<PAGE>

                                                                   EXHIBIT 10.28


                                                                 [Third Tranche]



          NEITHER THESE WARRANTS NOR THE SHARES UNDERLYING THESE WARRANTS HAVE
          BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933 OR THE LAWS OF ANY
          STATE. THEY MAY NOT BE SOLD OR OTHERWISE TRANSFERRED UNLESS THEY ARE
          REGISTERED UNDER SUCH ACT AND APPLICABLE STATE SECURITIES LAWS IF
          NECESSARY, OR AN EXEMPTION FROM REGISTRATION IS AVAILABLE. THESE
          WARRANTS AND THE SHARES UNDERLYING THESE WARRANTS ARE ALSO SUBJECT TO
          ADDITIONAL RESTRICTIONS ON TRANSFER SET FORTH IN THAT CERTAIN AMENDED
          AND RESTATED SHAREHOLDERS' AGREEMENT, A COPY OF WHICH MAY BE OBTAINED
          FROM INTRALINKS, INC.


115,385 Warrants                                                 June 30, 1999

                             WARRANT CERTIFICATE

                               INTRALINKS, INC.

          This warrant certificate ("Warrant Certificate") certifies that for
value received R. W. Johnson Pharmaceutical Research Institute ("PRI") or
registered assigns (the "Holder") is the owner of the number of warrants (the
"Warrants") specified above, each of which entitles the Holder thereof to
purchase, at any time after such warrants vest in accordance with the terms
hereof and on or before the Expiration Date (as hereinafter defined), one fully
paid and non-assessable share of Common Stock, $.01 par value (the "Common
Stock"), of IntraLinks, Inc. (the "Company"), for the Purchase Price (defined in
Section 1 below) in lawful money of the United States of America (subject to
adjustment as hereinafter provided).

     1.   Warrant; Purchase Price
          -----------------------

     Each Warrant initially shall entitle the Holder to purchase one share of
Common Stock of the Company, and the purchase price payable upon exercise of the
Warrant (the "Purchase Price") shall initially be $13.00 per share of Common
Stock, subject to adjustment as hereinafter provided. The Purchase Price and
number of shares of Common Stock issuable upon exercise of this Warrant are
subject to adjustment as provided in Section 5 hereof. The shares of Common
Stock issuable upon exercise of the Warrant (and/or other shares of stock so
issuable by reason of any adjustments pursuant to Section 5) are sometimes
referred to herein as the "Warrant Shares."
<PAGE>

     2.    Exercise; Expiration Date; No Fractional Shares; Reservation of
           ---------------------------------------------------------------
Shares
------

     2.1.  The Warrants are exercisable, at the option of the Holder, in whole
or in part in accordance with the terms hereof and on or before the Expiration
Date as hereinafter described, upon surrender of this Warrant Certificate to the
Company together with a duly completed Notice of Exercise, in the form attached
hereto as Exhibit A, and payment of the Purchase Price. In the case of exercise
          ---------
of less than the entire Warrant represented by this Warrant Certificate, the
Company shall cancel the Warrant Certificate upon the surrender thereof and
shall execute and deliver a new Warrant Certificate for the balance of such
Warrant. The Warrants shall be exercisable according to net revenues realized by
the Company's IntraPharma subsidiary (including net revenues derived from PRI)
for the three-year period commencing on the date hereof. In the event that such
net revenues reach $3,000,000 within the three-year period, the Warrants will be
100% exercisable and pro rata for net revenues less than such amount. The
cumulative net revenue of IntraPharma will be determined and the percent
exercisability of these Warrants will be calculated every six months, starting
with the date hereof. At any time, PRI may exercise all or a portion of the
then-exercisable Warrants. Notwithstanding anything contained herein to the
contrary, all of the Warrants shall immediately vest and become exercisable upon
the sale of any shares of the Company owned by Johnson & Johnson Development
Corporation or its permitted assigns as a result of and pursuant to Section
4.1(c) of the Amended and Restated Shareholders' Agreement of even date herewith
by and among the Company and its shareholders.

     2.2.  The term "Expiration Date" shall mean 5:00 p.m. New York time five
years from the date hereof, or if such day shall in the State of New York be a
holiday or a day on which banks are authorized to close, then 5:00 p.m. New York
time the next following day which in the State of New York is not a holiday or a
day on which banks are authorized to close.

