Document:

<PAGE>   1

                                                                    EXHIBIT 10.1

                              THE MEDICINES COMPANY

                            1998 STOCK INCENTIVE PLAN

1.   PURPOSE

The purpose of this 1998 Stock Incentive Plan (the "Plan") of The Medicines
Company, a Delaware corporation (the "Company"), is to advance the interests of
the Company's stockholders by enhancing the Company's ability to attract, retain
and motivate persons who make (or are expected to make) important contributions
to the Company by providing such persons with equity ownership opportunities and
performance-based incentives and thereby better aligning the interests of such
persons with those of the Company's stockholders. Except where the context
otherwise requires, the term "Company" shall include any present or future
subsidiary corporations of The Medicines Company as defined in Section 424(f) of
the Internal Revenue Code of 1986, as amended, and any regulations promulgated
thereunder (the "Code").

2.   ELIGIBILITY

All of the Company's employees, officers, directors, consultants and advisors
and any individuals who have accepted an offer for employment, are eligible to
be granted options, restricted stock awards, or other stock-based awards (each,
an "Award") under the Plan. Each person who has been granted an Award under the
Plan shall be deemed a "Participant".

3.   ADMINISTRATION, DELEGATION

     (a)  ADMINISTRATION BY BOARD OF DIRECTORS. The Plan will be administered by
the Board of Directors of the Company (the "Board"). The Board shall have
authority to grant Awards and to adopt, amend and repeal such administrative
rules, guidelines and practices relating to the Plan as it shall deem advisable.
The Board may correct any defect, supply any omission or reconcile any
inconsistency in the Plan or any Award in the manner and to the extent it shall
deem expedient to carry the Plan into effect and it shall be the sole and final
judge of such expediency. All decisions by the Board shall be made in the
Board's sole discretion and shall be final and binding on all persons having or
claiming any interest in the Plan or in any Award. No director or person acting
pursuant to the authority delegated by the Board shall be liable for any action
or determination relating to or under the Plan made in good faith.

     (b)  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 make Awards and exercise such other powers under the Plan
as the Board may determine, provided that the Board shall fix the maximum number
of shares subject to Awards and the maximum number of shares for any one
Participant to be made by such executive officers.

     (c)  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"). If and when the common
stock, $0.001 par value

<PAGE>   2

per share, of the Company (the "Common Stock") is registered under the
Securities Exchange Act of 1934, as amended (the "Exchange Act"), the Board
shall appoint one such Committee of not less than two members, each member of
which shall be an "outside director" within the meaning of Section 162(m) of the
Code and a "non-employee director" as defined in Rule 16b-3 promulgated under
the Exchange Act. All references in the Plan to the "Board" shall mean the Board
or a Committee of the Board or the executive officer referred to in Section 3(b)
of this Plan, to the extent that the Board's powers or authority under the Plan
have been delegated to such Committee or executive officer.

4.   STOCK AVAILABLE FOR AWARDS

     (a)  NUMBER OF SHARES. Subject to adjustment under Section 8, Awards may be
made under the Plan for up to 725,500 shares of Common Stock. If any Award
expires or is terminated, surrendered or canceled without having been fully
exercised or is forfeited in whole or in part or results in any Common Stock not
being issued, the unused Common Stock covered by such Award shall again be
available for the grant of Awards under the Plan, subject, however, in the case
of Incentive Stock Options (as hereinafter defined), to any limitation required
under the Code. 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 4(c), for
Awards granted after the Common Stock is registered under the Exchange Act, the
maximum number of shares of Common Stock with respect to which an Award may be
granted to any Participant under the Plan shall be 500,000 per calendar year.
The per-Participant limit described in this Section 4(b) shall be construed and
applied consistently with Section 162(m) of the Code.

     (c)  ADJUSTMENT TO COMMON STOCK. In the event of any stock split, stock
dividend, recapitalization, reorganization, merger, consolidation, combination,
exchange of shares, liquidation, spin-off or other similar change in
capitalization or event, or any distribution to holders of Common Stock other
than a normal cash dividend, (i) the number and class of securities available
under this Plan, (ii) the number and class of security and exercise price per
share subject to each outstanding Option, (iii) the repurchase price per
security subject to each outstanding Restricted Stock Award, and (iv) the terms
of each other outstanding stock-based Award shall be appropriately adjusted by
the Company (or substituted Awards may be made, if applicable) to the extent the
Board shall determine, in good faith, that such an adjustment (or substitution)
is necessary and appropriate. If this Section 4(c) applies and Section 8(c) also
applies to any event, Section 8(c) shall be applicable to such event, and this
Section 4(c) shall not be applicable.

