Document:

exv10w54

Exhibit 10.54

Severance Plan for International Senior Vice Presidents

As a Senior Vice President, you are entitled to severance benefits in the event your employment is
terminated by Biogen Idec other than For Cause or for reason of death or Disability (as these terms
are defined in the Biogen Idec 2008 Omnibus Equity Plan).

Benefits

Your severance benefits are comprised of (i) a lump sum payment (as calculated below), (ii) upon
completion of the appropriate forms, continuation of your participation in Biogen Idec’s group
medical and dental insurance plans, to the same extent provided for under local statute and to the
same extent such insurance is then provided to regular employees of Biogen Idec, including payment
by you of a portion of the insurance premiums (i.e., the “Insurance Benefit”) and (iii) the
reasonable cost of up to nine months of executive-level outplacement services from a recognized
provider of such services, at the expense of Biogen Idec (upon receipt of appropriate
documentation).

The lump sum severance payment is calculated as follows:

[9 + (A x 2)] x B = lump sum payment

	 	where:	 	 A is the number of full years of service with Biogen Idec (but A x 2 may not exceed 9),
and B is the monthly equivalent of your target annual cash compensation at the time of your
termination (i.e., one-twelfth of the sum of your then annual base salary plus target annual
bonus).

The following are examples of how the lump sum payment and Insurance Benefit Period are determined:

If your employment with Biogen Idec is terminated after 10 months of employment, you will
receive a lump sum payment equal to nine months of your target annual cash compensation and, if
applicable, continue to participate in Biogen Idec’s group medical and dental plans for nine
months, unless you become eligible to participate in another employer’s medical and dental
plans before that date.

If your employment with Biogen Idec is terminated after five years, you will receive a lump sum
payment equal to 18 months [9+9] of your target annual cash compensation and, if applicable,
continue to participate in Biogen Idec’s group medical and dental plans for 18 months, unless
you become eligible to participate in another employer’s medical and dental plans before that
date.

If at any time within two years following a Corporate Transaction or Corporate Change in Control
(as these terms are defined in Biogen Idec’s 2008 Omnibus Equity Plan) your employment is
terminated by Biogen Idec or the succeeding corporate entity, other than For Cause or for reason of
death or Disability (as these terms are defined in Biogen Idec’s 2008 Omnibus Equity Plan), or you
experience an Involuntary Employment Action (defined below) and as a result you terminate your
employment with Biogen Idec or the succeeding corporate entity, then, regardless of the length of
your service with Biogen Idec and the succeeding corporate entity, and in lieu of the formula set
forth above, you will receive a lump sum payment equivalent to 18 months of your target annual cash
compensation at the time of your termination or at the time of a Corporate Transaction or Corporate
Change in Control, whichever is higher. If applicable, you will additionally be entitled to
continue participating in Biogen Idec’s group medical and dental plans for 18 months, unless you
become eligible to participate in another employer’s medical and dental plans before that date.
The term “Involuntary Employment Action” shall have the definition set forth in Biogen Idec’s 2008
Omnibus Equity Plan, provided, however, that the term “Corporate
Transaction” used in that definition shall be deemed to mean either a Corporate Transaction or
Change in Control, as the case may be, and provided also that prior to your termination of
employment you have notified the Chief Legal Counsel or the Head of Human Resources of Biogen Idec
in writing of the basis for your Involuntary Employment Action, you have given such notice within
one year of the circumstances giving rise to your Involuntary Employment Action and Biogen Idec
does not cure such circumstances within 30 days after the date of your notice.

	 	 	 
	Effective October 13, 2008
	 	Page 1 of 2

 

 

Severance Plan for International Senior Vice Presidents

Delivery of Benefits

Payment and provision of all the benefits provided under this arrangement are conditioned on your
execution and delivery of all necessary forms and an irrevocable general release in favor of Biogen
Idec, in form and substance reasonably acceptable to Biogen Idec, with respect to any and all
claims relating to your employment and the termination of your employment with Biogen Idec. If you
retire or voluntarily terminate your employment with Biogen Idec, or Biogen Idec terminates your
employment For Cause or for reason of death or Disability (as these terms are defined in Biogen
Idec’s 2008 Omnibus Equity Plan), or you do not provide the requisite general release, you will not
be eligible to receive the severance benefits described above.

If all other conditions of this arrangement are met, a lump sum payment (less applicable taxes and
other mandatory deductions as required by law) will be paid to you following the termination of
your employment, no later than the first to occur of: a) 90 days following your termination of
your employment with Biogen Idec and b) March 15 of the year following the calendar year in which
termination of employment occurs.

To the extent that such benefit is applicable, the Insurance Benefit will continue until the
earlier of (i) the date you become eligible to participate in the medical and dental insurance plan
of another employer or (ii) the date that is [9 + (A x 2)] months, but not more than 18 months (or
18 months in the case of a Corporate Transaction or Change in Control), following the termination
of your employment with Biogen Idec (the “Insurance Benefit Period”).

General

Biogen Idec shall administer and shall have the discretionary authority to adopt rules for the
management and operation of this arrangement, to interpret the provisions of the arrangement and to
construe the terms of the severance arrangement in its sole discretion. The decision of Biogen
Idec, or the duly authorized delegate, is final and conclusive for all purposes.

The severance arrangement may be amended, modified, suspended or terminated by Biogen Idec at any
time; provided that the severance arrangement may not be amended or terminated without your written
consent for a period of two years following a Corporate Transaction or a Change in Control.

