies.  At any meeting of the stockholders, each
               ------------------
stockholder shall have one vote for each share of stock entitled to vote at such
meeting held of record by such stockholder and a proportionate vote for each
fractional share so held, unless otherwise provided in the Certificate of
Incorporation.  Each stockholder of record entitled to vote at a meeting of
stockholders, or to express consent or dissent to corporate action in writing
without a meeting (to the extent not otherwise prohibited by the Certificate of
Incorporation or these By-laws), may vote or express such consent or dissent in
person or may authorize another person or persons to vote or act for such
stockholder by written proxy executed by such stockholder or his or her
authorized agent or by a transmission permitted by law and delivered to the
Secretary of the Corporation.  No such proxy shall be voted or acted upon after
three years from the date of its execution, unless the proxy expressly provides
for a longer period.  Any copy, facsimile telecommunication or other reliable
reproduction of the writing or transmission created pursuant to this Section 1.8
may be substituted or used in lieu of the original writing or transmission for
any and all purposes for which the original writing or transmission could be
used,
<PAGE>

                                      -3-

provided that such copy, facsimile telecommunication or reproduction shall be a
complete reproduction of the entire original writing or transmission.

          In the election of directors, voting shall be by written ballot, and
for any other action, voting need not be by ballot.

          The Corporation may, and to the extent required by law or the
Certificate of Incorporation, shall, in advance of any meeting of stockholders,
appoint one or more inspectors to act at such meeting and make a written report
thereof.  The Corporation may designate one or more persons as alternate
inspectors to replace any inspector who fails to act.  If no inspector or
alternate is able to act at a meeting of stockholders, the person presiding at
such meeting may, and to the extent required by law or the Certificate of
Incorporation, shall, appoint one or more inspectors to act at such meeting.
Each inspector, before entering upon the discharge of his duties, shall take and
sign an oath faithfully to execute the duties of inspector with strict
impartiality and according to the best of his or her ability.

          1.9  Action at Meeting.  When a quorum is present at any meeting of
               -----------------
stockholders, the holders of a majority of the stock present or represented and
voting on a matter (or if there are two or more classes of stock entitled to
vote as separate classes, then in the case of each such class, the holders of a
majority of the stock of that class present or represented and voting on such
matter) shall decide any matter to be voted upon by the stockholders at such
meeting (other than the election of directors), except when a different vote is
required by express provision of law, the Certificate of Incorporation or these
By-Laws.  Any election of directors by the stockholders shall be determined by a
plurality of the votes cast by the stockholders entitled to vote at such
election, except as otherwise provided by the Certificate of Incorporation. For
the purposes of this paragraph, Broker Non-Votes represented at the meeting but
not permitted to vote on a particular matter shall not be counted, with respect
to the vote on such matter, in the number of (a) votes cast, (b) votes cast
affirmatively, or (c) votes cast negatively.

          1.10 Introduction of Business at Meetings.
               ------------------------------------

               A.   Annual Meetings of Stockholders.
                    -------------------------------

                    (1)  Nominations of persons for election to the Board of
       Directors and the proposal of business to be considered by the
       stockholders may be made at an annual meeting of stockholders (a)
       pursuant to the Corporation's notice of meeting, (b) by or at the
       direction of the Board of Directors or (c) by any stockholder of the
       Corporation who was a stockholder of record at the time of giving of
       notice provided for in this Section 1.10, who is entitled to vote at the
       meeting and who complies with the notice procedures set forth in this
       Section 1.10.

                    (2)  For nominations or other business to be properly
       brought before an annual meeting by a stockholder pursuant to clause (c)
       of paragraph (A)(1) of this Section 1.10, the stockholder must have given
       timely notice thereof in writing to the Secretary of the Corporation and
       such other business must otherwise be a proper matter for stockholder
       action. To be timely, a stockholder's notice shall be delivered to the
       Secretary at the principal executive offices of the Corporation not later
       than the close of business on the one hundred
<PAGE>

                                      -4-

       twentieth (120th) day nor earlier than the close of business on the one
       hundred fiftieth (150th) day prior to the first anniversary of the date
       of the proxy statement delivered to stockholders in connection with the
       preceding year's annual meeting; provided, however, that if either (i)
       the date of the annual meeting is more than thirty (30) days before or
       more than sixty (60) days after the first anniversary date of the
       preceding year's annual meeting or (ii) no proxy statement was delivered
       to stockholders in connection with the preceding year's annual meeting,
       notice by the stockholder to be timely must be so delivered not earlier
       than the close of business on the ninetieth (90th) day prior to such
       annual meeting and not later than the close of business on the later of
       the sixtieth (60th) day prior to such annual meeting or the close of
       business on the tenth (10th) day following the day on which public
       announcement of the date of such meeting is first made by the
       Corporation. Such stockholder's notice shall set forth (a) as to each
       person whom the stockholder proposes to nominate for election or
       reelection as a director, all information relating to such person that is
       required to be disclosed in solicitations of proxies for election of
       directors, or is otherwise required, in each case pursuant to Regulation
       14A under the Securities Exchange Act of 1934, as amended (the "Exchange
       Act") (including such person's written consent to being named in the
       proxy statement as a nominee and to serving as a director if elected);
       (b) as to any other business that the stockholder proposes to bring
       before the meeting, a brief description of the business desired to be
       brought before the meeting, the reasons for conducting such business at
       the meeting and any material interest in such business of such
       stockholder and the beneficial owner, if any, on whose behalf the
       proposal is made; and (c) as to the stockholder giving the notice and the
       beneficial owner, if any, on whose behalf the nomination or proposal is
       made (i) the name and address of such stockholder, as they appear on the
       Corporation's books, and of such beneficial owner and (ii) the class and
       number of shares of capital stock of the Corporation that are owned
       beneficially and held of record by such stockholder and such beneficial
       owner.

                    (3)  Notwithstanding anything in the second sentence of
       paragraph (A)(2) of this Section 1.10 to the contrary, in the event that
       the number of directors to be elected to the Board of Directors of the
       Corporation is increased and there is no public announcement by the
       Corporation naming all of the nominees for director or specifying the
       size of the increased Board of Directors at least seventy (70) days prior
       to the first anniversary of the preceding year's annual meeting (or, if
       the annual meeting is held more than thirty (30) days before or sixty
       (60) days after such anniversary date, at least seventy (70) days prior
       to such annual meeting), a stockholder's notice required by this Section
       1.10 shall also be considered timely, but only with respect to nominees
       for any new positions created by such increase, if it shall be delivered
       to the Secretary at the principal executive office of the Corporation not
       later than the close of business on the tenth (10th) day following the
       day on which such public announcement is first made by the Corporation.

               B.   Special Meetings of Stockholders.  Only such business shall
                    --------------------------------
       be conducted at a special meeting of stockholders as shall have been
       brought before the meeting pursuant to the Corporation's notice of
       meeting.  Nominations of persons for election to the Board of Directors
       may be made at a special meeting of stockholders at which directors are
       to be elected pursuant to the Corporation's notice of meeting (a) by or
       at the direction of the Board
<PAGE>

                                      -5-

       of Directors or (b) provided that the Board of Directors has determined
       that directors shall be elected at such meeting, by any stockholder of
       the Corporation who is a stockholder of record at the time of giving of
       notice of the special meeting, who shall be entitled to vote at the
       meeting and who complies with the notice procedures set forth in this
       Section 1.10. If the Corporation calls a special meeting of stockholders
       for the purpose of electing one or more directors to the Board of
       Directors, any such stockholder may nominate a person or persons (as the
       case may be), for election to such position(s) as specified in the
       Corporation's notice of meeting, if the stockholder's notice required by
       paragraph (A)(2) of this Section 1.10 shall be delivered to the Secretary
       at the principal executive offices of the Corporation not earlier than
       the ninetieth (90th) day prior to such special meeting nor later than the
       later of (x) the close of business on the sixtieth (60th) day prior to
       such special meeting or (y) the close of business on the tenth (10th) day
       following the day on which public announcement is first made of the date
       of such special meeting and of the nominees proposed by the Board of
       Directors to be elected at such meeting.

C.        General.
          -------

               (1)  Only such persons who are nominated in accordance with the
       procedures set forth in this Section 1.10 shall be eligible to serve as
       directors and only such business shall be conducted at a meeting of
       stockholders as shall have been brought before the meeting in accordance
       with the procedures set forth in this Section 1.10. Except as otherwise
       provided by law, the Certificate of Incorporation or these By-Laws, the
       chairman of the meeting shall have the power and duty to determine
       whether a nomination or any business proposed to be brought before the
       meeting was made or proposed, as the case may be, in accordance with the
       procedures set forth in this Section 1.10 and, if any proposed nomination
       or business is not in compliance herewith, to declare that such defective
       proposal or nomination shall be disregarded.

               (2)  For purposes of this Section 1.10, "public announcement"
       shall mean disclosure in a press release reported by the Dow Jones News
       Service, Associated Press, PR Newswire, Reuters or comparable national
       news service or in a document publicly filed by the Corporation with the
       Securities and Exchange Commission pursuant to Section 13, 14 or 15(d) of
       the Exchange Act.

               (3)  Notwithstanding the foregoing provisions of this Section
       1.10, a stockholder shall also comply with all applicable requirements of
       the Exchange Act and the rules and regulations thereunder with respect to
       the matters set forth herein.  Nothing in this Section 1.10 shall be
       deemed to affect any rights (i) of stockholders to request inclusion of
       proposals in the Corporation's proxy statement pursuant to Rule 14a-8
       under the Exchange Act or (ii) of the holders of any series of Preferred
       Stock to elect directors under specified circumstances.

     1.11  Action without Meeting.  Stockholders of the Corporation may not
           ----------------------
take any action by written consent in lieu of a meeting.  Notwithstanding any
other provision of law, the Certificate of Incorporation or these By-Laws, and
notwithstanding the fact that a lesser percentage may be specified
<PAGE>

                                      -6-

by law, the affirmative vote of the holders of at least sixty-six and two-thirds
percent (66-2/3%) of the votes which all the stockholders would be entitled to
cast at any annual election of directors or class of directors shall be required
to amend or repeal, or to adopt any provision inconsistent with, this Section
1.11.

                             ARTICLE 2 - Directors
                             ---------------------

     2.1  General Powers.  The business and affairs of the Corporation shall be
          --------------
managed by or under the direction of a Board of Directors, who may exercise all
of the powers of the Corporation except as otherwise provided by law or the
Certificate of Incorporation. In the event of a vacancy in the Board of
Directors, the remaining directors, except as otherwise provided by law or the
Certificate of Incorporation, may exercise the powers of the full Board of
Directors until the vacancy is filled. Without limiting the foregoing, the Board
of Directors may:

     (a)  declare dividends from time to time in accordance with law;

     (b)  purchase or otherwise acquire any property, rights or privileges on
  such terms as it shall determine;

     (c)  authorize the creation, making and issuance, in such form as it may
  determine, of written obligations of every kind, negotiable or non-negotiable,
  secured or unsecured, to borrow funds and guarantee obligations, and to do all
  things necessary in connection therewith;

     (d)  remove any officer of the Corporation with or without cause, and from
  time to time to devolve the powers and duties of any officer upon any other
  person for the time being;

     (e)  confer upon any officer of the Corporation the power to appoint,
  remove and suspend subordinate officers, employees and agents;

     (f)  adopt from time to time such stock option, stock purchase, bonus or
  other compensation plans for directors, officers, employees, consultants and
  agents of the Corporation and its subsidiaries as it may determine;

     (g)  adopt from time to time such insurance, retirement, and other benefit
  plans for directors, officers, employees, consultants and agents of the
  Corporation and its subsidiaries as it may determine; and

     (h)  adopt from time to time regulations, not inconsistent herewith, for
  the management of the Corporation's business and affairs.