5.   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, including conditions
relating to applicable federal or state securities laws, as it considers
necessary or advisable. An Option which is not intended to be an Incentive Stock
Option (as hereinafter defined) shall be designated a "Nonstatutory Stock
Option".

                                      -2-

<PAGE>   3

     (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 only be granted 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 Company shall have no liability to a Participant, or any
other party, if an Option (or any part thereof) which is intended to be an
Incentive Stock Option is not an Incentive Stock Option.

     (c)  EXERCISE PRICE. The Board shall establish the exercise price 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 subject to such terms and conditions as the Board may specify in the
applicable option agreement.

     (e)  EXERCISE OF OPTION. Options may be exercised by delivery to the
Company of a written notice of exercise signed by the proper person or by any
other form of notice (including electronic notice) approved by the Board
together with payment in full as specified in Section 5(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 granted under the Plan shall be paid for as follows:

          (1)  in cash or by check payable to the order of the Company;

          (2)  except as the Board may, in its sole discretion, otherwise
provide in an option agreement, 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;

          (3)  at such times as the Common Stock is registered under the
Exchange Act, delivery of shares of Common Stock owned by the Participant valued
at their fair market value as determined by (or in a manner approved by) the
Board in good faith ("Fair Market Value"), which Common Stock was owned by the
Participant at least six months prior to such delivery;

          (4)  to the extent permitted by the Board, in its sole discretion, (A)
by delivery of a promissory note of the Participant to the Company on terms
determined by the Board or (B) by payment of such other lawful consideration as
the Board may determine; or

          (5)  any combination of the above permitted forms of payment.

6.   RESTRICTED STOCK

     (a)  GRANTS. The Board may grant Awards entitling recipients to acquire
shares of Common Stock, subject to the right of the Company to repurchase all or
part of such shares at their issue price or other stated or formula price (or to
require forfeiture of such shares if issued at no cost) from the recipient in
the event that conditions specified by the Board in the applicable

                                      -3-

<PAGE>   4

Award are not satisfied prior to the end of the applicable restriction period or
periods established by the Board for such Award (each, "Restricted Stock
Award").

     (b)  TERMS AND CONDITIONS. The Board shall determine the terms and
conditions of any such Restricted Stock Award, including the conditions for
repurchase (or forfeiture) and the issue price, if any. 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). At 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, in a manner determined by the Board, by a Participant 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.

7.   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 the grant
of shares based upon certain conditions, the grant of securities convertible
into Common Stock and the grant of stock appreciation rights.

8.   ADJUSTMENTS FOR CHANGES IN COMMON STOCK AND CERTAIN OTHER EVENTS

     (a)  CHANGES IN CAPITALIZATION. In the event of any stock split, reverse
stock split, stock dividend, recapitalization, combination of shares,
reclassification of shares, spin-off or other similar change in capitalization
or event, or any distribution to holders of Common Stock other than a normal
cash dividend, (i) the number and class of securities available under this Plan,
(ii) the per-participant limit set forth in Section 4(b), (iii) the number and
class of securities and exercise price per share subject to each outstanding
Option, (iv) the repurchase price per share subject to each outstanding
Restricted Stock Award, and (v) the terms of each other outstanding Award shall
be appropriately adjusted by the Company (or substituted Awards may be made, if
applicable) to the extent the Board shall determine, in good faith, that such an
adjustment (or substitution) is necessary and appropriate. If this Section 8(a)
applies and Section 8(c) also applies to any event, Section 8(c) shall be
applicable to such event, and this Section 8(a) shall not be applicable.

     (b)  LIQUIDATION OR DISSOLUTION. In the event of a proposed liquidation or
dissolution of the Company, the Board shall upon written notice to the
Participants provide that all then unexercised Options will (i) become
exercisable in full as of a specified time at least 10 business days prior to
the effective date of such liquidation or dissolution and (ii) terminate
effective upon such liquidation or dissolution, except to the extent exercised
before such effective date. The Board may specify the effect of a liquidation or
dissolution on any Restricted Stock Award or other Award granted under the Plan
at the time of the grant of such Award.

     (c)  ACQUISITION AND CHANGE IN CONTROL EVENTS

          (1)  DEFINITIONS

                                      -4-

<PAGE>   5

               (a)  An "Acquisition Event" shall mean:

                    (i)  any merger or consolidation of the Company with or into
                         another entity as a result of which the Common Stock is
                         converted into or exchanged for the right to receive
                         cash, securities or other property; or

                    (ii) any exchange of shares of the Company for cash,
                         securities or other property pursuant to a statutory
                         share exchange transaction.

