<PAGE>   1
   

                                                                    EXHIBIT 10.9
    


                              TRANSITION AGREEMENT

This TRANSITION AGREEMENT ("Agreement"), dated as of April 27, 1999 ("Effective
Date"), is entered into by and between Connetics Corporation, a Delaware
corporation ("Connetics") and InterMune Pharmaceuticals, Inc., a California
corporation ("InterMune"). Connetics and InterMune are also referred to as a
"Party" or "Parties" to this Agreement.

                                        BACKGROUND

A.    Connetics is party to a License Agreement with Genentech, Inc. dated May
      5, 1998, as amended, ("Genentech License") pursuant to which Genentech
      licensed to Connetics certain rights to Actimmune (as defined below).

B.    Connetics has sublicensed to InterMune its rights under the Genentech
      License and under the Supply Agreement between Connetics and Genentech
      dated May 5, 1998 ("Genentech Supply Agreement"), all done pursuant to the
      Exclusive Sublicense Agreement between Connetics and InterMune dated as of
      August 21, 1998, as amended and restated effective April 27, 1999.
   

C.    The Genentech Supply Agreement includes provisions for Connetics to
      transfer manufacturing of Actimmune to a third party manufacturer [*], 
      and Connetics desires to create an incentive for InterMune (as
      Connetics' sublicensee) to accelerate the transfer of manufacturing.
    

D.    InterMune and Connetics have entered into a Term Sheet as of February 26,
      1999 (the "Term Sheet") pursuant to which, among other things, InterMune
      agreed that Connetics will have the right to book certain net revenues,
      expenses and net profits related to sales of Actimmune Units for the
      treatment of CGD (defined below) until December 31, 2001 (the "CGD
      Revenues").

E.    InterMune and Connetics have entered into that certain Collaboration
      Agreement (the "Collaboration Agreement") and certain other related
      documents as of even date herewith, which collectively set forth the
      transaction contemplated by the Term Sheet (the "Transaction").

F.    In connection with the Transaction, InterMune and Connetics desire to
      enter into this Transition Agreement to outline the mechanism by which
      Connetics shall book the CGD Revenues. 

NOW, THEREFORE, in consideration of the premises and the mutual covenants
contained in this Agreement, and intending to be legally bound, the Parties
agree as follows:



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<PAGE>   2
                                    AGREEMENT

                                    SECTION 1
                                   DEFINITIONS

      1.1 ACTIMMUNE. "Actimmune" means the filled and finished form of the
protein encoded by the interferon gamma-1b gene, and sold and distributed under
the trademark ACTIMMUNE(R), which is owned by Genentech and licensed to
Connetics and its sublicensees under the Genentech License.
   

      1.2 ACTIMMUNE GROSS MARGIN. "Actimmune Gross Margin" means Actimmune Net
Sales less all applicable [*].

      1.3 ACTIMMUNE GROSS SALES. "Actimmune Gross Sales" means [*].

      1.4 ACTIMMUNE NET SALES. "Actimmune Net Sales" means Actimmune Gross Sales
less adjustments for the following: [*].

      1.5 ACTIMMUNE UNITS. "Actimmune Units" means vials of ACTIMMUNE(R) that
are sold [*].

      1.6 BASELINE. "Baseline" means [*] Actimmune Units in 1999; [*]
Actimmune Units in 2000; and [*] Actimmune Units in 2001, adjusted as
applicable pursuant to Section 2.3(c). For clarity, the Parties intend that the
applicable Baseline shall represent the sales of Actimmune Units for the
treatment of CGD in each of the foregoing years.
    

      1.7 CGD. "CGD" means chronic granulomatous disease, which is the only FDA
approved indication for the sale of Actimmune as of the Effective Date.

      1.8 COLLECTION PERIOD. "Collection Period" means one full calendar month
during the Period.

      1.9 CORD DISTRIBUTION COSTS. "CORD Distribution Costs" means the actual
monthly payment by InterMune to CORD Logistics, Inc., for distribution services
for sales of Actimmune up to the Baseline.