This arrangement is unfunded. This arrangement will benefit and bind Biogen Idec and its
successors and permitted assigns and you and your heirs, executors and legal representatives. You
do not have any right to transfer or assign your benefits under this arrangement.

			
	 	 	 
	Effective October 13, 2008
	 	Page 2 of 2exv10w59

Exhibit 10.59

SECOND AMENDMENT TO

EMPLOYMENT AGREEMENT

THIS AMENDMENT by and between BIOGEN IDEC INC. (the “Company”) and James C. Mullen (the
“Executive”), dated as of December 4, 2008.

WHEREAS, the Executive and the Company are parties to an Employment Agreement dated as of June 20,
2003, as amended effective February 7, 2006 (the “June 20, 2003 Agreement”); and

WHEREAS, the Executive and the Company desire to amend the June 20, 2003 Agreement as set forth
herein.

NOW THEREFORE, it is hereby agreed as follows:

	1.	 	Clause (G) of Section 4(c)(ii) of the June 20, 2003 Agreement (and the text following such
clause) is hereby restated in its entirety, as follows:
	 
	 	 	“(G) a material reduction of the Annual Base Salary under Section 3(a) or a material failure
to pay benefits provided or referred to under this Agreement, unless any such action under
subclause (A) through (G) is remedied by the Company within thirty (30) days after receipt
of notice thereof given by the Executive.”
	 
	2.	 	The last sentence of Section 4(c)(iii) of the June 20, 2003 Agreement is hereby restated in
its entirety, as follows:
	 
	 	 	“An event shall not be deemed to constitute Good Reason if the Executive fails to deliver
Notice of Termination for Good Reason within ninety (90) days of his actual knowledge of the
event.”
	 
	3.	 	A new sentence is hereby added to the end of Section 5(f)(ii), as follows:
	 
	 	 	“In the event that the reduction described in the preceding sentence shall apply, such
reduction shall be effected by reducing the amount of cash severance payable to the
Executive pursuant to clause (i) of Section 5(a) by the amount provided for in the preceding
sentence. ”
	 
	4.	 	A new Section 11 is hereby added to the June 20, 2003 Agreement as follows:
	 
	11.	 	SECTION 409A COMPLIANCE

          For purposes of bringing this Agreement into compliance with, or providing an exemption from,
Section 409A of the Code and the regulations and guidance promulgated thereunder (“Section 409A”)
the Company and the Executive agree as follows:

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     (i) Reimbursements payable to the Executive under the Agreement shall be paid to the Executive
within sixty (60) days following the date upon which the Executive becomes entitled to the
reimbursement, but in no event later than the end of the calendar year following the year in which
the reimbursable expense is incurred (or, in the case of payments under Section 8, the year
following the year in which you become entitled to reimbursement). Tax gross-up payments payable to
the Executive under this Agreement shall be paid to the Executive within sixty (60) days following
the date upon which the tax resulting in the gross-up is paid, but in no event later than the end
of the calendar year following the year in which the tax resulting in the gross-up is paid. In
addition, such reimbursements and tax gross-up payments shall be made in a manner that complies
with all the requirements of Treasury Regulation Section 1.409A-3(i)(l)(iv). In no event shall
reimbursements and payments provided under the Agreement be subject to liquidation or exchange in a
manner which violates Treasury Regulation Section 1.409A-3(i)(l)(iv). Reimbursements to the
Executive with respect to taxes shall be calculated based on the Executive’s actual federal, state
and local tax rates, notwithstanding anything to the contrary set forth herein.

     (ii) Payments to the Executive of bonus amounts described in Section 3(b) hereof shall be made
in no event later than the last day of the “applicable 2 1/2 month period,” as such term is defined
in Treasury Regulation Section 1.409A-l(b)(4)(i)(A) in order that such amounts be treated as a
short-term deferral for purposes of Section 409A.

     (iii) Notwithstanding anything to the contrary herein, if the Executive is a “specified
employee” (within the meaning of Section 409A(a)(2)(B)(i) of the Code) with respect to the Company,
(1) payment to the Executive of any amounts (or benefits) otherwise payable to or in respect of the
Executive under this Agreement pursuant to the Executive’s termination of employment with the
Company which are deferred compensation under Section 409A, shall be delayed for a period of six
(6) months following such termination, and shall be paid on the first business day following the
expiration of such six (6) month period and (2) any payments and benefits not required to be so
delayed shall be paid or provided in accordance with this Agreement.

     (iv) For purposes of amounts under this Agreement which are subject to Section 409A, the
Executive’s employment with the Company will not be treated as terminated unless and until such
termination of employment constitutes a “separation from service” for purposes of Section 409A.

	5.	 	Except as expressly modified by the terms of this Amendment, the provisions of the June 20,
2003 Agreement shall continue in full force and effect.
	 
	6.	 	This Amendment may be executed in several counterparts, each of which shall be deemed an
original and which together shall constitute one and the same instrument.

This Amendment shall be governed by, and construed in accordance with, the laws of The Commonwealth
of Massachusetts, without reference to principles of conflicts of laws.

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IN WITNESS WHEREOF, the Executive and the Company have executed this Amendment under seal, as of
the day and year first above written.

	 	 	 	 	 
	 	BIOGEN IDEC INC.

 	 
	 	By:  	/s/ Bruce R. Ross
 	 
	 	 	Name:  	Bruce R. Ross 	 
	 	 	Title:  	Chairman 	 
	 
	 	 	 
	 	By:  	                                                     /s/ James C. Mullen
 	 
	 	 	James C. Mullen 	 

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