               (b)  A "Change in Control Event" shall mean:

                    (i)  any sale or transfer of all or substantially all of the
                         assets of the Company to another corporation or entity,
                         any merger, consolidation or reorganization of the
                         Company into or with another corporation or entity,
                         with the result that, upon conclusion of the
                         transaction, the voting securities of the Company
                         immediately prior thereto do not represent (either by
                         remaining outstanding or by being converted into voting
                         securities of the surviving entity) more than 50% of
                         the combined voting power of the voting securities of
                         the continuing or surviving entity of such
                         consolidation, merger or reorganization; or

                    (ii) following the date on which the Company becomes subject
                         to the periodic reporting requirements under Section 13
                         of the Exchange Act, a disclosure that any person (as
                         the term "person" is used in Section 13(d)(3) or
                         Section 14(d)(2) of the Exchange Act), other than (A)
                         any shareholder who, prior to the Company becoming
                         subject to such reporting requirements of Section 13 of
                         the Exchange Act, previously held at least 30% of the
                         combined voting power of outstanding voting securities
                         of the Company, (B) the Company or (C) any corporation
                         owned directly or indirectly by the stockholders of the
                         Company in substantially the same proportion as their
                         ownership of stock of the Company, becomes the
                         beneficial owner as the term "beneficial owner" is
                         defined under Rule 13d-3 or any successor rule or
                         regulation thereto under the Exchange Act) of
                         securities representing 30% or more of the combined
                         voting power of the then outstanding voting securities
                         of the Company; or

                   (iii) such time as individuals who as of the date of the
                         initial adoption of this Plan constitute the Board of
                         Directors of the Company, and any new director (other
                         than a director

                                      -5-

<PAGE>   6
                        designated by a person who has entered into an agreement
                        with the Company to effect any transaction described in
                        clause (i) or (ii) of this section) whose election by
                        the Board or nomination for election by the Company's
                        stockholders was approved by a vote of at least
                        two-thirds of the directors then still in office who
                        were either directors at the beginning of the period or
                        whose election or whose nomination for election was
                        previously so approved, cease for any reason to
                        constitute a majority of the Board of Directors.

               (c)  "Cause" shall mean (i) conviction of any felony or any crime
                    involving moral turpitude or dishonesty; (ii) participation
                    in a fraud or act of dishonesty against the Company (or, if
                    applicable, a successor corporation to the Company); (iii)
                    willful and material breach of the Company's policies (or,
                    if applicable, a successor corporation to the Company); (iv)
                    intentional and material damage to the Company's property
                    (or, if applicable, a successor corporation to the company);
                    or (v) material breach of the Participant's confidentiality
                    obligations or duties under the Participant's
                    non-disclosure, non-competition or other similar agreement
                    with the Company (or, if applicable, a successor corporation
                    to the Company).

               (d)  "Termination Event" shall mean the termination of the
                    Participant's employment (i) by the Company or the acquiring
                    or succeeding corporation without Cause; (ii) as a result of
                    his death or disability (within the meaning of Section
                    22(4)(3) of the Code); or (iii) by the Participant upon
                    written notice given promptly after the Company's or the
                    acquiring or succeeding corporation's taking any of the
                    following actions, which actions shall not have been cured
                    within a 30-day period following such notice: (A) the
                    principal place of the performance of the Participant's
                    responsibilities (the "Principal Location") is changed to a
                    location outside of a 30 mile radius from the Principal
                    Location immediately prior to the Change in Control Event;
                    (B) there is a material reduction in the Participant's
                    responsibilities without Cause; (C) there is a material
                    reduction in the Participant's salary; or (D) there is a
                    significant diminution in the scope of the Participant's
                    responsibilities without the Participant's agreement
                    (excluding increases in responsibility and sideways moves to
                    jobs with similar descriptions).

          (2)  EFFECT ON OPTIONS

               (a)  ACQUISITION EVENT. Upon the occurrence of an Acquisition
                    Event (regardless of whether such event also constitutes a
                    Change in Control Event), or the execution by the Company of
                    any agreement

                                      -6-

<PAGE>   7

                    with respect to an Acquisition Event (regardless of whether
                    such event will result in a Change in Control Event), the
                    Board shall provide that all outstanding Options shall be
                    assumed, or equivalent options shall be substituted, by the
                    acquiring or succeeding corporation (or an affiliate
                    thereof); PROVIDED THAT (i) any options substituted for
                    Incentive Stock Options shall satisfy, in the determination
                    of the Board, the requirements of Section 424(a) of the Code
                    and (ii) if such Acquisition Event also constitutes a Change
                    in Control Event, except to the extent specifically provided
                    to the contrary in the instrument evidencing any Option or
                    any other agreement between a Participant and the Company,
                    such assumed or substituted options shall become immediately
                    exercisable in full if, on or prior to the first anniversary
                    of the date of the consummation of the Change in Control
                    Event, a Termination Event occurs.