      1.10 GNE ROYALTIES. "GNE Royalties" means the amount of royalties payable
to Genentech, Inc. pursuant to Section 8.3 of the Genentech License for
Actimmune Net Sales.

      1.11 PERIOD. "Period" means the time from April 1, 1999 through December
31, 2001.



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      1.12 PRODUCT COST. "Product Cost" means actual cost paid by InterMune to
the manufacturer for each Actimmune Unit, regardless of whether the manufacturer
is Genentech or a third party manufacturer qualified pursuant to the
manufacturing transition contemplated by Section 3.

      1.13 PRODUCT MANAGEMENT COSTS. "Product Management Costs" means
InterMune's actual costs to manage sales of Actimmune Units for the treatment of
CGD up to the Baseline, including all expenses and services related to sales of
such Actimmune Units, such as maintenance of safety databases, etc., tracked on
a regular basis and properly accounted for, at hourly rates to be agreed on by
the Parties.

                                    SECTION 2
                          SERVICES PERFORMED; PAYMENTS

      2.1 SERVICES. During the Period, InterMune shall perform, or have
performed, order entry, packaging, shipping, invoicing, and credit and
collection services (subject to Section 2.3(b)) related to sales of Actimmune
Units. All such services shall be performed on a timely basis consistent with
standard industry practices.

      2.2 PRODUCT MANAGEMENT COSTS. Except for Product Management Costs,
InterMune shall receive no separate consideration for providing services under
this Agreement. No later than thirty (30) days after the end of each Collection
Period, InterMune shall invoice Connetics for Product Management Costs for such
Collection Period, and Connetics shall remit payment on such invoices within
thirty (30) days after receipt of the invoice. InterMune's invoice shall be
accompanied by a statement itemizing such Product Management Costs, including a
list of all relevant projects, services provided, travel and other expenses.
InterMune agrees that it will not include in Product Management Costs any
non-headcount related expenses or extraordinary expenses without first obtaining
Connetics' authorization to incur such expenses. Any expenses incurred with the
consent of the Commercialization Committee formed pursuant to Section 2.7 shall
be deemed to have been authorized by Connetics for purposes of this Section 2.2.

      2.3 ACCOUNTING FOR ACTIMMUNE UNIT SALES; PAYMENTS TO CONNETICS.

            (a) Recording Revenue. During the Period, InterMune agrees that
      Connetics shall be entitled to book the Actimmune Net Sales until the
      total Actimmune Units sold reaches the Baseline applicable for each
      calendar year during the Period, all in accordance with generally accepted
      accounting principles, and InterMune will not book such Net Sales or
      otherwise record the revenue related to the Net Sales that Connetics is
      entitled to book pursuant to this Agreement. For clarification, the
      payment which Connetics receives from InterMune pursuant to subsection (c)
      below, and the sales of Actimmune Units represented thereby, shall accrue
      to the total Actimmune Net Sales booked by Connetics for 1999. InterMune
      shall be entitled to book the Actimmune Net Sales for sales of all
      Actimmune Units above the Baseline, after the Baseline is met in a given
      calendar year.

            (b) Payments to Connetics. InterMune shall pay to Connetics the
      amount of Actimmune Gross Margin each Collection Period, until the total
      Actimmune Units sold


                                  Page 3 of 13
<PAGE>   4
   
      reaches the applicable Baseline in each calendar year during the Period,
      according to the following schedule: no later than [*] business days after
      the end of each Collection Period, InterMune shall (i) submit to Connetics
      the reports required pursuant to Section 2.4 for the Collection Period
      just ended, and (ii) remit payment for the Collection Period immediately
      preceding such Collection Period, together with a statement as described
      in Section 2.4. For purposes of this Agreement, payments for a given
      Collection Period shall be due on the [*] business day after the end of
      the first full calendar month following that Collection Period ("Due
      Date"). To the extent that InterMune has not received payment for sales of
      Actimmune Units for a given Collection Period, InterMune's remittance on
      the Due Date may exclude any such unpaid amounts, but InterMune shall
      remit such amount withheld from Actimmune Gross Margin on the next Due
      Date, regardless of whether InterMune has received payment.
      Notwithstanding the foregoing, if such unpaid amount from a purchaser of
      Actimmune Units remains unpaid six (6) months after the date of invoice
      ("Bad Debt"), then Connetics shall reimburse InterMune for such Bad Debt
      within thirty (30) days following the end of such six month period. In
      such case, InterMune shall provide to Connetics the necessary
      documentation in its possession for the accounting for and collection of
      such Bad Debt, and shall permit Connetics to pursue collection for such
      Bad Debt.