     2.3.  No fractional shares shall be issued upon exercise (in whole or in
part) of the Warrants and the number of shares of Common Stock to be issued
shall be rounded down to the nearest whole share, and there shall be no payment
to the Holder for any such rounded fractional shares.

     2.4.  The Company covenants that it will at all times reserve and keep
available out of its authorized capital stock, solely for the purpose of issue
upon exercise of the Warrants, such number of shares of Common Stock as shall
then be issuable upon the exercise of all outstanding Warrants. The Company
covenants that all shares of capital stock which shall be issuable upon exercise
of the Warrants shall, upon issuance in accordance with the terms hereof, be
duly and validly issued and fully paid and non-assessable and free from all
taxes, liens, encumbrances and charges with respect to the issue thereof, and
that upon issuance the Company shall use its commercially reasonable efforts to
cause such shares to be listed on each national securities exchange, if any, on
which the other shares of such outstanding capital stock of the Company are then
listed.

     3.    Registration and Transfer on Company Books
           ------------------------------------------

                                       2
<PAGE>

     3.1.  The Company shall maintain books for the registration and transfer of
the Warrants and the registration and transfer of the Warrant Shares.

     3.2.  Prior to due presentment for registration of transfer of this Warrant
Certificate, or the Warrant Shares, the Company may deem and treat the
registered Holder as the absolute owner thereof.

     3.3.  The Warrants shall be freely assignable by PRI to any affiliate of
PRI, provided that such affiliate, prior to the assignment by PRI, represents to
the Company that it is purchasing the Warrants for investment purposes only and
not with a view of or towards subsequent transfer (except to an affiliate) or
resale and that such sale or transfer is permitted under the securities laws.


     4.    Loss or Mutilation
           ------------------

     Upon receipt by the Company of reasonable evidence of the ownership of and
the loss, theft, destruction or mutilation of any Warrant Certificate and, in
the case of loss, theft or destruction, of indemnity reasonably satisfactory to
the Company, or, in the case of mutilation, upon surrender and cancellation of
the mutilated Warrant Certificate, the Company shall execute and deliver in lieu
thereof a new Warrant Certificate representing an equal number of Warrant
Shares.

     5.   Adjustment of Purchase Price and Number of Shares
          Deliverable; Reorganizations and Recapitalizations
          --------------------------------------------------

     5.1. The number of Warrant Shares purchasable upon the exercise of the
Warrants and the Purchase Price with respect to the Warrant Shares shall be
subject to adjustment as follows:

          (a) In case the Company shall (i) declare a dividend or make a
distribution on its Common Stock payable in shares of its capital stock, (ii)
subdivide its outstanding shares of Common Stock through stock split or
otherwise, (iii) combine its outstanding shares of Common Stock into a smaller
number of shares of Common Stock, or (iv) issue by reclassification of its
Common Stock (including any reclassification in connection with a consolidation
or merger in which the Company is the continuing corporation) other securities
of the Company, the number and/or nature of Warrant Shares purchasable upon
exercise of the Warrants immediately prior thereto shall be adjusted so that the
Holder shall be entitled to receive the kind and number of Warrant Shares or
other securities of the Company which he or it would have owned or have been
entitled to receive after the happening of any of the events described above,
had such Warrants been exercised immediately prior to the happening of such
event or any record date with respect thereto. Any adjustment made pursuant to
this paragraph (a) shall become effective retroactively as of the record date of
such event.

          (b) In the event of any capital reorganization or any reclassification
of the capital stock of the Company or in case of the consolidation or merger of
the Company with another corporation (other than a consolidation or merger in
which the outstanding shares of the

                                       3
<PAGE>

Company's Common Stock are not converted into or exchanged for other rights or
interests), or in the case of any sale, transfer or other disposition to another
corporation of all or substantially all the properties and assets of the
Company, the Holder of the Warrants shall thereafter be entitled to purchase
(and it shall be a condition to the consummation of any such reorganization,
reclassification, consolidation, merger, sale, transfer or other disposition
that appropriate provisions shall be made so that such Holder shall thereafter
be entitled to purchase) the kind and amount of shares of stock and other
securities and property (including cash) which the Holder would have been
entitled to receive had such Warrant been exercised immediately prior to the
effective date of such reorganization, reclassification, consolidation, merger,
sale, transfer or other disposition; and in any such case appropriate
adjustments shall be made in the application of the provisions of this Section 5
with respect to rights and interest thereafter of the Holder of the Warrants to
the end that the provisions of this Section 5 shall thereafter be applicable, as
near as reasonably may be, in relation to any shares or other property
thereafter purchasable upon the exercise of the Warrants. The provisions of this
Section 5.1(b) shall similarly apply to successive reorganizations,
reclassifications, consolidations, mergers, sales, transfers or other
dispositions.