     2.2  Number; Election and Qualification.  The number of directors which
          ----------------------------------
shall constitute the whole Board of Directors shall be determined by resolution
of the Board of Directors, but in no event shall be less than three. The number
of directors may be decreased at any time and from time to time by a majority of
the directors then in office, but only to eliminate vacancies existing by reason
of the death,
<PAGE>

                                      -7-

resignation, removal or expiration of the term of one or more directors. The
directors shall be elected at the annual meeting of stockholders (or, if so
determined by the Board of Directors pursuant to Section 10 hereof, at a special
meeting of stockholders), by such stockholders as have the right to vote on such
election. Directors need not be stockholders of the Corporation.

     2.3  Classes of Directors.  The Board of Directors shall be and is divided
          --------------------
into three classes: Class I, Class II and Class III. No one class shall have
more than one director more than any other class.

     2.4  Terms in Office.  Each director shall serve for a term ending on the
          ---------------
date of the third annual meeting following the annual meeting at which such
director was elected; provided, however, that each initial director in Class I
shall serve for a term ending on the date of the annual meeting next following
the end of the Corporation's fiscal year ending July 1, 2000; each initial
director in Class II shall serve for a term ending on the date of the annual
meeting next following the end of the Corporation's fiscal year ending June 30,
2001; and each initial director in Class III shall serve for a term ending on
the date of the annual meeting next following the end of the Corporation's
fiscal year ending June 29, 2002.

     2.5  Allocation of Directors Among Classes in the Event of Increases or
          ------------------------------------------------------------------
Decreases in the Number of Directors.  In the event of any increase or decrease
- ------------------------------------
in the authorized number of directors, (i) each director then serving as such
shall nevertheless continue as a director of the class of which he or she is a
member until the expiration of such director's current term or his or her prior
death, removal or resignation and (ii) the newly created or eliminated
directorships resulting from such increase or decrease shall be apportioned by
the Board of Directors among the three classes of directors, subject to the
second sentence of Section 2.3. To the extent possible, consistent with the
foregoing rule, any newly created directorships shall be added to those classes
whose terms of office are to expire at the earliest dates following such
allocation, unless otherwise provided for from time to time by resolution
adopted by a majority of the directors then in office, although less than a
quorum. No decrease in the number of directors constituting the whole Board of
Directors shall shorten the term of an incumbent Director.

     2.6  Tenure.  Notwithstanding any provisions to the contrary contained
          ------
herein, each director shall hold office until his or her successor is elected
and qualified, or until his or her earlier death, resignation or removal.

     2.7  Vacancies.  Unless and until filled by the stockholders, any vacancy
          ---------
in the Board of Directors, however occurring, including a vacancy resulting from
an enlargement thereof, may be filled by vote of a majority of the directors
then in office, although less than a quorum, or by a sole remaining director. A
director elected to fill a vacancy shall be elected for the unexpired term of
his or her predecessor in office, if any, and a director chosen to fill a
position resulting from an increase in the number of directors shall hold office
until the next election of directors of the class for which such director was
chosen and until his or her successor is elected and qualified, or until his or
her earlier death, resignation or removal.

     2.8  Resignation.  Any director may resign by delivering his or her
          -----------
written resignation to the Corporation at its principal office or to the
President or Secretary.  Such resignation shall be effective
<PAGE>

                                      -8-

upon receipt unless it is specified to be effective at some other time or upon
the happening of some other event.

     2.9  Regular Meetings.  Regular meetings of the Board of Directors may be
          ----------------
held without notice at such time and place, either within or without the State
of Delaware, as shall be determined from time to time by the Board of Directors;
provided that any director who is absent when such a determination is made shall
be given notice of the determination.

     2.10 Special Meetings.  Special meetings of the Board of Directors may be
          ----------------
held at any time and place, within or without the State of Delaware, designated
in a call by the Chairman of the Board (if any), the President, two or more
directors, or by one director in the event that there is only a single director
in office.

     2.11 Notice of Special Meetings.  Notice of any special meeting of
          --------------------------
directors shall be given to each director by the Secretary or by the officer or
one of the directors calling the meeting.  Notice shall be duly given to each
director (i) by giving notice to such director in person or by telephone at
least forty-eight (48) hours in advance of the meeting, (ii) by sending a
telegram or delivering written notice by facsimile transmission or by hand, to
his or her last known business or home address at least forty-eight (48) hours
in advance of the meeting, or (iii) by mailing written notice to his or her last
known business or home address at least seventy-two (72) hours in advance of the
meeting.  A notice or waiver of notice of a meeting of the Board of Directors
need not specify the purposes of the meeting.

     2.12 Meetings by Telephone Conference Calls.  Directors or any members of
          --------------------------------------
any committee designated by the Board of Directors may participate in a meeting
of the Board of Directors or such committee by means of conference telephone or
similar communications equipment by means of which all persons participating in
the meeting can hear each other, and participation by such means shall be deemed
to constitute presence in person at such meeting.

     2.13 Quorum.  A majority of the total number of the whole Board of
          ------
Directors shall constitute a quorum at all meetings of the Board of Directors.
In the event one or more of the directors shall be disqualified to vote at any
meeting, then the required quorum shall be reduced by one for each such director
so disqualified; provided, however, that in no case shall less than one-third
(1/3) of the total number of the whole Board of Directors constitute a quorum.
In the absence of a quorum at any such meeting, a majority of the directors
present may adjourn the meeting from time to time without further notice other
than announcement at the meeting, until a quorum shall be present.

     2.14 Action at Meeting.  At any meeting of the Board of Directors at which
          -----------------
a quorum is present, the vote of a majority of those present shall be sufficient
to take any action, unless a different vote is specified by law, the Certificate
of Incorporation or these By-Laws.

     2.15 Action by Written Consent.  Any action required or permitted to be
          -------------------------
taken at any meeting of the Board of Directors or of any committee of the
Board of Directors may be taken without a meeting, if all members of the Board
of Directors or committee, as the case may be, consent to such action in
writing, and the written consents are filed with the minutes of proceedings of
the Board of Directors or committee.
<PAGE>

                                      -9-

     2.16  Removal.  Unless otherwise provided in the Certificate of
           -------
Incorporation, any one or more or all of the directors may be removed with cause
only by the holders of at least sixty-six and two-thirds percent (66-2/3%) of
the shares then entitled to vote at an election of directors.  Directors may not
be removed without cause.

     2.17  Committees.  The Board of Directors may, by resolution passed by a
           ----------
majority of the whole Board, designate one or more committees, each committee
to consist of one or more of the directors of the Corporation.  The Board of
Directors may designate one or more directors as alternate members of any
committee, who may replace any absent or disqualified member at any meeting of
such committee.  In the absence or disqualification of a member of a committee,
the member or members of such committee present at any meeting and not
disqualified from voting, whether or not such member or members constitute a
quorum, may unanimously appoint another member of the Board of Directors to act
at such meeting in the place of any such absent or disqualified member.  Any
such committee, to the extent provided in the resolution of the Board of
Directors and subject to the provisions of the General Corporation Law of the
State of Delaware, shall have and may exercise all the powers and authority of
the Board of Directors in the management of the business and affairs of the
Corporation and may authorize the seal of the Corporation to be affixed to all
papers which may require it.  Each such committee shall keep minutes and make
such reports as the Board of Directors may from time to time request.  Except as
the Board of Directors may otherwise determine or as provided herein, any
committee may make rules for the conduct of its business, but unless otherwise
provided by the directors or in such rules, its business shall be conducted as
nearly as possible in the same manner as is provided in these By-Laws for the
Board of Directors.  Adequate provisions shall be made for notice to members of
all meeting of committees.  One-third (1/3) of the members of any committee
shall constitute a quorum unless the committee shall consist of one (1) or two
(2) members, in which event one (1) member shall constitute a quorum; and all
matters shall be determined by a majority vote of the members present.  Action
may be taken by any committee without a meeting if all members thereof consent
thereto in writing, and the writing or writings are filed with the minutes of
the proceedings of such committee.

     2.18 Compensation of Directors.  Directors may be paid such compensation
          -------------------------
for their services and such reimbursement for expenses of attendance at meetings
as the Board of Directors may from time to time determine. No such payment shall
preclude any director from serving the Corporation or any of its parent or
subsidiary corporations in any other capacity and receiving compensation for
such service.

     2.19 Amendments to Article.  Notwithstanding any other provisions of law,
          ---------------------
the Certificate of Incorporation or these By-Laws, and notwithstanding the fact
that a lesser percentage may be specified by law, the affirmative vote of the
holders of a least sixty-six and two-thirds percent (66-2/3%) of the votes which
all the stockholders would be entitled to cast at any annual election of
directors or class of directors shall be required to amend or repeal, or to
adopt any provision inconsistent with, this Article 2.
<PAGE>

                                      -10-


                             ARTICLE 3 - Officers
                             --------------------


     3.1  Enumeration.  The officers of the Corporation shall consist of a
          -----------
President, a Secretary, a Treasurer and such other officers with such other
titles as the Board of Directors shall determine, including, but not limited to,
a Chairman of the Board, a Vice-Chairman of the Board, and one or more Vice
Presidents, Assistant Treasurers and Assistant Secretaries. The Board of
Directors may appoint such other officers as it may deem appropriate.

     3.2  Election.  The President, Treasurer and Secretary shall be elected
          --------
annually by the Board of Directors at its first meeting following the annual
meeting of stockholders. Other officers may be appointed by the Board of
Directors at such meeting or at any other meeting.

     3.3  Qualification.  No officer need be a stockholder.  Any two or more
          -------------
offices may be held by the same person.

     3.4  Tenure.  Except as otherwise provided by law, by the Certificate of
          ------
Incorporation or by these By-Laws, each officer shall hold office until his or
her successor is elected and qualified, unless a different term is specified in
the vote choosing or appointing such officer, or until his or her earlier death,
resignation or removal.

     3.5  Resignation and Removal.  Any officer may resign by delivering his or
          -----------------------
her written resignation to the Chairman of the Board (if any), to the Board of
Directors at a meeting thereof, to the Corporation at its principal office or to
the President or Secretary. Such resignation shall be effective upon receipt
unless it is specified to be effective at some other time or upon the happening
of some other event.

     Any officer may be removed at any time, with or without cause, by vote of a
majority of the entire number of directors then in office.