                         Notwithstanding the foregoing, if the acquiring or
                    succeeding corporation (or an affiliate thereof) does not
                    agree to assume, or substitute for, such Options, then the
                    Board shall (x) upon written notice to the Participants,
                    provide that all then unexercised Options will become
                    exercisable in full as of a specified time (the
                    "Acceleration Time") prior to the Acquisition Event and will
                    terminate immediately prior to the consummation of such
                    Acquisition Event, except to the extent exercised by the
                    Participants before the consummation of such Acquisition
                    Event, and/or (y) in the event of an Acquisition Event under
                    the terms of which holders of Common Stock will receive upon
                    consummation thereof a cash payment for each share of Common
                    Stock surrendered pursuant to such Acquisition Event (the
                    "Acquisition Price"), provide that all outstanding Options
                    shall terminate upon consummation of such Acquisition Event
                    and each Participant shall receive, in exchange therefor, a
                    cash payment equal to the amount (if any) by which (A) the
                    Acquisition Price multiplied by the number of shares of
                    Common Stock subject to such outstanding Options (whether or
                    not then exercisable), exceeds (B) the aggregate exercise
                    price of such Options.

               (b)  CHANGE IN CONTROL EVENT THAT IS NOT AN ACQUISITION EVENT.
                    Following the occurrence of a Change in Control Event that
                    does not also constitute an Acquisition Event, except to the
                    extent specifically provided to the contrary in the
                    instrument evidencing any Option or any other agreement
                    between a Participant and the Company, each such Option
                    shall become immediately exercisable in full if, on or prior
                    to the first anniversary of the date of the consummation of
                    the Change in Control Event, a Termination Event occurs.

                                      -7-

<PAGE>   8

          (3)  EFFECT ON RESTRICTED STOCK AWARDS

               (a)  ACQUISITION EVENT THAT IS NOT A CHANGE IN CONTROL EVENT.
                    Upon the occurrence of an Acquisition Event that is not a
                    Change in Control Event, the repurchase and other rights of
                    the Company under each outstanding Restricted Stock Award
                    shall inure to the benefit of the Company's successor and
                    shall apply to the cash, securities or other property which
                    the Common Stock was converted into or exchanged for
                    pursuant to such Acquisition Event in the same manner and to
                    the same extent as they applied to the Common Stock subject
                    to such Restricted Stock Award.

               (b)  CHANGE IN CONTROL EVENT. Upon the occurrence of a Change in
                    Control Event (regardless of whether such event also
                    constitutes an Acquisition Event), except to the extent
                    specifically provided to the contrary in the instrument
                    evidencing any Restricted Stock Award or any other agreement
                    between a Participant and the Company, each such Restricted
                    Stock Award shall immediately become free from all
                    conditions or restrictions if, on or prior to the first
                    anniversary of the date of the consummation of the Change in
                    Control Event, a Termination Event occurs.

          (4)  EFFECT ON OTHER AWARDS

               (a)  ACQUISITION EVENT THAT IS NOT A CHANGE IN CONTROL EVENT. The
                    Board shall specify the effect of an Acquisition Event that
                    is not a Change in Control Event on any other Award granted
                    under the Plan at the time of the grant of such Award.

               (b)  CHANGE IN CONTROL EVENT. Upon the occurrence of a Change in
                    Control Event (regardless of whether such event also
                    constitutes an Acquisition Event), except to the extent
                    specifically provided to the contrary in the instrument
                    evidencing any Award or any other agreement between a
                    Participant and the Company, each such Award shall
                    immediately become fully exercisable, realizable, vested or
                    free from conditions or restrictions if, on or prior to the
                    first anniversary of the date of the consummation of the
                    Change in Control Event, a Termination Event occurs

9.   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.

                                      -8-

<PAGE>   9

     (b)  DOCUMENTATION. Each Award under the Plan shall be evidenced by a
written instrument in such form as the Board shall determine. Each Award may
contain terms and conditions in addition to those set forth in the Plan.

     (c)  BOARD DISCRETION. Except as otherwise provided by the Plan, each Award
may be made alone or in addition or in relation to any other Award. The terms of
each Award need not be identical, and the Board need not treat Participants
uniformly.