            (c) Gross Margin for the First Quarter of 1999. InterMune will make
      a one-time payment to Connetics on the Effective Date equal to Actimmune
      Gross Margin for the period from January 15, 1999 to March 31, 1999, in
      the amount of [*], together with supporting documentation as described
      in this Article 2. The amount paid will count toward the total Actimmune
      Net Sales booked by Connetics for 1999, as set forth in paragraph (a)
      above.

            (d) Overdue Payments. For each Collection Period, if InterMune fails
      to remit payment by the Due Date, the amount due shall accrue interest at
      the rate of [*] per year until the amount due together with all accrued
      interest are paid in full. If InterMune fails for [*] consecutive
      Collection Periods to remit payment by the Due Date, InterMune hereby
      agrees that Connetics shall have the right (at its sole option) to modify
      the payment structure described in subsection (b) above so that Connetics
      collects all revenue with respect to sales of Actimmune Units, withholds
      the Actimmune Gross Margin, and remits the balance to InterMune. In such
      event:
    

                        (i) InterMune shall take all action necessary to provide
                  Connetics with the necessary permissions and authorization to
                  make such modifications to the payment structure, in
                  accordance with a payment and reporting schedule equivalent to
                  that set forth in Subsection (b) above;

                        (ii) The provisions of Sections 2.4 and 2.6 shall apply
                  mutatis mutandis; and

                        (iii) At the termination or expiration of this
                  Agreement, Connetics' right to collect revenues for the sales
                  of Actimmune Units shall terminate and InterMune shall
                  thereafter have the right to collect all revenues for such
                  sales. Connetics shall



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                                  Page 4 of 13
<PAGE>   5

                  take all action necessary to provide InterMune with the
                  necessary permissions and authorization to allow InterMune to
                  collect such revenues.

   
            (e) Sales Below Baseline. The Parties agree that, if Actimmune Unit
      sales are [*] or more below the Baseline (on a quarterly-adjusted basis)
      for a period of [*] days following [*] they will meet to evaluate the
      effect of [*] on sales volume compared with historical trends and other
      market dynamics. If the sales of Actimmune Units remain below the Baseline
      for the second [*] day period following such [*] the Parties agree to
      re-set the Baseline, provided that such lower sales are not attributable
      to an extraordinary circumstance, such as an interruption in supply. If,
      however, sales of Actimmune Units increase during such second [*] day
      period, the Parties agree to review the market dynamics and trends from
      prior years with respect to CGD patients, and to make a final decision
      regarding whether and to what extent to re-set the Baseline. The revised
      Baseline number shall be deemed to be the Baseline for all relevant
      purposes of this Agreement beginning with the date the revised Baseline is
      agreed upon (or such earlier date as the Parties may agree). If the
      Parties cannot agree on an appropriate adjustment to the Baseline
      following [*] as set forth in this subsection, then the proposals of each
      Party shall be referred for resolution according to the mechanism set
      forth in Section 5.9.

            (f) Sales Above the Baseline. During [*] if Actimmune Net Sales in
      any given calendar quarter exceed the Baseline (as may be adjusted
      pursuant to subsection (e) above) for that quarter by more than [*],
      Connetics agrees that it will [*] for the purpose of offsetting any
      deferred net profits that InterMune might have realized for such quarter
      had it been entitled to book those Actimmune Net Sales. The Parties agree
      to [*] in an amount that approximates the profits deferred by InterMune
      for Actimmune Unit sales above Baseline for the relevant quarter, [*]
      InterMune's right to book sales after Baseline is met for the year. [*] to
      be mutually agreed upon at the time of [*].