     Except as the Board of Directors may otherwise determine, no officer who
resigns or is removed shall have any right to any compensation as an officer for
any period following his or her resignation or removal, or any right to damages
on account of such removal, whether his or her compensation be by the month or
by the year or otherwise, unless such compensation is expressly provided in a
duly authorized written agreement with the Corporation.

     3.6  Vacancies.  The Board of Directors may fill any vacancy occurring in
          ---------
any office for any reason and may, in its discretion, leave unfilled for such
period as it may determine any offices other than those of President, Treasurer
and Secretary. Each such successor shall hold office for the unexpired term of
his predecessor and until his or her successor is elected and qualified, or
until his or her earlier death, resignation or removal.

     3.7  Chairman of the Board and Vice-Chairman of the Board.  The Chairman
          ----------------------------------------------------
of the Board, if any, shall preside at all meetings of the Board of Directors
and stockholders at which he or she is present and shall perform such duties and
possess such powers as are designated by the Board of
<PAGE>

                                      -11-

Directors. If the Board of Directors appoints a Vice-Chairman of the Board, he
or she shall, in the absence or disability of the Chairman of the Board, perform
the duties and exercise the powers of the Chairman of the Board and shall
perform such other duties and possess such other powers as may from time to time
be designated by the Board of Directors.

     3.8   President.  The President shall, subject to the direction of the
           ---------
Board of Directors, have general charge and supervision of the business of the
Corporation. Unless otherwise provided by the Board of Directors, and provided
that there is no Chairman of the Board or that the Chairman and Vice-Chairman,
if any, are not available, the President shall preside at all meetings of the
stockholders, and, if a director, at all meetings of the Board of Directors.
Unless the Board of Directors has designated another officer as the Chief
Executive Officer, the President shall be the Chief Executive Officer of the
Corporation. The President shall perform such other duties and shall have such
other powers as the Board of Directors may from time to time prescribe. The
President shall have the power to enter into contracts and otherwise bind the
Corporation in matters arising in the ordinary course of the Corporation's
business.

     3.9   Vice Presidents.  Any Vice President shall perform such duties and
           ---------------
possess such powers as the Board of Directors or the President may from time to
time prescribe. In the event of the absence, inability or refusal to act of the
President, the Vice President (or if there shall be more than one, the Vice
Presidents in the order determined by the Board of Directors) shall perform the
duties of the President and, when so performing, shall have all the powers of
and be subject to all the restrictions upon the President. The Board of
Directors may assign to any Vice President the title of Executive Vice
President, Senior Vice President or any other title selected by the Board of
Directors. Unless otherwise determined by the Board of Directors, any Vice
President shall have the power to enter into contracts and otherwise bind the
Corporation in matters arising in the ordinary course of the Corporation's
business.

     3.10  Secretary and Assistant Secretaries. The Secretary shall perform such
           -----------------------------------
duties and shall have such powers as the Board of Directors or the President may
from time to time prescribe. In addition, the Secretary shall perform such
duties and have such powers as are incident to the office of secretary,
including without limitation the duty and power to give notices of all meetings
of stockholders and special meetings of the Board of Directors, to attend all
meetings of stockholders and the Board of Directors and keep a record of the
proceedings, to maintain a stock ledger and prepare lists of stockholders and
their addresses as required, to be custodian of corporate records and the
corporate seal and to affix and attest to the same on documents.

     Any Assistant Secretary shall perform such duties and possess such powers
as the Board of Directors, the President or the Secretary may from time to time
prescribe. In the event of the absence, inability or refusal to act of the
Secretary, the Assistant Secretary (or if there shall be more than one, the
Assistant Secretaries in the order determined by the Board of Directors) shall
perform the duties and exercise the powers of the Secretary.

     In the absence of the Secretary or any Assistant Secretary at any meeting
of stockholders or directors, the person presiding at the meeting shall
designate a temporary secretary to keep a record of the meeting.
<PAGE>

                                      -12-

     3.11  Treasurer and Assistant Treasurers. The Treasurer shall perform such
           ----------------------------------
duties and shall have such powers as the Board of Directors or the President may
from time to time prescribe. In addition, the Treasurer shall perform such
duties and have such powers as are incident to the office of treasurer,
including without limitation the duty and power to keep and be responsible for
all funds and securities of the Corporation, to deposit funds of the Corporation
in depositories selected in accordance with these By-Laws, to disburse such
funds as ordered by the Board of Directors, to make proper accounts for such
funds, and to render as required by the Board of Directors statements of all
such transactions and of the financial condition of the Corporation.

     The Assistant Treasurers shall perform such duties and possess such powers
as the Board of Directors, the President or the Treasurer may from time to time
prescribe. In the event of the absence, inability or refusal to act of the
Treasurer, the Assistant Treasurer (or if there shall be more than one, the
Assistant Treasurers in the order determined by the Board of Directors) shall
perform the duties and exercise the powers of the Treasurer.

     3.12  Salaries.  Officers of the Corporation shall be entitled to such
           --------
salaries, compensation or reimbursement as shall be fixed or allowed from time
to time by the Board of Directors.

     3.13  Action with Respect to Securities of Other Corporations.  Unless
           -------------------------------------------------------
otherwise directed by the Board of Directors, the President or any officer of
the Corporation authorized by the President, shall have power to vote and
otherwise act on behalf of the Corporation, in person or by proxy, at any
meeting of stockholders of or with respect to any action of stockholders of any
other corporation in which the Corporation may hold securities and otherwise to
exercise any and all rights and powers which this Corporation may possess by
reason of its ownership of securities in such other corporation.


                           ARTICLE 4 - Capital Stock
                           -------------------------

     4.1   Issuance of Stock. Unless otherwise voted by the stockholders and
           -----------------
subject to the provisions of the Certificate of Incorporation, the whole or any
part of any unissued balance of the authorized capital stock of the Corporation
or the whole or any part of any issued, authorized capital stock of the
Corporation held in its treasury may be issued, sold, transferred or otherwise
disposed of by vote of the Board of Directors in such manner, for such
consideration and on such terms as the Board of Directors may determine.

     4.2   Certificates of Stock.  Every holder of stock of the Corporation
           ---------------------
shall be entitled to have a certificate, in such form as may be prescribed by
law and by the Board of Directors, certifying the number and class of shares
owned by such stockholder in the Corporation. Each such certificate shall be
signed by, or in the name of the Corporation by, the Chairman or Vice-Chairman,
if any, of the Board of Directors, or the President or a Vice President, and the
Treasurer or an Assistant Treasurer, or the Secretary or an Assistant Secretary
of the Corporation. Any or all of the signatures on such certificate may be a
facsimile.
<PAGE>

                                      -13-

     Each certificate for shares of stock which are subject to any restriction
on transfer pursuant to the Certificate of Incorporation, the By-Laws,
applicable securities laws or any agreement among any number of shareholders or
among such holders and the Corporation shall have conspicuously noted on the
face or back of such certificate either the full text of such restriction or a
statement of the existence of such restriction.

     4.3  Transfers. Except as otherwise established by rules and regulations
          ---------
adopted by the Board of Directors, and subject to applicable law, shares of
stock may be transferred on the books of the Corporation by the surrender to the
Corporation or its transfer agent of the certificate representing such shares,
properly endorsed or accompanied by a written assignment or power of attorney
properly executed, and with such proof of authority or the authenticity of
signature as the Corporation or its transfer agent may reasonably require.
Except as may be otherwise required by law, by the Certificate of Incorporation
or by these By-Laws, the Corporation shall be entitled to treat the record
holder of stock as shown on its books as the owner of such stock for all
purposes, including the payment of dividends and the right to vote with respect
to such stock, regardless of any transfer, pledge or other disposition of such
stock, until the shares have been transferred on the books of the Corporation in
accordance with the requirements of these By-Laws.

     4.4  Lost, Stolen or Destroyed Certificates. The Corporation may issue a
          --------------------------------------
new certificate of stock in place of any previously issued certificate alleged
to have been lost, stolen, or destroyed, upon such terms and conditions as the
President may prescribe, including the presentation of reasonable evidence of
such loss, theft or destruction and the giving of such indemnity as the
President may require for the protection of the Corporation or any transfer
agent or registrar.

     4.5  Record Date. The Board of Directors may fix in advance a date as a
          -----------
record date for the determination of the stockholders entitled to notice of or
to vote at any meeting of stockholders or, to the extent permitted by the
Certificate of Incorporation and these By-laws, to express consent (or dissent)
to corporate action in writing without a meeting, or entitled to receive payment
of any dividend or other distribution or allotment of any rights in respect of
any change, conversion or exchange of stock, or for the purpose of any other
lawful action. Such record date shall not be more than 60 nor less than 10 days
before the date of such meeting, nor more than 60 days prior to any other action
to which such record date relates.

     If no record date is fixed, the record date for determining stockholders
entitled to notice of or to vote at a meeting of stockholders shall be at the
close of business on the day before the day on which notice is given, or, if
notice is waived, at the close of business on the day before the day on which
the meeting is held. The record date for determining stockholders entitled to
express consent to corporate action in writing without a meeting (to the extent
permitted by the Certificate of Incorporation and these By-laws) when no prior
action by the Board of Directors is necessary, shall be the day on which the
first written consent is expressed. The record date for determining stockholders
for any other purpose shall be at the close of business on the day on which the
Board of Directors adopts the resolution relating to such purpose.
<PAGE>

                                      -14-

     A determination of stockholders of record entitled to notice of or to vote
at a meeting of stockholders shall apply to any adjournment of the meeting;
provided, however, that the Board of Directors may fix a new record date for the
adjourned meeting.


                        ARTICLE 5 - General Provisions
                        ------------------------------

     5.1  Fiscal Year. The fiscal year of the Corporation shall be fixed by
          -----------
resolution of the Board of Directors.

     5.2  Corporate Seal. The corporate seal shall be in such form as shall be
          --------------
approved by the Board of Directors.

     5.3  Notices. Except as otherwise specifically provided herein or required
          -------
by law or the Certificate of Incorporation, all notices required to be given to
any person pursuant to these by-laws shall be in writing and may in every
instance be effectively given by hand delivery to the recipient thereof, by
depositing such notice in the mails, postage paid, or by sending such notice by
prepaid telegram or facsimile transmission. Any such notice shall be addressed
to such person at his or her last known address as the same appears on the books
of the Corporation. The time when such notice is received shall be deemed to be
the time of the giving of the notice.

     5.4  Waiver of Notice. Whenever any notice whatsoever is required to be
          ----------------
given by law, by the Certificate of Incorporation or by these By-Laws, a waiver
of such notice either in writing signed by the person entitled to such notice or
such person's duly authorized attorney, or by telegraph, facsimile transmission
or any other available method, whether before, at or after the time stated in
such waiver, or the appearance of such person or persons at such meeting in
person or by proxy, shall be deemed equivalent to such notice.

     5.5  Evidence of Authority. A certificate by the Secretary, or an Assistant
          ---------------------
Secretary, or a temporary Secretary, as to any action taken by the stockholders,
directors, a committee or any officer or representative of the Corporation
shall, as to all persons who rely on the certificate in good faith, be
conclusive evidence of such action.