     (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, the Participant's legal
representative, conservator, guardian or Designated Beneficiary may exercise
rights under the Award.

     (e)  WITHHOLDING. Each Participant shall pay to the Company, or make
provision satisfactory to the Board 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. Except as the Board may otherwise
provide in an Award, Participants may satisfy such tax obligations in whole or
in part by delivery of shares of Common Stock, including shares retained from
the Award creating the tax obligation, valued at their Fair Market Value. 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.

     (f)  AMENDMENT OF AWARD. 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 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.

     (g)  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.

     (h)  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 restrictions in full or in part or that any other 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.

10.  MISCELLANEOUS

                                      -9-

<PAGE>   10

     (a)  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, except as expressly provided in the
applicable Award.

     (b)  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 of such shares.

     (c)  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 earlier of (i) the date on
which the Plan was adopted by the Board or (ii) the date the Plan was approved
by the Company's stockholders, but Awards previously granted may extend beyond
that date.

     (d)  AMENDMENT OF PLAN. The Board may amend, suspend or terminate the Plan
or any portion thereof at any time.

     (e)  GOVERNING LAW. The provisions of the Plan and all Awards made
hereunder shall be governed by and interpreted in accordance with the laws of
the State of Delaware, without regard to any applicable conflicts of law.

                                      -10-

<PAGE>   11
                              THE MEDICINES COMPANY
                     AMENDMENT TO 1998 STOCK INCENTIVE PLAN

             Adopted by the Board of Directors on December 15, 1998

SECTION 4 AS AMENDED AND RESTATED. Section 4(a) of the 1998 Stock Incentive Plan
of The Medicines Company shall be deleted in its entirety and the following
shall be substituted in its place:

4.       STOCK AVAILABLE FOR AWARDS

         a. NUMBER OF SHARES. Subject to adjustment under Section 8, Awards may
be made under the Plan for up to 1,483,917 shares of Common Stock. If any Award
expires or is terminated, surrendered or canceled without having been fully
exercised or is forfeited in whole or in part or results in any Common Stock not
being issued, the unused Common Stock covered by such Award shall again be
available for the grant of Awards under the Plan, subject, however, in the case
of Incentive Stock Options (as hereinafter defined), to any limitation required
under the Code. Shares issued under the Plan may consist, in whole or in part,
of authorized but unissued shares or treasury shares.

<PAGE>   12

                              THE MEDICINES COMPANY
                       1998 STOCK INCENTIVE PLAN AMENDMENT

                             As of February 7, 2000

SECTION 4 AS AMENDED AND RESTATED. Section 4(a) of the 1998 Stock Incentive Plan
of The Medicines Company shall be deleted in its entirety and the following
shall be substituted in its place:

         "a. NUMBER OF SHARES. Subject to adjustment under Section 8, Awards may
             be made under the Plan for up to 1,983,917 shares of Common Stock.
             If any Award expires or is terminated, surrendered or canceled
             without having been fully exercised or is forfeited in whole or in
             part or results in any Common Stock not being issued, the unused
             Common Stock covered by such Award shall again be available for the
             grant of Awards under the Plan, subject, however, in the case of
             Incentive Stock Options (as hereinafter defined), to any limitation
             required under the Code. Shares issued under the Plan may consist,
             in whole or in part, of authorized but unissued shares or treasury
             shares."<PAGE>   1

                                                                    EXHIBIT 10.2

                              THE MEDICINES COMPANY

                        2000 EMPLOYEE STOCK PURCHASE PLAN

                                  May 15, 2000

The purpose of this Plan is to provide eligible employees of The Medicines
Company (the "Company") and certain of its subsidiaries with opportunities to
purchase shares of the Company's common stock, $0.001 par value (the "Common
Stock"), commencing on [_____],2000. Three Hundred Fifty Thousand (350,000)
shares of Common Stock in the aggregate have been approved for this purpose.
This Plan is intended to qualify as an "employee stock purchase plan" as defined
in Section 423 of the Internal Revenue Code of 1986, as amended (the "Code"),
and the regulations promulgated thereunder, and shall be interpreted consistent
therewith.

         1.       ADMINISTRATION. The Plan will be administered by the Company's
Board of Directors (the "Board") or by a Committee appointed by the Board (the
"Committee"). The Board or the Committee has authority to make rules and
regulations for the administration of the Plan and its interpretation and
decisions with regard thereto shall be final and conclusive.