      2.4 MONTHLY STATEMENTS AND REPORTS TO BE PROVIDED BY INTERMUNE. On the
[*] business day of each month, InterMune shall furnish to Connetics:
    

            (a) with respect to the Collection Period just ended, a report or
      reports (in a format reasonably acceptable to Connetics), listing the
      quantities of Actimmune Units sold and related sales dollars (itemized by
      customer and/or distributor), cost of Actimmune Units sold, inventory of
      Actimmune Units as of the end of the Collection Period, accounts
      receivable aging summary, returns, chargebacks, and rebates; and

            (b) with respect to the Collection Period ended a month earlier,
      payment of the Actimmune Gross Margin together with a statement that
      reconciles the payment submitted with the reports submitted for the same
      Collection Period in the prior month, and which includes all the
      information necessary to calculate Actimmune Gross Sales, Actimmune Net
      Sales, Actimmune Gross Margin and the payment made to Connetics. The
      principal



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                                  Page 5 of 13
<PAGE>   6
      financial officer of InterMune shall certify that such monthly statement
      complies with this Agreement.

   
In addition to the periodic reporting outlined above, InterMune shall continue
to permit Connetics [*] as InterMune might use during the term of this
Agreement. The initial report pursuant to subsection 2.4(a) shall be due on May
4, 1999, and the initial statement and payment pursuant to subsection 2.4(b)
shall be due on June 2, 1999. InterMune's obligation to submit reports,
statements and payments shall continue after the term of this Agreement, until
all Collection Periods during the term have been fully accounted for.

      2.5 ROYALTY PAYMENTS TO GENENTECH. InterMune shall remit to Genentech any
amounts payable on Actimmune Net Sales for third party royalties and for GNE
Royalties, all as required by the Genentech License. InterMune covenants and
agrees to remit the full amount of such royalties directly to Genentech or the
applicable third party, and shall [*] after the Effective Date and during the
term of this Agreement.

      2.6 AUDIT. During the term of this Agreement, and for [*] years after 
expiration or termination of this Agreement, InterMune shall permit an
independent auditor, reasonably acceptable to InterMune, to have access to
InterMune's records as may be necessary to verify the accuracy of the statements
provided to Connetics under this Agreement, including Actimmune Gross Sales,
Actimmune Net Sales, and Actimmune Gross Margin, and to assure that InterMune
has complied with the payment terms of this Agreement. Such records shall be
open during reasonable business hours for examination at Connetics' expense, and
not more often than once each calendar year, by such independent auditor (who
shall be required to enter into a binder of confidentiality with InterMune).
    

      2.7 COMMERCIALIZATION COMMITTEE. The Parties shall establish a
Commercialization Committee which shall be responsible for monitoring progress,
managing information exchange between the Parties, deciding key strategies and
solving problems with respect to commercialization and promotion of Actimmune
for the CGD market. At the first meeting of the Commercialization Committee, the
members shall establish a regular meeting time and structure, and appoint a
secretary whose responsibility it will be to coordinate the timing, notice, and
agendas for Commercialization Committee meetings.

                                    SECTION 3
                          MANUFACTURING COST TRANSITION
   
      3.1 OFFSET TO TRANSITION COSTS. The Parties anticipate that the transfer
of manufacturing to a third party manufacturer could result in a substantial
reduction in the Product Cost for Actimmune. As an incentive to InterMune to
complete the transfer of manufacturing of Actimmune to a third party
manufacturer pursuant to Section 4.1 of the Genentech Supply Agreement before
May 2001, and in consideration of an increase in Actimmune Gross Margin during
the Period by virtue of such lower Product Cost, Connetics agrees to reimburse
InterMune for [*] of InterMune's actual costs to effect such transfer of
manufacturing up to a maximum
    



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                                  Page 6 of 13
<PAGE>   7
   
payment of [*] subject to adjustment as follows for each subsequent quarter that
the transfer is not complete:

<TABLE>
<CAPTION>
Amount Payable by Connetics*             If Transfer is Complete by:
---------------------------              ---------------------------
<S>                                      <C>
         [*]                                         [*]
</TABLE>

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

* The amounts payable by Connetics listed above assume [*] as of the Effective
Date). Accordingly, if the transition is completed by the target date but
results in a [*] the amount payable by Connetics shall be [*]. By way of
example, if the transfer is completed before [*].