     5.6  Facsimile Signatures. In addition to the provisions for use of
          --------------------
facsimile signatures elsewhere specifically authorized in these By-Laws,
facsimile signatures of any officer or officers of the Corporation may be used
whenever and as authorized by the Board of Directors or a committee thereof.

     5.7  Reliance upon Books, Reports and Records. Each director, each member
          ----------------------------------------
of any committee designated by the Board of Directors, and each officer of the
Corporation shall, in the performance of his or her duties, be fully protected
in relying in good faith upon the books of account or other records of the
Corporation and upon such information, opinions, reports or statements presented
to the Corporation by any of its officers or employees or committees of the
Board of Directors so designated, or by any other person as to matters which
such director or committee member reasonably believes are within such other
person's professional or expert competence and who has been selected with
reasonable care by or on behalf of the Corporation.
<PAGE>

                                      -15-

     5.8   Time Periods. In applying any provision of these By-Laws that
           ------------
requires that an act be done or not be done a specified number of days prior to
an event or that an act be done during a period of a specified number of days
prior to an event, calendar days shall be used, the day of the doing of the act
shall be excluded, and the day of the event shall be included.

     5.9   Certificate of Incorporation. All references in these By-Laws to the
           ----------------------------
Certificate of Incorporation shall be deemed to refer to the Certificate of
Incorporation of the Corporation, as amended and in effect from time to time.

     5.10  Transactions with Interested Parties. No contract or transaction
           ------------------------------------
between the Corporation and one or more of the directors or officers, or between
the Corporation and any other corporation, partnership, association, or other
organization in which one or more of the directors or officers are directors or
officers, or have a financial interest, shall be void or voidable solely for
this reason, or solely because such director or officer is present at or
participates in the meeting of the Board of Directors or a committee of the
Board of Directors which authorizes the contract or transaction or solely
because his, her or their votes are counted for such purpose, if:

     (1)   The material facts as to his or her relationship or interest and as
     to the contract or transaction are disclosed or are known to the Board of
     Directors or the committee, and the Board or committee in good faith
     authorizes the contract or transaction by the affirmative vote of a
     majority of the disinterested directors, even though the disinterested
     directors be less than a quorum;

     (2)   The material facts as to his or her relationship or interest and as
     to the contract or transaction are disclosed or are known to the
     stockholders entitled to vote thereon, and the contract or transaction is
     specifically approved in good faith by vote of the stockholders; or

     (3)   The contract or transaction is fair as to the Corporation as of the
     time it is authorized, approved or ratified, by the Board of Directors, a
     committee of the Board of Directors, or the stockholders.

     Common or interested directors may be counted in determining the presence
of a quorum at a meeting of the Board of Directors or of a committee which
authorizes the contract or transaction.

     5.11  Severability. Any determination that any provision of these By-Laws
           ------------
is for any reason inapplicable, illegal or ineffective shall not affect or
invalidate any other provision of these By-Laws.

     5.12  Pronouns. All pronouns used in these By-Laws shall be deemed to refer
           --------
to the masculine, feminine or neuter, singular or plural, as the identity of the
persons or persons so designated may require.
<PAGE>

                                      -16-

                            ARTICLE 6 - Amendments
                            ----------------------

     6.1  By the Board of Directors. Except as is otherwise set forth in these
          -------------------------
By-Laws, these By-Laws may be altered, amended or repealed, or new by-laws may
be adopted, by the affirmative vote of a majority of the directors present at
any regular or special meeting of the Board of Directors at which a quorum is
present.

     6.2  By the Stockholders. Except as otherwise set forth in these By-Laws,
          -------------------
these By-Laws may be altered, amended or repealed or new by-laws may be adopted
by the affirmative vote of the holders of sixty-six and two-thirds percent (66-
2/3%) of the shares of the capital stock of the Corporation issued and
outstanding and entitled to vote at any regular meeting of stockholders, or at
any special meeting of stockholders, provided notice of such alteration,
amendment, repeal or adoption of new by-laws shall have been stated in the
notice of such special meeting.


                          ARTICLE 7 - Indemnification
                          ---------------------------

     7.1  Actions Other Than by or in the Right of the Corporation. The
          --------------------------------------------------------
Corporation shall indemnify and hold harmless, to the fullest extent permitted
by applicable law as it presently exists or may hereafter be amended, any person
who was or is a party or is threatened to be made a party or is otherwise
involved in any threatened, pending or completed action, suit or proceeding,
whether civil, criminal, administrative or investigative (other than an action
by or in the right of the Corporation) by reason of the fact that such person,
or a person for whom such person is the legal representative, is or was a
director, trustee, partner, officer, employee or agent of the Corporation, or is
or was serving at the request of the Corporation as a director, officer,
employee or agent of another corporation, partnership, joint venture, trust or
other enterprise or non-profit entity, against all liability, losses, expenses
(including attorneys' fees), judgments, fines, and amounts paid in settlement
actually and reasonably incurred by such person in connection with such action,
suit or proceeding if such person acted in good faith and in a manner he or she
reasonably believed to be in or not opposed to the best interest of the
Corporation, and, with respect to any criminal action or proceeding, had no
reasonable cause to believe his or her conduct was unlawful. The termination of
any action, suit or proceeding by judgment, order, settlement, conviction, or
upon a plea of nolo contendere or its equivalent, shall not, of itself, create a
presumption that such person did not act in good faith and in a manner which he
or she reasonably believed to be in or not opposed to the best interest of the
Corporation, and, with respect to any criminal action or proceeding, had
reasonable cause to believe that his or her conduct was unlawful.

     7.2  Actions by or in the Right of the Corporation.  The Corporation
          ---------------------------------------------
shall indemnify any person who was or is a party or is threatened to be made a
party to any threatened, pending or completed action or suit by or in the right
of the Corporation to procure a judgment in its favor by reason of the fact that
he or she is or was a director, trustee, partner, officer, employee or agent of
the Corporation, or is or was serving at the request of the Corporation as a
director, officer, employee or agent of another corporation, partnership, joint
venture, trust or other enterprise or non-profit entity against expenses
(including attorneys' fees) actually and reasonably incurred by him or her in
connection with the defense or settlement of such action or suit if such person
acted in good faith and in a manner such person reasonably believed to be in or
not opposed to the best interests of the Corporation; except that no
<PAGE>

                                      -17-

indemnification shall be made in respect of any claim, issue or matter as to
which such person shall have been adjudged to be liable for negligence or
misconduct in the performance of his duty to the Corporation unless and only to
the extent that the Court of Chancery of the State of Delaware or the court in
which such action or suit was brought shall determine upon application that
despite the adjudication of liability but in view of all the circumstances of
the case, such person fairly and reasonably entitled to indemnity for such
expenses which the Court of Chancery of the State of Delaware or such other
court shall deem proper.

     7.3  Success on the Merits. To the extent that any person referred to in
          ---------------------
Sections 7.1 or 7.2 has been successful on the merits or otherwise in defense of
any action, suit or proceeding referred to therein, or in defense of any claim,
issue or matter therein, he or she shall be indemnified against expenses
(including attorneys' fees) actually and reasonably incurred by him or her in
connection therewith.

     7.4. Authorization. Any indemnification under Sections 7.1, 7.2 or 7.3
          -------------
(unless ordered by a court) shall be made by the Corporation only as authorized
in the specific case upon a determination that indemnification of the director,
trustee, partner, officer, employee or agent is proper in the circumstances
because he has met the applicable standard of conduct set forth in Sections 7.1
and 7.2. Such determination shall be made: (a) by the Board of Directors, by a
majority vote of directors who are not parties to such action, suit or
proceeding (whether or not a quorum), or (b) if there are no disinterested
directors or if a majority of disinterested directors so directs, by independent
legal counsel (who may be regular legal counsel to the corporation) in a written
opinion, or (c) by the stockholders.

     7.5  Expense Advance. Expenses (including attorneys' fees) incurred by an
          ---------------
officer or director of the Corporation in defending any pending or threatened
civil, criminal, administrative or investigative action, suit or proceeding may
be paid by the Corporation in advance of the final disposition of such action,
suit or proceeding as authorized by the Board of Directors in the manner
provided in Section 7.4 of this Article upon receipt of an undertaking by or on
behalf of such officer or director to repay such amount, if it shall ultimately
be determined that he is not entitled to be indemnified by the Corporation as
authorized in this Article. Such expenses (including attorneys' fees) incurred
by other employees or agents of the Corporation may be so paid upon such terms
and conditions, if any, as the Board of Directors deems appropriate.

     7.6  Nonexclusivity.  The indemnification and advancement of expenses
          --------------
provided by, or granted pursuant to, the other Sections of this Article shall
not be deemed exclusive of any other rights to which any person seeking
indemnification or advancement of expenses may be entitled under any statute,
by-law, agreement, vote of stockholders or disinterested directors or otherwise,
both as to action in his or her official capacity and as to action in another
capacity while holding such office, and shall continue as to a person who has
ceased to be a director, officer, employee or agent and shall inure to the
benefit of the heirs, executors and administrators of such a person.

     7.7  Insurance. The Corporation shall have power to purchase and maintain
          ---------
insurance on behalf of any person who is or was a director, officer, employee or
agent of the Corporation, or is or was serving at the request of the Corporation
as a director, trustee, partner, officer, employee or agent of another
corporation, partnership, joint venture, trust or other enterprise or non-profit
entity against any
<PAGE>

                                      -18-

liability asserted against and incurred by such person in any such capacity, or
arising out of his or her status as such, whether or not the Corporation would
have the power to indemnify such person against such liability under the
provisions of this Article or Section 145 of the Delaware General Corporation
Law.

     7.8   "The Corporation". For the purposes of this Article, references to
           -----------------
"the Corporation" shall include the resulting corporation and, to the extent
that the Board of Directors of the resulting corporation so decides, all
constituent corporations (including any constituent of a constituent) absorbed
in a consolidation or merger which, if its separate existence had continued,
would have had power and authority to indemnify its directors, officers and
employees or agents so that any person who is or was a director, officer,
employee or agent of such a constituent corporation or is or was serving at the
request of such constituent corporation as director, trustee, partner, officer,
employee or agent of another corporation, partnership, joint venture, trust or
other enterprise or non-profit entity shall stand in the same position under the
provisions of this Article with respect to the resulting or surviving
corporation as he or she would have with respect to such constituent corporation
if its separate existence had continued.

     7.9   Other Indemnification. The Corporation's obligation, if any, to
           ---------------------
indemnify any person who was or is serving at its request as a director,
trustee, partner, officer, employee or agent of another corporation,
partnership, joint venture, trust or other enterprise or non-profit entity shall
be reduced by any amount such person may collect as indemnification from such
other corporation, partnership, joint venture, trust or other enterprise or non-
profit entity or from insurance.

     7.10  Other Definitions. For purposes of this Article, references to "other
           -----------------
enterprises" shall include employee benefit plans; references to "fines" shall
include any excise taxes assessed on a person with respect to an employee
benefit plan; and references to "serving at the request of the Corporation"
shall include any service as a director, trustee, officer, employee or agent of
the Corporation which imposes duties on, or involves services by, such director,
trustee, officer, employee, or agent with respect to an employee benefit plan,
its participants, or beneficiaries; and a person who acted in good faith and in
a manner he reasonably believed to be in the interest of the participants and
beneficiaries of an employee benefit plan shall be deemed to have acted in a
manner "not opposed to the best interests of the Corporation" as referred to in
this Article.