         2.       ELIGIBILITY. All employees of the Company, including Directors
who are employees, and all employees of any subsidiary of the Company (as
defined in Section 424(f) of the Code) designated by the Board or the Committee
from time to time (a "Designated Subsidiary"), are eligible to participate in
any one or more of the offerings of Options (as defined in Section 9) to
purchase Common Stock under the Plan provided that:

                  (a)      they are customarily employed by the Company or a
         Designated Subsidiary for more than 20 hours a week and for more than
         five months in a calendar year; and

                  (b)      they have been employed by the Company or a
         Designated Subsidiary for at least [insert number of months not greater
         than 24] months prior to enrolling in the Plan; and

                                      -6-
<PAGE>   2
                  (c)      they are employees of the Company or a Designated
         Subsidiary on the first day of the applicable Plan Period (as defined
         below).

         No employee may be granted an option hereunder if such employee,
immediately after the option is granted, owns 5% or more of the total combined
voting power or value of the stock of the Company or any subsidiary. For
purposes of the preceding sentence, the attribution rules of Section 424(d) of
the Code shall apply in determining the stock ownership of an employee, and all
stock which the employee has a contractual right to purchase shall be treated as
stock owned by the employee.

         3.       OFFERINGS. The Company will make one or more offerings
("Offerings") to employees to purchase stock under this Plan. Offerings will
begin each [_____] and [_____], or the first business day thereafter (the
"Offering Commencement Dates"). Each Offering Commencement Date will begin a
[_____] month period (a "Plan Period") during which payroll deductions will be
made and held for the purchase of Common Stock at the end of the Plan Period.
The Board or the Committee may, at its discretion, choose a different Plan
Period of twelve (12) months or less for subsequent Offerings. Notwithstanding
anything to the contrary, the first Plan Period shall begin on the first date
that the Common Stock is publicly traded following the Company's initial public
offering ("IPO") and shall end on [_____].

         4.       PARTICIPATION. An employee eligible on the Offering
Commencement Date of any Offering may participate in such Offering by completing
and forwarding a payroll deduction authorization form to the employee's
appropriate payroll office at least ___ days prior to the applicable Offering
Commencement Date. The form will authorize a regular payroll deduction from the
Compensation received by the employee during the Plan Period. Unless an employee
files a new form or withdraws from the Plan, his deductions and purchases will
continue at the same rate for future Offerings under the Plan as long as the
Plan remains in effect. The term "Compensation" means the amount of money
reportable on the employee's Federal Income Tax Withholding Statement, excluding
overtime, shift premium, incentive or bonus awards, allowances and
reimbursements for expenses such as relocation allowances for travel expenses,
income or gains on the exercise of Company stock options or stock appreciation
rights, and similar items, whether or not shown on the employee's Federal Income
Tax Withholding Statement, but including, in the case of salespersons, sales
commissions to the extent determined by the Board or the Committee.

         5.       DEDUCTIONS. The Company will maintain payroll deduction
accounts for all participating employees. With respect to any Offering made
under this Plan, an employee may

                                      -7-

<PAGE>   3
authorize a payroll deduction in any dollar amount up to a maximum of ____% of
the Compensation he or she receives during the Plan Period or such shorter
period during which deductions from payroll are made. Payroll deductions may be
at the rate of [_____]%, [_____]%, [_____]% or [_____]% of Compensation with any
change in compensation during the Plan Period to result in an automatic
corresponding change in the dollar amount withheld.] [The minimum payroll
deduction is such percentage of compensation as may be established from time to
time by the Board or the Committee.

         No employee may be granted an Option (as defined in Section 9) which
permits his rights to purchase Common Stock under this Plan and any other
employee stock purchase plan (as defined in Section 423(b) of the Code) of the
Company and its subsidiaries, to accrue at a rate which exceeds $25,000 of the
fair market value of such Common Stock (determined at the Offering Commencement
Date of the Plan Period) for each calendar year in which the Option is
outstanding at any time.

         6.       DEDUCTION CHANGES. An employee may decrease or discontinue his
payroll deduction once during any Plan Period, by filing a new payroll deduction
authorization form. However, an employee may not increase his payroll deduction
during a Plan Period. If an employee elects to discontinue his payroll
deductions during a Plan Period, but does not elect to withdraw his funds
pursuant to Section 8 hereof, funds deducted prior to his election to
discontinue will be applied to the purchase of Common Stock on the Exercise Date
(as defined below).

         7.       INTEREST. Interest will not be paid on any employee accounts,
except to the extent that the Board or the Committee, in its sole discretion,
elects to credit employee accounts with interest at such per annum rate as it
may from time to time determine.