      3.2 COMPLETION OF MANUFACTURING TRANSFER. For purposes of this Agreement,
the transfer of manufacturing from Genentech to a third party manufacturer shall
be deemed to be complete in the first Collection Period for which [*].
    
      3.3 PAYMENT TERMS. Any payment by Connetics pursuant to this Section 3
shall be payable in cash no later than thirty (30) days following completion of
the manufacturing transfer as set forth in Section 3.2.

                                    SECTION 4
                                 CONFIDENTIALITY
   
      4.1 CONFIDENTIAL INFORMATION OBLIGATIONS. As used herein, "Confidential
Information" means all information that a Party discloses to the other Party
under this Agreement, provided that "Confidential Information" shall not include
such information excluded under Section 4.2. Except to the extent expressly
authorized by this Agreement or otherwise agreed in writing by the Parties, each
Party agrees that, during the term of this Agreement and for [*]
after the expiration or termination of this Agreement, it shall keep
confidential and shall not publish or otherwise
    



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                                  Page 7 of 13
<PAGE>   8

disclose and shall not use for any purpose other than as provided for in this
Agreement any Confidential Information furnished to it by the other Party
pursuant to this Agreement.

      4.2 EXCEPTIONS. The obligations set forth in Section 4.1 shall not apply
to any Information that the receiving Party can demonstrate by competent
evidence:

      (a) was already known to the receiving Party, other than under an
      obligation of confidentiality, at the time of disclosure by the other
      Party;

      (b) was generally available to the public or otherwise part of the public
      domain at the time of its disclosure to the receiving Party by the other
      Party;

      (c) became generally available to the public or otherwise part of the
      public domain after its disclosure and other than through any act or
      omission of the receiving Party in breach of this Agreement;

      (d) was disclosed to the receiving Party, other than under an obligation
      of confidentiality to a third Party, by a third Party who had no
      obligation to the disclosing Party not to disclose such information to
      others; or

      (e) is independently developed by the receiving Party without using any of
      the other Party's Confidential Information.

      4.3 PERMITTED DISCLOSURE. Notwithstanding the limitations in this Article
4, each Party may disclose Confidential Information belonging to the other Party
(or otherwise subject to this Article 4), to the extent such disclosure is
reasonably necessary in the following instances, but solely for the limited
purpose of such necessity:

      (a) regulatory and tax filings;

      (b) prosecuting or defending litigation;

      (c) complying with applicable governmental laws or regulations or valid
      court orders; or

      (d) disclosure to affiliates, employees, consultants or agents who agree
      to be bound by similar terms of confidentiality and non-use at least
      equivalent in scope to those set forth in this Article 4.

Notwithstanding the foregoing, in the event a Party is required to make a
disclosure of the other Party's Confidential Information pursuant to Section
4.4, it will give reasonable advance notice to the other Party of such
disclosure and endeavor in good faith to secure confidential treatment of such
information. In any event, the Parties agree to take all reasonable action to
avoid disclosure of Confidential Information hereunder. Further, the Parties
agree to consult with one another on the provisions of this Agreement to be
redacted in any filings made by a Party with the United States Securities and
Exchange Commission or as otherwise required by law.


                                  Page 8 of 13
<PAGE>   9
                                    SECTION 5
                               GENERAL PROVISIONS

   
      5.1 NO OFFSET. Neither Party shall be entitled to offset any amounts due
to the other Party under this Agreement against any amounts due from such other
Party pursuant to this Agreement or other agreements between the Parties.
Notwithstanding the foregoing sentence, any amounts due to a Party under this
Agreement that are [*] or more days overdue may be offset by such Party
against any amounts such Party owes the other Party under this Agreement.
    

      5.2 SURVIVAL. The payment and reporting obligations set forth in Article
2, and the provisions of Section 2.6 and Article 4 shall survive any expiration
or termination of this Agreement, as will all rights accrued and obligations
incurred hereunder prior to such expiration or termination.