     7.11  Continuation of Indemnification. The indemnification and advancement
           -------------------------------
of expenses provided by, or granted pursuant to, this Article shall, unless
otherwise provided when authorized or ratified, continue as a person who has
ceased to be a director, trustee, partner, officer, employee or agent and shall
inure to the benefit of the heirs, executors and administrators of such a
person.

<PAGE>

                                                                     EXHIBIT 4.4
                                                                     -----------

                                MATRIXONE, INC.

                                1999 Stock Plan
                                ---------------

1.   Purpose and Eligibility
     -----------------------

     The purpose of this 1999 Stock Plan (the "Plan") of MatrixOne, Inc. (the
                                               ----
"Company") is to provide stock options and other equity interests in the Company
- --------
(each an "Award") to employees, officers, directors, consultants and advisors of
          -----
the Company and its Subsidiaries, all of whom are eligible to receive Awards
under the Plan. Any person to whom an Award has been granted under the Plan is
called a "Participant". Additional definitions are contained in Section 8.
          -----------

2.   Administration
     --------------

     a.   Administration by Board of Directors.  The Plan will be administered
          ------------------------------------
by the Board of Directors of the Company (the "Board"). The Board, in its sole
                                               -----
discretion, shall have the authority to grant and amend Awards, to adopt, amend
and repeal rules relating to the Plan and to interpret and correct the
provisions of the Plan and any Award. All decisions by the Board shall be final
and binding on all interested persons. Neither the Company nor any member of the
Board shall be liable for any action or determination relating to the Plan.

     b.   Appointment of Committees.  To the extent permitted by applicable law,
          -------------------------
the Board may delegate any or all of its powers under the Plan to one or more
committees or subcommittees of the Board (a "Committee"). All references in the
                                             ---------
Plan to the "Board" shall mean such Committee or the Board.
             -----

     c.   Delegation to Executive Officers. To the extent permitted by
          --------------------------------
applicable law, the Board may delegate to one or more executive officers of the
Company the power to grant Awards and exercise such other powers under the Plan
as the Board may determine, provided that the Board shall fix the maximum number
of Awards to be granted and the maximum number of shares issuable to any one
Participant pursuant to Awards granted by such executive officers and shall
establish such other terms and conditions to the power of the executive officers
as the Board so chooses.

3.   Stock Available for Awards
     --------------------------

     a.   Number of Shares.  Subject to adjustment under Section 3(c), the
          ----------------
aggregate number of shares of Common Stock of the Company (the "Common Stock")
                                                                ------------
that may be issued pursuant to the Plan is 1,500,000 shares. If any Award
expires, or is terminated, surrendered or forfeited, in whole or in part, the
unissued Common Stock covered by such Award shall again be available for the
grant of Awards under the Plan. If shares of Common Stock issued pursuant to the
Plan are repurchased by, or are surrendered or forfeited to, the Company at no
more than cost,
<PAGE>

such shares of Common Stock shall again be available for the grant of Awards
under the Plan; provided, however, that the cumulative number of such shares
that may be so reissued under the Plan will not exceed 1,500,000 shares. Shares
issued under the Plan may consist in whole or in part of authorized but unissued
shares or treasury shares.

     b.   Per-Participant Limit.  Subject to adjustment under Section 3(c), no
          ---------------------
Participant may be granted Awards during any one fiscal year to purchase more
than 300,000 shares of Common Stock.

     c.   Adjustment to Common Stock.  In the event of any stock split, stock
          --------------------------
dividend, extraordinary cash dividend, recapitalization, reorganization, merger,
consolidation, combination, exchange of shares, liquidation, spin-off, split-up,
or other similar change in capitalization or event, (i) the number and class of
securities available for Awards under the Plan and the per-Participant share
limit, (ii) the number and class of securities, vesting schedule and exercise
price per share subject to each outstanding Option, (iii) the repurchase price
per security subject to repurchase, and (iv) the terms of each other outstanding
stock-based Award shall be adjusted by the Company (or substituted Awards may be
made) to the extent the Board shall determine, in good faith, that such an
adjustment (or substitution) is appropriate. If Section 7(e)(i) applies for any
event, this Section 3(c) shall not be applicable.

4.   Stock Options
     -------------

     a.   General.  The Board may grant options to purchase Common Stock (each,
          -------
an "Option") and determine the number of shares of Common Stock to be covered by
    ------
each Option, the exercise price of each Option and the conditions and
limitations applicable to the exercise of each Option and the Common Stock
issued upon the exercise of each Option, including vesting provisions,
repurchase provisions and restrictions relating to applicable federal or state
securities laws, as it considers advisable.

     b.   Incentive Stock Options.  An Option that the Board intends to be an
          -----------------------
"incentive stock option" as defined in Section 422 of the Code (an "Incentive
                                                                    ---------
Stock Option") shall be granted only to employees of the Company and shall be
- ------------
subject to and shall be construed consistently with the requirements of Section
422 of the Code. The Board and the Company shall have no liability if an Option
or any part thereof that is intended to be an Incentive Stock Option does not
qualify as such. An Option or any part thereof that does not qualify as an
Incentive Stock Option, or an Option that could qualify but is intentionally not
granted as an Incentive Stock Option, is referred to herein as a "Nonstatutory
                                                                  ------------
Stock Option".
- ------------

     c.   Exercise Price.  The Board shall establish the exercise price (or
          --------------
determine the method by which the exercise price shall be determined) at the
time each Option is granted and specify it in the applicable option agreement.

     d.   Duration of Options.  Each Option shall be exercisable at such times
          -------------------
and be subject to such terms and conditions as the Board may specify in the
applicable option agreement.

                                      -2-
<PAGE>

     e.   Exercise of Option.  Options may be exercised only by delivery to the
          ------------------
Company of a written notice of exercise signed by the proper person together
with payment in full as specified in Section 4(f) for the number of shares for
which the Option is exercised.

     f.   Payment Upon Exercise.  Common Stock purchased upon the exercise of an
          ---------------------
Option shall be paid for by one or any combination of the following forms of
payment:

          (i)   by check payable to the order of the Company;

          (ii)  except as otherwise explicitly provided in the applicable option
agreement, and only if the Common Stock is then publicly traded, delivery of an
irrevocable and unconditional undertaking by a creditworthy broker to deliver
promptly to the Company sufficient funds to pay the exercise price, or delivery
by the Participant to the Company of a copy of irrevocable and unconditional
instructions to a creditworthy broker to deliver promptly to the Company cash or
a check sufficient to pay the exercise price; or

          (iii) to the extent explicitly provided in the applicable option
agreement, by (x) delivery of shares of Common Stock owned by the Participant
valued at fair market value (as determined by the Board or as determined
pursuant to the applicable option agreement), or (y) payment of such other
lawful consideration as the Board may determine.

5.   Restricted Stock
     ----------------

     a.   Grants.  The Board may grant Awards entitling recipients to acquire
          ------
shares of Common Stock, subject to (i) delivery to the Company by the
Participant of a check in an amount at least equal to the par value of the
shares purchased, and (ii) the right of the Company to repurchase all or part of
such shares at their issue price or other stated or formula price from the
Participant in the event that conditions specified by the Board in the
applicable Award are not satisfied prior to the end of the applicable
restriction period or periods established by the Board for such Award (each, a
"Restricted Stock Award").
- -----------------------

     b.   Terms and Conditions. The Board shall determine the terms and
          --------------------
conditions of any such Restricted Stock Award. Any stock certificates issued in
respect of a Restricted Stock Award shall be registered in the name of the
Participant and, unless otherwise determined by the Board, deposited by the
Participant, together with a stock power endorsed in blank, with the Company (or
its designee). After the expiration of the applicable restriction periods, the
Company (or such designee) shall deliver the certificates no longer subject to
such restrictions to the Participant or, if the Participant has died, to the
beneficiary designated by a Participant, in a manner determined by the Board, to
receive amounts due or exercise rights of the Participant in the event of the
Participant's death (the "Designated Beneficiary"). In the absence of an
                          ----------------------
effective designation by a Participant, Designated Beneficiary shall mean the
Participant's estate.

                                      -3-
<PAGE>

6.   Other Stock-Based Awards
     ------------------------

     The Board shall have the right to grant other Awards based upon the Common
Stock having such terms and conditions as the Board may determine, including,
without limitation, the grant of shares based upon certain conditions, the grant
of securities convertible into Common Stock and the grant of stock appreciation
rights, phantom stock awards or stock units.

7.   General Provisions Applicable to Awards
     ---------------------------------------

     a.   Transferability of Awards. Except as the Board may otherwise determine
          -------------------------
or provide in an Award, Awards shall not be sold, assigned, transferred, pledged
or otherwise encumbered by the person to whom they are granted, either
voluntarily or by operation of law, except by will or the laws of descent and
distribution, and, during the life of the Participant, shall be exercisable only
by the Participant. References to a Participant, to the extent relevant in the
context, shall include references to authorized transferees. Notwithstanding the
foregoing, Nonstatutory Stock Options shall also be assignable or transferable
pursuant to: (i) a valid domestic relations order or (ii) to: (A) parents of the
grantee, (B) issue of the parents of the grantee, (C) parents of the grantee's
spouse, (D) issue of the parents of the grantee's spouse, (E) spouses of any
such issue, (F) the legal guardian of any such issue and/or spouses, (G) one or
more trusts for the primary benefit of any such issue, spouses and/or charitable
organizations described in provision (I) below, which trusts are either
irrevocable or restricted by their terms such that they may not be amended to
provide distribution of any Stock Right to anyone other than such issue,
spouses, and/or charitable organizations, (H) the custodian for any such issue
under the Uniform Transfers to Minors Act or corresponding statute of any
jurisdiction, or (I) a charitable organization described in Section 170(c) of
the Internal Revenue Code, or any successor thereto (the "Code") including but
not limited to private foundations and supporting organizations which have been
established by the grantee during the grantee's lifetime, and which have
obtained tax exempt status under Section 501(c)(3) of the Code; and in each such
case only to the extent that such transfer is authorized by either the Chief
Executive Officer or the Chief Financial Officer of the Company; and thereafter
the transferee shall have all such rights of the grantee, provided, however,
that any provisions relating to employment or business relationship of the
grantee (such as option termination provisions) shall be deemed to survive such
transfer and the grantee's actual period of employment or business relationship
shall be the relevant measurement period for purposes thereof.

     b.   Documentation.  Each Award under the Plan shall be evidenced by a
          -------------
written instrument in such form as the Board shall determine or as executed by
an officer of the Company pursuant to authority delegated by the Board. Each
Award may contain terms and conditions in addition to those set forth in the
Plan provided that such terms and conditions do not contravene the provisions of
the Plan.

     c.   Board Discretion. The terms of each type of Award need not be
          ----------------
identical, and the Board need not treat Participants uniformly.