         8.       WITHDRAWAL OF FUNDS. An employee may at any time prior to the
close of business on the last business day in a Plan Period and for any reason
permanently draw out the balance accumulated in the employee's account and
thereby withdraw from participation in an Offering. Partial withdrawals are not
permitted. The employee may not begin participation again during the remainder
of the Plan Period. The employee may participate in any subsequent Offering in
accordance with terms and conditions established by the Board or the Committee.

         9.       PURCHASE OF SHARES. On the Offering Commencement Date of each
Plan Period, the Company will grant to each eligible employee who is then a
participant in the Plan an option ("Option") to purchase on the last business
day of such Plan Period (the "Exercise Date"), at the

                                      -8-
<PAGE>   4
Option Price hereinafter provided for, the largest number of whole shares of
Common Stock of the Company as does not exceed the number of shares determined
by multiplying $2,083 by the number of full months in the Offering Period and
dividing the result by the closing price (as defined below) on the Offering
Commencement Date of such Plan Period.

         The purchase price for each share purchased will be 85% of the closing
price of the Common Stock on (i) the first business day of such Plan Period or
(ii) the Exercise Date, whichever closing price shall be less. Such closing
price shall be (a) the closing price on any national securities exchange on
which the Common Stock is listed, (b) the closing price of the Common Stock on
the Nasdaq National Market or (c) the average of the closing bid and asked
prices in the over-the-counter-market, whichever is applicable, as published in
THE WALL STREET JOURNAL; provided that, with respect to the first Plan Period,
the closing price on the Offering Commencement Date shall be the initial public
offering price provided for in the underwriting agreement entered into by the
Company in connection with the IPO. If no sales of Common Stock were made on
such a day, the price of the Common Stock for purposes of clauses (a) and (b)
above shall be the reported price for the next preceding day on which sales were
made.

         Each employee who continues to be a participant in the Plan on the
Exercise Date shall be deemed to have exercised his Option at the Option Price
on such date and shall be deemed to have purchased from the Company the number
of full shares of Common Stock reserved for the purpose of the Plan that his
accumulated payroll deductions on such date will pay for, but not in excess of
the maximum number determined in the manner set forth above.

         Any balance remaining in an employee's payroll deduction account at the
end of a Plan Period will be automatically refunded to the employee, except that
any balance which is less than the purchase price of one share of Common Stock
will be carried forward into the employee's payroll deduction account for the
following Offering, unless the employee elects not to participate in the
following Offering under the Plan, in which case the balance in the employee's
account shall be refunded.

         10.      ISSUANCE OF CERTIFICATES. Certificates representing shares of
Common Stock purchased under the Plan may be issued only in the name of the
employee, in the name of the employee and another person of legal age as joint
tenants with rights of survivorship, or (in the Company's sole discretion) in
the name of a brokerage firm, bank or other nominee holder designated by the
employee. The Company may, in its sole discretion and in compliance with
applicable laws, authorize the use of book entry registration of shares in lieu
of issuing stock certificates.

                                      -9-
<PAGE>   5
         11.      RIGHTS ON RETIREMENT, DEATH OR TERMINATION OF EMPLOYMENT. In
the event of a participating employee's termination of employment prior to the
last business day of a Plan Period, no payroll deduction shall be taken from any
pay due and owing to an employee and the balance in the employee's account shall
be paid to the employee or, in the event of the employee's death, (a) to a
beneficiary previously designated in a revocable notice signed by the employee
(with any spousal consent required under state law) or (b) in the absence of
such a designated beneficiary, to the executor or administrator of the
employee's estate or (c) if no such executor or administrator has been appointed
to the knowledge of the Company, to such other person(s) as the Company may, in
its discretion, designate. If, prior to the last business day of the Plan
Period, the Designated Subsidiary by which an employee is employed shall cease
to be a subsidiary of the Company, or if the employee is transferred to a
subsidiary of the Company that is not a Designated Subsidiary, the employee
shall be deemed to have terminated employment for the purposes of this Plan.

         12.      OPTIONEES NOT STOCKHOLDERS. Neither the granting of an Option
to an employee nor the deductions from his pay shall constitute such employee a
stockholder of the shares of Common Stock covered by an Option under this Plan
until such shares have been purchased by and issued to him.

         13.      RIGHTS NOT TRANSFERABLE. Rights under this Plan are not
transferable by a participating employee other than by will or the laws of
descent and distribution, and are exercisable during the employee's lifetime
only by the employee.

         14.      APPLICATION OF FUNDS. All funds received or held by the
Company under this Plan may be combined with other corporate funds and may be
used for any corporate purpose.