   
      5.3 TERM AND TERMINATION. The term of this Agreement shall coincide with
the Period, and this Agreement will expire with no further action required by
either Party on December 31, 2001. In addition, either Party may terminate this
Agreement on no less than [*] days' notice to the other Party for material
breach of this Agreement by that Party.
    

      5.4 WAIVER. No waiver by either Party of any breach or default of any of
the covenants or agreements set forth in this Agreement shall be deemed a waiver
as to any subsequent or similar breach or default.

      5.5 ASSIGNMENT. This Agreement shall be binding upon and inure to the
benefit of the Parties and their permitted successors and assigns; provided,
however, that neither Party shall assign any of its rights and obligations under
this Agreement without the prior written consent of the other Party, except as
incident to the merger, consolidation, reorganization or acquisition of stock or
assets affecting substantially all of the assets or actual voting control of the
assigning Party. Any assignment or attempted assignment by either Party in
violation of the terms of this Section 4.2 shall be null and void and of no
legal effect.

      5.6 NOTICES. Any notice or other communication required or permitted to be
given to either Party shall be in writing and shall be deemed to have been
properly given and to be effective on the date of delivery if delivered in
person or by facsimile or five (5) days after mailing by registered or certified
mail, postage paid, to the other Party at the following address:

      In the case of InterMune:        InterMune, Inc.



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                                  Page 9 of 13
<PAGE>   10

                                       3294 West Bayshore Road
                                       Palo Alto, CA 94303
                                       Fax: (650) 858-2937
                                       Attention: President

      In the case of Connetics:        Connetics Corporation
                                       3400 West Bayshore Road
                                       Palo Alto, CA 94303
                                       Fax: (650) 843-2899
                                       Attention: Chief Executive Officer

Either Party may change its address for communications by a notice to the other
Party in accordance with this Section. 

      5.7 HEADINGS. The headings of the several sections are inserted for
convenience of reference only and are not intended to be a part of or to affect
the meaning or interpretation of this Agreement.

      5.8 AMENDMENT. No amendment or modification hereof shall be valid or
binding upon the Parties unless made in writing and signed by both Parties.

      5.9 GOVERNING LAW. This Agreement shall be governed exclusively by the
laws of the California, as such law applies to contracts entered into between
and to be performed by California residents entirely in California.

      5.10 DISPUTE RESOLUTION.

            (a) In the event of any controversy or claim arising out of,
relating to or in connection with any provision of this Agreement, or the rights
or obligations of the Parties, the Parties shall try to settle their differences
amicably between themselves by referring the disputed matter to the President of
InterMune and the Chief Executive Officer of Connetics for discussion and
resolution. Either Party may initiate such informal dispute resolution by
sending written notice of the dispute to the other Party, and within ten (10)
days after such notice such representatives of the Parties shall meet for
attempted resolution by good faith negotiations.

            (b) If such personnel are unable to resolve such dispute within
thirty (30) days of initiating such negotiations, either Party may seek to have
such dispute resolved by binding arbitration under this Section 5.9. The
arbitration shall be held in Palo Alto, California according to the Commercial
Arbitration Rules of the American Arbitration Association (the "Rules"). The
arbitration will be conducted by a panel of three (3) arbitrators who are
knowledgeable in the subject matter that is at issue in the dispute, are not
affiliated directly or indirectly with either Party, and are selected by mutual
agreement of the Parties. Failing such agreement, the arbitrators shall be
selected appointed as provided in the Rules. During the arbitration, the Parties
shall have such discovery rights as the arbitrators may allow, consistent with
the discovery permitted by the Federal Code of Civil Procedure. In conducting
the arbitration, the arbitrators shall apply the rules of evidence applicable in
California, and shall be able to decree any and all relief of an equitable
nature, including but not limited to such relief as a temporary restraining
order, a preliminary injunction, or a


                                 Page 10 of 13
<PAGE>   11
permanent injunction, as well as specific performance. The arbitrators shall
also be able to award direct and indirect damages, but shall not award any other
form of damage (e.g., punitive or exemplary damages).