                                      -4-
<PAGE>

     d.   Termination of Status.  The Board shall determine the effect on an
          ---------------------
Award of the disability, death, retirement, authorized leave of absence or other
change in the employment or other status of a Participant and the extent to
which, and the period during which, the Participant, or the Participant's legal
representative, conservator, guardian or Designated Beneficiary, may exercise
rights under the Award.

     e.   Acquisition of the Company
          --------------------------

          (i)  Consequences of an Acquisition.
               ------------------------------

               (A)  Acquisition Intended to be Accounted for as a Pooling-of-
                    ---------------------------------------------------------
Interests.  Upon the consummation of an Acquisition intended to be accounted for
- ---------
as a pooling of interests: (x) all outstanding Awards shall remain the
obligation of the Company or be assumed by the surviving or acquiring entity,
and there shall be automatically substituted for the shares of Common Stock then
subject to such Awards the consideration payable with respect to the outstanding
shares of Common Stock in connection with the Acquisition and (y) the vesting
provisions of all then unvested Awards shall become accelerated by a period of
24 months.

               (B)  Acquisition Intended to be Accounted for under the Purchase
                    -----------------------------------------------------------
Method. Unless otherwise expressly provided in the applicable Option or Award,
- ------
upon the occurrence of an Acquisition intended to be accounted for under the
purchase method, (x) the vesting provisions of all then unvested Awards shall
become accelerated by a period of 24 months and (y) the Board or the board of
directors of the surviving or acquiring entity (as used in this Section
7(e)(i)(B), also the "Board"), shall, as to outstanding Awards (on the same
                      -----
basis or on different bases, as the Board shall specify), make appropriate
provision for the continuation of such Awards by the Company or the assumption
of such Awards by the surviving or acquiring entity and by substituting on an
equitable basis for the shares then subject to such Awards either (i) the
consideration payable with respect to the outstanding shares of Common Stock in
connection with the Acquisition, (ii) shares of stock of the surviving or
acquiring corporation or (iii) such other securities as the Board deems
appropriate, the fair market value of which (as determined by the Board in its
sole discretion) shall not materially differ from the fair market value of the
shares of Common Stock subject to such Awards immediately preceding the
Acquisition. In addition to or in lieu of the foregoing, with respect to
outstanding Options, the Board may, upon written notice to the affected
optionees, provide (a) that one or more Options then outstanding shall become
immediately exercisable in full; (b) that such Options must be exercised within
a specified number of days of the date of such notice, at the end of which
period such Options shall terminate; or (c) that one or more Options then
outstanding shall be terminated in exchange for a cash payment equal to the
excess of the fair market value (as determined by the Board in its sole
discretion) for the shares subject to such Options over the exercise price
thereof.

               (C)  Acquisition Defined.  An "Acquisition" shall mean: (x) the
                    -------------------       -----------
sale of the Company by merger in which the shareholders of the Company in their
capacity as such no longer own a majority of the outstanding equity securities
of the Company (or its successor); or (y) any sale of all or substantially all
of the assets or capital stock of the Company (other than in a

                                      -5-
<PAGE>

spin-off or similar transaction) or (z) any other acquisition of the business of
the Company, as determined by the Board.

          (ii)   Assumption of Options Upon Certain Events.  In connection with
                 -----------------------------------------
a merger or consolidation of an entity with the Company or the acquisition by
the Company of property or stock of an entity, the Board may grant Awards under
the Plan in substitution for stock and stock-based awards issued by such entity
or an affiliate thereof. The substitute Awards shall be granted on such terms
and conditions as the Board considers appropriate in the circumstances.

          (iii)  Pooling-of Interests-Accounting.  If the Company proposes to
                 -------------------------------
engage in an Acquisition intended to be accounted for as a pooling-of-interests,
and in the event that the provisions of this Plan or of any Award hereunder, or
any actions of the Board taken in connection with such Acquisition, are
determined by the Company's or the acquiring company's independent public
accountants to cause such Acquisition to fail to be accounted for as a pooling-
of-interests, then such provisions or actions shall be amended or rescinded by
the Board, without the consent of any Participant, to be consistent with
pooling-of-interests accounting treatment for such Acquisition.

          (iv)   Parachute Awards. Notwithstanding the provisions of Section
                 ----------------
7(e)(i)(A), if, in connection with an Acquisition described therein, a tax under
Section 4999 of the Code would be imposed on the Participant (after taking into
account the exceptions set forth in Sections 280G(b)(4) and 280G(b)(5) of the
Code), then the number of Awards which shall become exercisable, realizable or
vested as provided in such section shall be reduced (or delayed), to the minimum
extent necessary, so that no such tax would be imposed on the Participant (the
Awards not becoming so accelerated, realizable or vested, the "Parachute
                                                               ---------
Awards"); provided, however, that if the "aggregate present value" of the
                                          -----------------------
Parachute Awards would exceed the tax that, but for this sentence, would be
imposed on the Participant under Section 4999 of the Code in connection with the
Acquisition, then the Awards shall become immediately exercisable, realizable
and vested without regard to the provisions of this sentence. For purposes of
the preceding sentence, the "aggregate present value" of an Award shall be
                             -----------------------
calculated on an after-tax basis (other than taxes imposed by Section 4999 of
the Code) and shall be based on economic principles rather than the principles
set forth under Section 280G of the Code and the regulations promulgated
thereunder. All determinations required to be made under this Section 7(e)(iv)
shall be made by the Company.

     f.   Withholding.  Each Participant shall pay to the Company, or make
          -----------
provisions satisfactory to the Company for payment of, any taxes required by law
to be withheld in connection with Awards to such Participant no later than the
date of the event creating the tax liability. The Board may allow Participants
to satisfy such tax obligations in whole or in part by transferring shares of
Common Stock, including shares retained from the Award creating the tax
obligation, valued at their fair market value (as determined by the Board or as
determined pursuant to the applicable option agreement). The Company may, to the
extent permitted by law, deduct any such tax obligations from any payment of any
kind otherwise due to a Participant.

                                      -6-
<PAGE>

     g.   Amendment of Awards.  The Board may amend, modify or terminate any
          -------------------
outstanding Award including, but not limited to, substituting therefor another
Award of the same or a different type, changing the date of exercise or
realization, and converting an Incentive Stock Option to a Nonstatutory Stock
Option, provided that, except as otherwise provided in Section 7(e)(iii), the
Participant's consent to such action shall be required unless the Board
determines that the action, taking into account any related action, would not
materially and adversely affect the Participant.

     h.   Conditions on Delivery of Stock.  The Company will not be obligated to
          -------------------------------
deliver any shares of Common Stock pursuant to the Plan or to remove
restrictions from shares previously delivered under the Plan until (i) all
conditions of the Award have been met or removed to the satisfaction of the
Company, (ii) in the opinion of the Company's counsel, all other legal matters
in connection with the issuance and delivery of such shares have been satisfied,
including any applicable securities laws and any applicable stock exchange or
stock market rules and regulations, and (iii) the Participant has executed and
delivered to the Company such representations or agreements as the Company may
consider appropriate to satisfy the requirements of any applicable laws, rules
or regulations.

     i.   Acceleration. The Board may at any time provide that any Options shall
          ------------
become immediately exercisable in full or in part, that any Restricted Stock
Awards shall be free of some or all restrictions, or that any other stock-based
Awards may become exercisable in full or in part or free of some or all
restrictions or conditions, or otherwise realizable in full or in part, as the
case may be, despite the fact that the foregoing actions may (i) cause the
application of Sections 280G and 4999 of the Code if a change in control of the
Company occurs, or (ii) disqualify all or part of the Option as an Incentive
Stock Option.

8.   Miscellaneous
     -------------

     a.  Definitions.
         -----------

               (i)   "Company," for purposes of eligibility under the Plan,
                      --------
shall include any present or future subsidiary corporations of MatrixOne, Inc.,
as defined in Section 424(f) of the Code (a "Subsidiary"), and any present or
                                             ----------
future parent corporation of MatrixOne, Inc., as defined in Section 424(e) of
the Code. For purposes of Awards other than Incentive Stock Options, the term
"Company" shall include any other business venture in which the Company has a
- --------
direct or indirect significant interest, as determined by the Board in its sole
discretion.

               (ii)  "Code" means the Internal Revenue Code of 1986, as amended,
                      ----
and any regulations promulgated thereunder.

               (iii) "employee" for purposes of eligibility under the Plan (but
                      --------
not for purposes of Section 4(b)) shall include a person to whom an offer of
employment has been extended by the Company.

                                      -7-
<PAGE>

     b.   No Right To Employment or Other Status.  No person shall have any
          --------------------------------------
claim or right to be granted an Award, and the grant of an Award shall not be
construed as giving a Participant the right to continued employment or any other
relationship with the Company. The Company expressly reserves the right at any
time to dismiss or otherwise terminate its relationship with a Participant free
from any liability or claim under the Plan.

     c.   No Rights As Stockholder.  Subject to the provisions of the applicable
          ------------------------
Award, no Participant or Designated Beneficiary shall have any rights as a
stockholder with respect to any shares of Common Stock to be distributed with
respect to an Award until becoming the record holder thereof.

     d.   Effective Date and Term of Plan.  The Plan shall become effective on
          -------------------------------
the date on which it is adopted by the Board. No Awards shall be granted under
the Plan after the completion of ten years from the date on which the Plan was
adopted by the Board, but Awards previously granted may extend beyond that date.

     e.   Amendment of Plan.  The Board may amend, suspend or terminate the Plan
          -----------------
or any portion thereof at any time, subject, in the case of amendments, to any
applicable statutory or regulatory requirements to obtain shareholder approval
when and if so required.

     f.   Governing Law. The provisions of the Plan and all Awards made
          -------------
hereunder shall be governed by and interpreted in accordance with the laws of
Delaware, without regard to any applicable conflicts of law.


                                    Adopted by the Board of Directors on
                                    January 20, 2000

                                    Approved by the stockholders on
                                    January 20, 2000

                                      -8-

<PAGE>

                                                                     EXHIBIT 4.7
                                                                     -----------

                                MATRIXONE, INC.

                       2000 EMPLOYEE STOCK PURCHASE PLAN



Article 1 - Purpose.
- -------------------

     This 2000 Employee Stock Purchase Plan (the "Plan") is intended to
encourage stock ownership by all eligible employees of MatrixOne, Inc. (the
"Company"), a Delaware corporation, and its participating subsidiaries (as
defined in Article 17) so that they may share in the growth of the Company by
acquiring or increasing their proprietary interest in the Company. The Plan is
designed to encourage eligible employees to remain in the employ of the Company
and its participating subsidiaries. The Plan is intended to constitute an
"employee stock purchase plan" within the meaning of Section 423(b) of the
Internal Revenue Code of 1986, as amended (the "Code").

Article 2 - Administration of the Plan.
- --------------------------------------

     The Plan may be administered by a committee appointed by the Board of
Directors of the Company (the "Committee"). The Committee shall consist of not
less than two members of the Company's Board of Directors. The Board of
Directors may from time to time remove members from, or add members to, the
Committee. Vacancies on the Committee, howsoever caused, shall be filled by the
Board of Directors. The Committee may select one of its members as Chairman, and
shall hold meetings at such times and places as it may determine. Acts by a
majority of the Committee, or acts reduced to or approved in writing by a
majority of the members of the Committee, shall be the valid acts of the
Committee.