         15.      ADJUSTMENT IN CASE OF CHANGES AFFECTING COMMON STOCK. In the
event of a subdivision of outstanding shares of Common Stock, or the payment of
a dividend in Common Stock, the number of shares approved for this Plan, and the
share limitation set forth in Section 9, shall be increased proportionately, and
such other adjustment shall be made as may be deemed equitable by the Board or
the Committee. In the event of any other change affecting the Common Stock, such
adjustment shall be made as may be deemed equitable by the Board or the
Committee to give proper effect to such event.

         16.      MERGER. If the Company shall at any time merge or consolidate
with another corporation and the holders of the capital stock of the Company
immediately prior to such merger or consolidation continue to hold at least 80%
by voting power of the capital stock of the

                                      -10-
<PAGE>   6
surviving corporation ("Continuity of Control"), the holder of each Option then
outstanding will thereafter be entitled to receive at the next Exercise Date
upon the exercise of such Option for each share as to which such Option shall be
exercised the securities or property which a holder of one share of the Common
Stock was entitled to upon and at the time of such merger or consolidation, and
the Board or the Committee shall take such steps in connection with such merger
or consolidation as the Board or the Committee shall deem necessary to assure
that the provisions of Section 15 shall thereafter be applicable, as nearly as
reasonably may be, in relation to the said securities or property as to which
such holder of such Option might thereafter be entitled to receive thereunder.

         In the event of a merger or consolidation of the Company with or into
another corporation which does not involve Continuity of Control, or of a sale
of all or substantially all of the assets of the Company while unexercised
Options remain outstanding under the Plan, (a) subject to the provisions of
clauses (b) and (c), after the effective date of such transaction, each holder
of an outstanding Option shall be entitled, upon exercise of such Option, to
receive in lieu of shares of Common Stock, shares of such stock or other
securities as the holders of shares of Common Stock received pursuant to the
terms of such transaction; or (b) all outstanding Options may be cancelled by
the Board or the Committee as of a date prior to the effective date of any such
transaction and all payroll deductions shall be paid out to the participating
employees; or (c) all outstanding Options may be cancelled by the Board or the
Committee as of the effective date of any such transaction, provided that notice
of such cancellation shall be given to each holder of an Option, and each holder
of an Option shall have the right to exercise such Option in full based on
payroll deductions then credited to his account as of a date determined by the
Board or the Committee, which date shall not be less than ten (10) days
preceding the effective date of such transaction.

         17.      AMENDMENT OF THE PLAN. The Board may at any time, and from
time to time, amend this Plan in any respect, except that (a) if the approval of
any such amendment by the shareholders of the Company is required by Section 423
of the Code, such amendment shall not be effected without such approval, and (b)
in no event may any amendment be made which would cause the Plan to fail to
comply with Section 423 of the Code.

         18.      INSUFFICIENT SHARES. In the event that the total number of
shares of Common Stock specified in elections to be purchased under any Offering
plus the number of shares purchased under previous Offerings under this Plan
exceeds the maximum number of shares issuable under this Plan, the Board or the
Committee will allot the shares then available on a pro rata basis.

                                      -11-
<PAGE>   7
         19.      TERMINATION OF THE PLAN. This Plan may be terminated at any
time by the Board. Upon termination of this Plan all amounts in the accounts of
participating employees shall be promptly refunded.

         20.      GOVERNMENTAL REGULATIONS. The Company's obligation to sell and
deliver Common Stock under this Plan is subject to listing on a national stock
exchange or quotation on the Nasdaq National Market (to the extent the Common
Stock is then so listed or quoted) and the approval of all governmental
authorities required in connection with the authorization, issuance or sale of
such stock.

         21.      GOVERNING LAW. The Plan shall be governed by
[Delaware/Massachusetts] law except to the extent that such law is preempted by
federal law.

         22.      ISSUANCE OF SHARES. Shares may be issued upon exercise of an
Option from authorized but unissued Common Stock, from shares held in the
treasury of the Company, or from any other proper source.

         23.      NOTIFICATION UPON SALE OF SHARES. Each employee agrees, by
entering the Plan, to promptly give the Company notice of any disposition of
shares purchased under the Plan where such disposition occurs within two years
after the date of grant of the Option pursuant to which such shares were
purchased.

         24.      EFFECTIVE DATE AND APPROVAL OF SHAREHOLDERS. The Plan shall
take effect on [_____], 2000 subject to approval by the shareholders of the
Company as required by Section 423 of the Code, which approval must occur within
twelve months of the adoption of the Plan by the Board.

                                             Adopted by the Board of Directors

                                             on May 15, 2000

                                             Approved by the stockholders on
                                             [_____], 2000

                                      -12-

Source: [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00010-of-00352.parquet"}, [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00010-of-00352.parquet"}]]