          (c) Whenever the number of Warrant Shares purchasable upon the
exercise of the Warrants is adjusted, as provided in this Section 5.1, the
Purchase Price with respect to the Warrant Shares shall be adjusted by
multiplying such Purchase Price immediately prior to such adjustment by a
fraction, of which the numerator shall be the number of Warrant Shares
purchasable upon the exercise of the Warrants immediately prior to such
adjustment, and of which the denominator shall be the number of Warrant Shares
so purchasable immediately thereafter.

     5.2. Whenever the number of Warrant Shares purchasable upon the exercise of
the Warrant or the Purchase Price of such Warrant Shares is adjusted, as herein
provided, the Company shall mail to the Holder, at the address of the Holder
shown on the books of the Company, a notice of such adjustment or adjustments,
prepared and signed by the Chief Financial Officer or Secretary of the Company,
which sets forth the number of Warrant Shares purchasable upon the exercise of
each Warrant and the Purchase Price of such Warrant Shares after such
adjustment, a brief statement of the facts requiring such adjustment and the
computation by which such adjustment was made.

     5.3. In the event that at any time prior to the expiration of the Warrants
and prior to their exercise:

          (a) the Company shall offer for subscription to the holders of the
Common Stock any additional shares of stock of any class or any other securities
convertible into Common Stock or any rights to subscribe thereto; or

          (b) the Company shall declare any stock split, stock dividend,
subdivision, combination, or similar distribution with respect to the Common
Stock, regardless of the effect of any such event on the outstanding number of
shares of Common Stock; or

                                       4
<PAGE>

          (c) the Company shall declare a dividend with respect to the Common
Stock, other than a dividend payable in shares of the Company's own Common
Stock;

          (d) there shall be a voluntary or involuntary dissolution,
liquidation, or winding up of the Company (other than in connection with a
consolidation, merger, or sale of all or substantially all of its property,
assets and business as an entity); or

          (e) there shall be any capital change in the Company as set forth in
Section  5.1(b);

(each such event hereinafter being referred to as a "Notification Event"), the
Company shall cause to be mailed to the Holder, not less than 10 days prior to
the record date, if any, in connection with such Notification Event (provided,
however, that if there is no record date, or if 10 days prior notice is
impracticable, as soon as practicable) written notice specifying the nature of
such event and the effective date of, or the date on which the books of the
Company shall close or a record shall be taken with respect to, such event. Such
notice shall also set forth facts indicating the effect of such action, if any
(to the extent such effect may be known at the date of such notice), on the
Purchase Price and the kind and amount of the shares of stock or other
securities or property deliverable upon exercise of the Warrant.

     6.   Voluntary Adjustment by the Company
          -----------------------------------

     The Company may, at its option, at any time during the term of the
Warrants, reduce the then current Purchase Price to any amount deemed
appropriate by the Board of Directors of the Company and/or extend the date of
the expiration of the Warrants.

     7.   Registration Rights
          -------------------

     The Warrant Shares shall have the registration rights set forth in the
Amended and Restated Registration Rights Agreement of even date herewith by and
among the Company, the Holder and the other securityholders of the Company named
therein.

     8.   Governing Law
          -------------

     This Warrant Certificate shall be governed by and construed in accordance
with the laws of the State of New York, without regard to the conflict of law
principles thereof.

                                       5
<PAGE>

          IN WITNESS WHEREOF, the Company has caused this Warrant Certificate to
be duly executed by its officers thereunto duly authorized and its corporate
seal to be affixed hereon, as of this 30th day of June, 1999.

                              INTRALINKS, INC.


                              By: /s/
                                  -------------------------
                                  Name:
                                  Title:

Attest:


__________________________________
Name:
Title:

                                       6
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                                                                       EXHIBIT A



                               NOTICE OF EXERCISE


          The undersigned hereby irrevocably elects to exercise, pursuant to
Section 2 of the Warrant Certificate accompanying this Notice of Exercise,
_______ Warrants of the total number of Warrants owned by the undersigned
pursuant to the accompanying Warrant Certificate, and herewith makes payment of
the Purchase Price of such shares in full.


                              Name of Holder

                              __________________________________
                              Signature


                              Address:

                              __________________________________

                              __________________________________

                              __________________________________