     The interpretation and construction by the Committee of any provisions of
the Plan or of any option granted under it shall be final, unless otherwise
determined by the Board of Directors. The Committee may from time to time adopt
such rules and regulations for carrying out the Plan as it may deem best,
provided that any such rules and regulations shall be applied on a uniform basis
to all employees under the Plan. No member of the Board of Directors or the
Committee shall be liable for any action or determination made in good faith
with respect to the Plan or any option granted under it.

     In the event the Board of Directors fails to appoint or refrains from
appointing a Committee, the Board of Directors shall have all power and
authority to administer the Plan. In such event, the word "Committee" wherever
used herein shall be deemed to mean the Board of Directors.

Article 3 - Eligible Employees.
- ------------------------------

     All employees of the Company or any of its participating subsidiaries whose
customary employment is more than 20 hours per week and for more than five
months in any calendar
<PAGE>

                                      -2-

year shall be eligible to receive options under the Plan to purchase common
stock of the Company, and all eligible employees shall have the same rights and
privileges hereunder. Persons who are eligible employees on the first business
day of any Payment Period (as defined in Article 5) shall receive their options
as of such day. Persons who become eligible employees after any date on which
options are granted under the Plan shall be granted options on the first day of
the next succeeding Payment Period on which options are granted to eligible
employees under the Plan. In no event, however, may an employee be granted an
option if such employee, immediately after the option was granted, would be
treated as owning stock possessing five percent or more of the total combined
voting power or value of all classes of stock of the Company or of any parent
corporation or subsidiary corporation, as the terms "parent corporation" and
"subsidiary corporation" are defined in Section 424(e) and (f) of the Code. For
purposes of determining stock ownership under this paragraph, the rules of
Section 424(d) of the Code shall apply, and stock which the employee may
purchase under outstanding options shall be treated as stock owned by the
employee.


Article 4 - Stock Subject to the Plan.
- -------------------------------------

     The stock subject to the options under the Plan shall be shares of the
Company's authorized but unissued common stock, par value $.01 per share (the
"Common Stock"), or shares of Common Stock reacquired by the Company, including
shares purchased in the open market. The aggregate number of shares which may be
issued pursuant to the Plan is 1,350,000, subject to adjustment as provided in
Article 12. If any option granted under the Plan shall expire or terminate for
any reason without having been exercised in full or shall cease for any reason
to be exercisable in whole or in part, the unpurchased shares subject thereto
shall again be available under the Plan.

Article 5 - Payment Period and Stock Options.
- --------------------------------------------

     The first Payment Period during which payroll deductions will be
accumulated under the Plan shall commence on the later to occur of May 1, 2000
and the first day of the first calendar month following effectiveness of the
Form S-8 registration statement filed with the Securities and Exchange
Commission covering the shares to be issued pursuant to the Plan and shall end
on October 31, 2000. For the remainder of the duration of the Plan, Payment
Periods shall consist of the six-month periods commencing on November 1 and May
1 and ending on April 30 and October 31 of each calendar year.

     Twice each year, on the first business day of each Payment Period, the
Company will grant to each eligible employee who is then a participant in the
Plan an option to purchase on the last day of such Payment Period, at the Option
Price hereinafter provided for, a maximum of 2,250 shares, on condition that
such employee remains eligible to participate in the Plan throughout the
remainder of such Payment Period and subject to the limitation set forth in
Article 4. The participant shall be entitled to exercise the option so granted
only to the extent of the participant's accumulated payroll deductions on the
last day of such Payment Period. If the participant's accumulated payroll
deductions on the last day of the Payment Period would
<PAGE>

                                      -3-

enable the participant to purchase more than 2,250 shares except for the 2,250-
share limitation, the excess of the amount of the accumulated payroll deductions
over the aggregate purchase price of the 2,250 shares shall be promptly refunded
to the participant by the Company, without interest. The Option Price per share
for each Payment Period shall be the lesser of (i) 85% of the average market
price of the Common Stock on the first business day of the Payment Period and
(ii) 85% of the average market price of the Common Stock on the last business
day of the Payment Period, in either event rounded up to the nearest cent. The
foregoing limitations on the number of shares subject to option and the Option
Price shall be subject to adjustment as provided in Article 12.

     For purposes of the Plan, the term "average market price" on any date means
(i) the average (on that date) of the high and low prices of the Common Stock on
the principal national securities exchange on which the Common Stock is traded,
if the Common Stock is then traded on a national securities exchange; or (ii)
the last reported sale price (on that date) of the Common Stock on the Nasdaq
National Market, if the Common Stock is not then traded on a national securities
exchange; or (iii) the average of the closing bid and asked prices last quoted
(on that date) by an established quotation service for over-the-counter
securities, if the Common Stock is not reported on the Nasdaq National Market;
or (iv) if the Common Stock is not publicly traded, the fair market value of the
Common Stock as determined by the Committee after taking into consideration all
factors which it deems appropriate, including, without limitation, recent sale
and offer prices of the Common Stock in private transactions negotiated at arm's
length.

     For purposes of the Plan, the term "business day" means a day on which
there is trading on the Nasdaq National Market or the aforementioned national
securities exchange, whichever is applicable pursuant to the preceding
paragraph; and if neither is applicable, a day that is not a Saturday, Sunday or
legal holiday in the Commonwealth of Massachusetts.

     No employee shall be granted an option which permits the employee's right
to purchase stock under the Plan, and under all other Section 423(b) employee
stock purchase plans of the Company and any parent or subsidiary corporations,
to accrue at a rate which exceeds $25,000 of fair market value of such stock
(determined on the date or dates that options on such stock were granted) for
each calendar year in which such option is outstanding at any time. The purpose
of the limitation in the preceding sentence is to comply with Section 423(b)(8)
of the Code. If the participant's accumulated payroll deductions on the last day
of the Payment Period would otherwise enable the participant to purchase Common
Stock in excess of the Section 423(b)(8) limitation described in this paragraph,
the excess of the amount of the accumulated payroll deductions over the
aggregate purchase price of the shares actually purchased shall be promptly
refunded to the participant by the Company, without interest.

Article 6 - Exercise of Option.
- ------------------------------

     Each eligible employee who continues to be a participant in the Plan on the
last day of a Payment Period shall be deemed to have exercised his or her option
on such date and shall be deemed to have purchased from the Company such number
of full shares of Common Stock
<PAGE>

                                      -4-

reserved for the purpose of the Plan as the participant's accumulated payroll
deductions on such date will pay for at the Option Price, subject to the 2,250
share limit of the option, and the Section 423(b)(8) limitation described in
Article 5. If the individual is not a participant on the last day of a Payment
Period, then he or she shall not be entitled to exercise his or her option. Only
full shares of Common Stock may be purchased under the Plan. Unused payroll
deductions remaining in a participant's account at the end of a Payment Period
by reason of the inability to purchase a fractional share shall be carried
forward to the next Payment Period.

Article 7 - Authorization for Entering the Plan.
- -----------------------------------------------

     An employee may elect to enter the Plan by filling out, signing and
delivering to the Company an authorization:

          A.  Stating the percentage to be deducted regularly from the
employee's pay;

          B.  Authorizing the purchase of stock for the employee in each Payment
Period in accordance with the terms of the Plan; and

          C.  Specifying the exact name or names in which stock purchased for
the employee is to be issued as provided under Article 11 hereof.

Such authorization must be received by the Company at least ten days before the
first day of the next succeeding Payment Period and shall take effect only if
the employee is an eligible employee on the first business day of such Payment
Period.

     Unless a participant files a new authorization or withdraws from the Plan,
the deductions and purchases under the authorization the participant has on file
under the Plan will continue from one Payment Period to succeeding Payment
Periods as long as the Plan remains in effect.

     The Company will accumulate and hold for each participant's account the
amounts deducted from his or her pay. No interest will be paid on these amounts.

Article 8 - Maximum Amount of Payroll Deductions.
- ------------------------------------------------

     An employee may authorize payroll deductions in an amount (expressed as a
whole percentage) not less than one percent (1%) but not more than ten percent
(10%) of the employee's total compensation, including base pay or salary and any
overtime, bonuses or commissions.

Article 9 - Change in Payroll Deductions.
- ----------------------------------------

     Deductions may not be increased or decreased during a Payment Period.
However, a participant may withdraw in full from the Plan.
<PAGE>

                                      -5-

Article 10 - Withdrawal from the Plan.
- -------------------------------------

     A participant may withdraw from the Plan (in whole but not in part) at any
time prior to the last day of a Payment Period by delivering a withdrawal notice
to the Company.

     To re-enter the Plan, an employee who has previously withdrawn must file a
new authorization at least ten days before the first day of the next Payment
Period in which he or she wishes to participate. The employee's re-entry into
the Plan becomes effective at the beginning of such Payment Period, provided
that he or she is an eligible employee on the first business day of the Payment
Period.

Article 11 - Issuance of Stock.
- ------------------------------

     Certificates for stock issued to participants shall be delivered as soon as
practicable after each Payment Period by the Company's transfer agent.

     Stock purchased under the Plan shall be issued only in the name of the
participant, or if the participant's authorization so specifies, in the name of
the participant and another person of legal age as joint tenants with rights of
survivorship.

Article 12 - Adjustments.
- ------------------------

     Upon the happening of any of the following described events, a
participant's rights under options granted under the Plan shall be adjusted as
hereinafter provided:

          A.   In the event that the shares of Common Stock shall be subdivided
or combined into a greater or smaller number of shares or if, upon a
reorganization, split-up, liquidation, recapitalization or the like of the
Company, the shares of Common Stock shall be exchanged for other securities of
the Company, each participant shall be entitled, subject to the conditions
herein stated, to purchase such number of shares of Common Stock or amount of
other securities of the Company as were exchangeable for the number of shares of
Common Stock that such participant would have been entitled to purchase except
for such action, and appropriate adjustments shall be made in the purchase price
per share to reflect such subdivision, combination or exchange; and

          B.   In the event the Company shall issue any of its shares as a stock
dividend upon or with respect to the shares of stock of the class which shall at
the time be subject to option hereunder, each participant upon exercising such
an option shall be entitled to receive (for the purchase price paid upon such
exercise) the shares as to which the participant is exercising his or her option
and, in addition thereto (at no additional cost), such number of shares of the
class or classes in which such stock dividend or dividends were declared or
paid, and such amount of cash in lieu of fractional shares, as is equal to the
number of shares thereof and the amount of cash in lieu of fractional shares,
respectively, which the participant would have received if the participant had
been the holder of the shares as to which the participant is
<PAGE>

                                      -6-

exercising his or her option at all times between the date of the granting of
such option and the date of its exercise.

     Upon the happening of any of the foregoing events, the class and aggregate
number of shares set forth in Article 4 hereof which are subject to options
which have been or may be granted under the Plan and the limitation set forth in
the second paragraph of Article 5 shall also be appropriately adjusted to
reflect the events specified in paragraphs A and B above. Notwithstanding the
foregoing, any adjustments made pursuant to paragraphs A or B shall be made only
after the Committee, based on advice of counsel for the Company, determines
whether such adjustments would constitute a "modification" (as that term is
defined in Section 424 of the Code). If the Committee determines that such
adjustments would constitute a modification, it may refrain from making such
adjustments.

