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                                                                   Exhibit 10.31


                               SEVERANCE AGREEMENT



                  THIS SEVERANCE AGREEMENT (the "Agreement") is made effective
as of September 13, 2000, between JNI Corporation, a Delaware corporation
("JNI"), and TERRY FLANAGAN ("Employee").

                                    RECITALS

         A.       Employee is presently employed as the President and Chief
         Executive Officer of JNI.

         B.       The terms and conditions of Employee's employment with JNI are
         consistent with JNI's employment policies and practices.

         C.       Employee and JNI desire to memorialize in writing their
         understanding regarding severance payments and vesting of options in
         the event of a termination "without cause" or voluntary resignation for
         "good reason."

         D.       Employee and JNI acknowledge that this Agreement supersedes
         any and all other agreements, either oral or in writing, between
         Employee and JNI and/or Jaymark, Inc. and all other subsidiaries or
         affiliates of JNI with respect to the matters discussed herein,
         including, but not limited to, the Severance and Change of Control
         Agreement between JNI and Employee approved by the Board of Directors
         on September 1, 1999.

                                    AGREEMENT

                  In consideration of the promises and of the mutual covenants
contained herein, and for other good and valuable consideration, receipt of
which is hereby acknowledged, the parties hereto do hereby agree as follows:

         1.       EFFECT OF CERTAIN TERMINATIONS

                  1.1 SEVERANCE COMPENSATION. If Employee's employment is
terminated without "cause," or Employee voluntarily resigns or retires with
"good reason," then (i) JNI shall pay to Employee, on the normal payroll dates
of JNI during the twelve-month period commencing on termination without cause or
resignation with good reason, severance compensation in an amount equal to 12
months' base salary plus a prorata bonus for the year during which the
termination or resignation occurs (based upon the performance standards and
other factors which would have applied to Employee's bonus for the full year)
and (ii) all options granted to Employee under JNI's 1997 Stock Option Plan or
its 1999 Stock Option Plan which, as of the date of such termination without
"cause" or voluntary resignation for "good reason," remain unexercised and
unvested, shall, to the extent permissible by law, become immediately vested in
full and exercisable otherwise in accordance with the terms of the stock option
agreements relating to such options. Notwithstanding the foregoing, if it is
determined that the amounts payable to Employee under this Agreement, when
considered together with any other


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amounts payable to Employee, cause such payments to be treated as excess
parachute payments within the meaning of Section 280G of the Internal Revenue
Code, JNI shall reduce the amount payable to Employee under this Section 1.1 to
an amount that will not subject Employee to the imposition of tax under Section
4999 of the Internal Revenue Code.

                  1.2 CHANGE IN CONTROL. A "Change in Control" means (i) the
acquisition by an individual person or entity acting in concert, directly or
indirectly, through one transaction or a series of related transactions, of more
than 50% of the outstanding voting securities of JNI, (ii) a merger or
consolidation of JNI with or into another entity after which the stockholders of
JNI immediately prior to such transaction hold less than 50% of the voting
securities of the surviving entity or (iii) a sale of all or substantially all
of the assets of JNI.

                  1.3 TERMINATION FOR "CAUSE." For purposes of this Agreement, a
termination for "cause" occurs if Employee is terminated for any of the
following reasons: (i) theft, dishonesty, or falsification of JNI records; (ii)
improper disclosure of JNI's confidential or proprietary information; (iii)
Employee's failure or inability to perform any reasonable assigned duties after
written notice from JNI of, and a reasonable opportunity cure, such failure or
inability; or (iv) Employee's conviction of any criminal act which impairs his
ability to perform his duties as an employee of JNI.

                  1.4 VOLUNTARY RESIGNATION FOR "GOOD REASON." Employee may
terminate his employment with JNI with "good reason" by serving notice of his
resignation or retirement to JNI with a description of the circumstances giving
rise to the good reason. "Good reason" means (i) Employee's compensation,
including salary, bonus and equity compensation, is materially reduced from the
compensation level in effect for Employee during the prior year (or such shorter
period of time as Employee was employed by JNI); (ii) any material diminution of
Employee's titles, responsibilities or duties with the Company, including, but
not limited to, the hiring of a new Chief Executive Officer (even if Employee
participates in the selection of the new Chief Executive Officer to facilitate
Employee's own voluntary retirement); or (iii) the occurrence of a Change of
Control.

                  1.5 PAYMENT UPON DEATH OR DISABILITY. Neither death nor
disability shall affect JNI's obligations hereunder.

                  1.6 HEALTH AND DENTAL COVERAGE. JNI will pay the monthly
premiums to continue Employee under JNI's health and dental insurance coverage,
including family coverage, for twelve (12) months from Employee's termination
without "cause" or voluntary resignation for "good cause."

                  1.7 OTHER INSURANCE COVERAGE. JNI will continue coverage of
Employee under JNI's long-term disability, accidental death and disability and
life insurance plans, if any, for twelve (12) months from Employee's termination
without "cause" or voluntary resignation for "good cause", provided JNI's
insurance carriers allow for such coverage continuation.

                  1.8 LEASE. In the event of a termination without "cause" or
voluntary resignation for "good reason," JNI will assume any remaining lease
payments on Employee's


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San Diego apartment (which currently expires in 2001) and, to the extent
practicable, take over the lease from Employee.

                  1.9 CONSULTING. During the twelve-month period following a
termination without cause or a resignation for "good reason," Employee will make
himself available on reasonable notice and at reasonable times to provide advice
and other consulting services as and when requested by the new chief executive
officer of JNI.

                  1.10 NO DUTY TO MITIGATE. Employee shall not be required to
mitigate the amount of any payment contemplated by this Agreement (whether by
seeking new employment or in any other manner).

         2.       GENERAL PROVISIONS.

                  2.1 SEVERABILITY. If any provision of this Agreement is held
by a court of competent jurisdiction to be invalid, void or unenforceable, the
remaining provisions shall nevertheless continue in full force without being
impaired or invalidated in any way.

                  2.2 SUCCESSORS AND ASSIGNS. The rights and obligations of JNI
under this Agreement shall ensure to the benefit of and shall be binding upon
the successors and assigns of JNI. Employee shall not be entitled to assign any
of his rights or obligations under this Agreement, other than to his estate as
provided in Section 1.5.

                  2.3 APPLICABLE LAW. This Agreement shall be interpreted,
construed, governed and enforced in accordance with the laws of the State of
California.

                  2.4 AMENDMENTS. No amendment or modification of the terms or
conditions of this Agreement shall be valid unless in subsequent writing and
signed by the parties thereto.

         IN WITNESS WHEREOF, the parties hereto execute this Agreement,
effective as of the date first above written.

EMPLOYEE:                                  JNI CORPORATION


/s/ TERRY M. FLANAGAN                    By: /s/ ERIC P. WENAAS
-----------------------------                  ---------------------------------
                                           Title: Chairman
                                                 -------------------------------
Address: 9775 Towne Center Drive         Address:  9775 Towne Centre Drive
        -------------------------                  San Diego, CA 92121
         San Diego, CA 92121
        -------------------------


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