            (c) The reasonable fees and expenses, of the arbitrators, along with
the reasonable legal fees and expenses of the prevailing Party (including all
expert witness fees and expenses), the fees and expenses of a court reporter,
and any expenses for a hearing room, shall be paid as follows: If the
arbitrators rule in favor of one Party on all disputed issues in the
arbitration, the losing Party shall pay 100% of such fees and expenses; if the
arbitrators rule in favor of one Party on some issues and the other Party on
other issues, the arbitrators shall issue with the rulings a written
determination as to how such fees and expenses shall be allocated between the
Parties. The arbitrators shall allocate fees and expenses in a way that bears a
reasonable relationship to the outcome of the arbitration, with the Party
prevailing on more issues, or on issues of greater value or gravity, recovering
a relatively larger share of its legal fees and expenses.

            (d) The decision of the arbitrators shall be final and may be
entered, sued on or enforced by the Party in whose favor it runs in any court of
competent jurisdiction at the option of such Party. Whether a claim, dispute or
other matter in question would be barred by the applicable statute of
limitations, which statute of limitations also shall apply to any claim or
disputes subject to arbitration under this Section, shall be determined by
binding arbitration pursuant to this Section.

      5.11 FORCE MAJEURE. Any delays in performance by any Party under this
Agreement shall not be considered a breach of this Agreement if and to the
extent caused by occurrences beyond the reasonable control of the Party
affected, including but not limited to acts of God, embargoes, governmental
restrictions, fire, flood, explosion, riots, wars, civil disorder, rebellion or
sabotage. The Party suffering such occurrence shall immediately notify the other
Party as soon as practicable, and any time for performance hereunder shall be
extended by the actual time of delay caused by the occurrence.

      5.12 INDEPENDENT CONTRACTORS. In making and performing this Agreement,
InterMune and Connetics act and shall act at all times as independent
contractors and nothing contained in this Agreement shall be construed or
implied to create an agency, partnership or employer and employee relationship
between InterMune and Connetics. At no time shall one Party make commitments or
incur any charges or expenses for or in the name of the other Party.

      5.13 SEVERABILITY. If any part of this Agreement is declared invalid by
any legally governing authority having jurisdiction over either Party, then such
declaration shall not affect the remainder of the Agreement and the Parties
shall revise the invalidated part in a manner that will render such provision
valid without impairing the Parties' original interest.

      5.14 CUMULATIVE RIGHTS. The rights, powers and remedies under this
Agreement shall be in addition to, and not in limitation of, all rights, powers
and remedies provided at law or in equity, or under any other agreement between
the Parties. All of such rights, powers and remedies shall be cumulative, and
may be exercised successively or cumulatively.

      5.15 COUNTERPARTS. This Agreement may be executed in two or more
counterparts, each of which shall be an original and all of which shall
constitute together the same document.


                                 Page 11 of 13
<PAGE>   12
      5.16 ENTIRE AGREEMENT. This Agreement, in conjunction with the other
"Intercompany Agreements" (as that term is described in the Collaboration
Agreement), embodies the entire understanding of the Parties with respect to the
subject matter of the Intercompany Agreements, and supersedes and terminates all
previous communications, representations or understandings, either oral or
written, between the Parties relating to the subject matter of the Intercompany
Agreements.


                           [INTENTIONALLY LEFT BLANK]
                             SIGNATURE PAGE FOLLOWS


                                 Page 12 of 13
<PAGE>   13

IN WITNESS WHEREOF, both InterMune and Connetics have executed this Agreement,
as of the day and year first written above.

INTERMUNE PHARMACEUTICALS, INC.     CONNETICS CORPORATION

By:    /s/ W. Scott Harkonen        By:    /s/ T. Wiggans   
       -------------------------           -------------------------------------
Name:  W. Scott Harkonen            Name:  Thomas G. Wiggans   
       -------------------------           -------------------------------------
Title: President                    Title: President and Chief Executive Officer
       -------------------------           -------------------------------------



                                 Page 13 of 13