     If the Company is to be consolidated with or acquired by another entity in
a merger, a sale of all or substantially all of the Company's assets or
otherwise (an "Acquisition"), the Committee or the board of directors of any
entity assuming the obligations of the Company hereunder (the "Successor Board")
shall, with respect to options then outstanding under the Plan, either (i) make
appropriate provision for the continuation of such options by arranging for the
substitution on an equitable basis for the shares then subject to such options
either (a) the consideration payable with respect to the outstanding shares of
the Common Stock in connection with the Acquisition, (b) shares of stock of the
successor corporation, or a parent or subsidiary of such corporation, or (c)
such other securities as the Successor Board deems appropriate, the fair market
value of which shall not materially exceed the fair market value of the shares
of Common Stock subject to such options immediately preceding the Acquisition;
or (ii) terminate each participant's options in exchange for a cash payment
equal to the excess of (a) the fair market value on the date of the Acquisition,
of the number of shares of Common Stock that the participant's accumulated
payroll deductions as of the date of the Acquisition could purchase, at an
option price determined with reference only to the first business day of the
applicable Payment Period and subject to the 2,250-share, Code Section 423(b)(8)
and fractional-share limitations on the amount of stock a participant would be
entitled to purchase, over (b) the result of multiplying such number of shares
by such option price.

     The Committee or Successor Board shall determine the adjustments to be made
under this Article 12, and its determination shall be conclusive.

Article 13 - No Transfer or Assignment of Employee's Rights.
- -----------------------------------------------------------

     An option granted under the Plan may not be transferred or assigned and may
be exercised only by the participant.

Article 14 - Termination of Employee's Rights.
- ---------------------------------------------

     Whenever a participant ceases to be an eligible employee because of
retirement, voluntary or involuntary termination, resignation, layoff,
discharge, death or for any other reason, his or her rights under the Plan shall
immediately terminate, and the Company shall
<PAGE>

                                      -7-

promptly refund, without interest, the entire balance of his or her payroll
deduction account under the Plan. Notwithstanding the foregoing, eligible
employment shall be treated as continuing intact while a participant is on
military leave, sick leave or other bona fide leave of absence, for up to 90
days, or for so long as the participant's right to re-employment is guaranteed
either by statute or by contract, if longer than 90 days.

     If a participant's payroll deductions are interrupted by any legal process,
a withdrawal notice will be considered as having been received from the
participant on the day the interruption occurs.

Article 15 - Termination and Amendments to Plan.
- -----------------------------------------------

     Unless terminated sooner, as provided below, the Plan shall terminate on
December 9, 2009. The Plan may be terminated at any time by the Company's Board
of Directors but such termination shall not affect options then outstanding
under the Plan. It will terminate in any case when all or substantially all of
the unissued shares of stock reserved for the purposes of the Plan have been
purchased. If at any time shares of stock reserved for the purpose of the Plan
remain available for purchase but not in sufficient number to satisfy all then
unfilled purchase requirements, the available shares shall be apportioned among
participants in proportion to the amount of payroll deductions accumulated on
behalf of each participant that would otherwise be used to purchase stock, and
the Plan shall terminate. Upon such termination or any other termination of the
Plan, all payroll deductions not used to purchase stock will be refunded,
without interest.

     The Committee or the Board of Directors may from time to time adopt
amendments to the Plan provided that, without the approval of the stockholders
of the Company, no amendment may (i) increase the number of shares that may be
issued under the Plan; (ii) change the class of employees eligible to receive
options under the Plan, if such action would be treated as the adoption of a new
plan for purposes of Section 423(b) of the Code; or (iii) cause Rule 16b-3 under
the Securities Exchange Act of 1934 to become inapplicable to the Plan.

Article 16 - Limits on Sale of Stock Purchased under the Plan.
- -------------------------------------------------------------

     The Plan is intended to provide shares of Common Stock for investment and
not for resale. The Company does not, however, intend to restrict or influence
any employee in the conduct of his or her own affairs. An employee may,
therefore, sell stock purchased under the Plan at any time the employee chooses,
subject to compliance with any applicable federal or state securities laws and
subject to any restrictions imposed under Article 21 to ensure that tax
withholding obligations are satisfied. THE EMPLOYEE ASSUMES THE RISK OF ANY
MARKET FLUCTUATIONS IN THE PRICE OF THE STOCK.
<PAGE>

                                      -8-

Article 17 - Participating Subsidiaries.
- ---------------------------------------

     The term "participating subsidiary" shall mean any present or future
subsidiary of the Company, as that term is defined in Section 424(f) of the
Code, which is designated from time to time by the Board of Directors to
participate in the Plan. The Board of Directors shall have the power to make
such designation before or after the Plan is approved by the stockholders.

Article 18 - Optionees Not Stockholders.
- ---------------------------------------

     Neither the granting of an option to an employee nor the deductions from
his or her pay shall constitute such employee a stockholder of the shares
covered by an option until such shares have been actually purchased by the
employee.

Article 19 - Application of Funds.
- ---------------------------------

     The proceeds received by the Company from the sale of Common Stock pursuant
to options granted under the Plan will be used for general corporate purposes.

Article 20 - Notice to Company of Disqualifying Disposition.
- -----------------------------------------------------------

     By electing to participate in the Plan, each participant agrees to notify
the Company in writing immediately after the participant transfers Common Stock
acquired under the Plan, if such transfer occurs within two years after the
first business day of the Payment Period in which such Common Stock was
acquired. Each participant further agrees to provide any information about such
a transfer as may be requested by the Company or any subsidiary corporation in
order to assist it in complying with the tax laws. Such dispositions generally
are treated as "disqualifying dispositions" under Sections 421 and 424 of the
Code, which have certain tax consequences to participants and to the Company and
its participating subsidiaries.

Article 21 - Withholding of Additional Income Taxes.
- ---------------------------------------------------

     By electing to participate in the Plan, each participant acknowledges that
the Company and its participating subsidiaries are required to withhold taxes
with respect to the amounts deducted from the participant's compensation and
accumulated for the benefit of the participant under the Plan, and each
participant agrees that the Company and its participating subsidiaries may
deduct additional amounts from the participant's compensation, when amounts are
added to the participant's account, used to purchase Common Stock or refunded,
in order to satisfy such withholding obligations. Each participant further
acknowledges that when Common Stock is purchased under the Plan, the Company and
its participating subsidiaries may be required to withhold taxes with respect to
all or a portion of the difference between the fair market value of the Common
Stock purchased and its purchase price, and each participant agrees that such
taxes may be withheld from compensation otherwise payable to such participant.
It is intended that tax withholding will be accomplished in such a manner that
the full amount of payroll deductions elected by the participant under Article 7
will be used to purchase Common Stock. However, if amounts sufficient to satisfy
applicable tax withholding
<PAGE>

                                      -9-

obligations have not been withheld from compensation otherwise payable to any
participant, then, notwithstanding any other provision of the Plan, the Company
may withhold such taxes from the participant's accumulated payroll deductions
and apply the net amount to the purchase of Common Stock, unless the participant
pays to the Company, prior to the exercise date, an amount sufficient to satisfy
such withholding obligations. Each participant further acknowledges that the
Company and its participating subsidiaries may be required to withhold taxes in
connection with the disposition of stock acquired under the Plan and agrees that
the Company or any participating subsidiary may take whatever action it
considers appropriate to satisfy such withholding requirements, including
deducting from compensation otherwise payable to such participant an amount
sufficient to satisfy such withholding requirements or conditioning any
disposition of Common Stock by the participant upon the payment to the Company
or such subsidiary of an amount sufficient to satisfy such withholding
requirements.

Article 22 - Governmental Regulations.
- -------------------------------------

     The Company's obligation to sell and deliver shares of Common Stock under
the Plan is subject to the approval of any governmental authority required in
connection with the authorization, issuance or sale of such shares.

     Government regulations may impose reporting or other obligations on the
Company with respect to the Plan. For example, the Company may be required to
identify shares of Common Stock issued under the Plan on its stock ownership
records and send tax information statements to employees and former employees
who transfer title to such shares.

Article 23 - Governing Law.
- --------------------------

     The validity and construction of the Plan shall be governed by the laws of
the State of Delaware, without giving effect to the principles of conflicts of
law thereof.

Article 24 - Approval of Board of Directors and Stockholders of the Company.
- ---------------------------------------------------------------------------

     The Plan was adopted by the Board of Directors on December 9, 1999 and was
approved by the stockholders of the Company on January 20, 2000.

<PAGE>

                                                                     EXHIBIT 5.1
                        Testa, Hurwitz & Thibeault, LLP



                                          April 20, 2000



MatrixOne, Inc.
Two Executive Drive
Chelmsford, MA 01824

   Re: Registration Statement on Form S-8 Relating to each of the 2000 Employee
       Stock Purchase Plan, the 1999 Stock Plan, the Amended and Restated 1996
       Stock Plan and the Amended and Restated 1987 Stock Option Plan
       (collectively, the "Plans")

Dear Sir or Madam:

     Reference is made to the above-captioned Registration Statement on Form S-8
(the "Registration Statement") filed by MatrixOne, Inc. (the "Company") on the
date hereof with the Securities and Exchange Commission under the Securities Act
of 1933, as amended, relating to an aggregate of 19,209,321 shares of Common
Stock, par value $0.01 per share, of the Company issuable pursuant to the Plans
(the "Shares").

     We have examined, are familiar with, and have relied as to factual matters
solely upon, copies of the Plans, the Company's Amended and Restated Certificate
of Incorporation, the Company's Amended and Restated By-Laws, the minute books
and stock records of the Company, and originals or certified copies of such
other certificates, documents, records and materials as we have deemed necessary
for the purpose of rendering this opinion.

     We are members of the Bar of the Commonwealth of Massachusetts and are not
expert in, and express no opinion regarding, the laws of any jurisdiction other
than the Commonwealth of Massachusetts, the General Corporation Law of the State
of Delaware and the United States of America.

     Based upon the foregoing, we are of the opinion that the Shares have been
duly authorized and, when issued and paid for in accordance with the terms of
the Plans, will be validly issued, fully paid and nonassessable.

     We hereby consent to the filing of this opinion as Exhibit 5.1 to the
Registration Statement.

                              Very truly yours,

                              /s/ TESTA, HURWITZ & THIBEAULT, LLP

<PAGE>

                                                                    EXHIBIT 23.1

                   CONSENT OF INDEPENDENT PUBLIC ACCOUNTANTS



   As independent public accountants, we hereby consent to the incorporation by
reference in this Registration Statement of our report dated August 27, 1999
(except with respect to the matters discussed in Notes 7 and 8 for which the
date is February 23, 2000 and Note 12 for which the date is February 2, 2000)
included in MatrixOne, Inc.'s registration statement (No. 333-92731) on Form S-
1.



                            /s/ ARTHUR ANDERSEN LLP





Boston, Massachusetts
April 19, 2000


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