Document:

Filed by Bowne Pure Compliance

Exhibit 10.3

INDEMNIFICATION AGREEMENT

This Indemnification Agreement made and entered into this 5th day of November, 2008
(the “Agreement”), by and between TomoTherapy Incorporated, a Wisconsin corporation (the
“Company”), and                                         , Indemnitee (“Indemnitee”):

WHEREAS, highly competent persons are becoming more reluctant to serve publicly held
corporations as directors, officers or in other capacities unless they are provided with adequate
protection through insurance and indemnification against inordinate risks of claims and actions
against them arising out of their service to and activities on behalf of corporations;

WHEREAS, the difficulties of obtaining adequate insurance and uncertainties relating to
indemnification have increased the difficulty of attracting and retaining such persons;

WHEREAS, Sections 180.0850 through 180.0859 of the Wisconsin Business Corporation Law (the
“WBCL”) provide both mandatory and discretionary indemnification for directors and officers of
Wisconsin corporations;

WHEREAS, the Board of Directors (the “Board”) of the Company has determined that the Company
should act to assure such persons that there will be increased certainty of such protection in the
future by providing, in addition to indemnification provided by law, certain indemnification
rights;

WHEREAS, it is reasonable, prudent, and necessary for the Company contractually to obligate
itself to indemnify such persons to the fullest extent permitted by applicable law so that they
will serve or continue to serve the Company free from undue concern that they will not be so
indemnified; and

WHEREAS, Indemnitee is willing to serve, continue to serve, and to take on additional service
for or on behalf of the Company on the condition that he or she be so indemnified;

NOW, THEREFORE, in consideration of the premises and the covenants contained herein, the
Company and Indemnitee do hereby covenant and agree as follows:

Section 1. Services by Indemnitee. Indemnitee agrees to serve as a director, officer,
employee, or agent (collectively, the “Representative”) of the Company. Indemnitee may at any time
and for any reason resign from such position (subject to any other contractual obligation or other
obligation imposed by operation of law), and the Company or any subsidiary shall have no obligation
to continue the Indemnitee in any such position.

Section 2. Indemnification. The Company shall indemnify Indemnitee to the fullest extent
permitted by applicable law in effect on the date hereof or as such laws may from time to time be
amended. Without diminishing the scope of the indemnification provided by this Section 2, the
indemnification rights of Indemnitee provided hereunder shall include, but shall not be limited to,
those rights set forth hereinafter, except to the extent expressly prohibited by applicable law.

 

 

 

Section 3. Action or Proceeding. In addition to the indemnification of Indemnitee provided
pursuant to the other provisions hereof, Indemnitee shall be entitled to the indemnification rights
provided in this Section 3 if he or she is a party or is threatened to be made a party to any
threatened, pending, or completed action, suit, or proceeding, whether civil, criminal,
administrative, or investigative in nature, by reason of the fact that he or she is or was a
Representative or fiduciary of the Company or is or was serving at the request of the Company as a
Representative or fiduciary of any other entity or by reason of anything done or not done by him or
her in such capacity. Pursuant to this Section 3, Indemnitee shall be indemnified against all
expenses (including attorneys’ fees), costs, judgments, penalties, fines, and amounts paid in
settlement or litigation actually and reasonably incurred by him or her in connection with such
action, suit, or proceeding (including, but not limited to, the investigation, defense, or appeal
thereof), unless such amounts were incurred because Indemnitee breached or failed to perform a duty
owed to the Company and the breach or failure to perform constitutes:

	 	(a)	 	a willful failure to deal fairly with the Company or its shareholders in
connection with a matter in which Indemnitee has a material conflict of
interest;
	 
	 	(b)	 	a violation of criminal law, unless Indemnitee had reasonable cause to
believe that his or her conduct was lawful or no reasonable cause to
believe that his or her conduct was unlawful;
	 
	 	(c)	 	a transaction from which Indemnitee derived an improper personal profit; or
	 
	 	(d)	 	willful misconduct.

Section 4. Indemnification for Costs, Charges, and Expenses of Successful Party.
Notwithstanding the other provisions of this Agreement and in addition to the rights to
indemnification set forth elsewhere herein, to the extent that Indemnitee has served as a witness
on behalf of the Company or has been successful on the merits or otherwise, including, without
limitation, the dismissal of an action, with or without prejudice, or in defense of any action,
suit, or proceeding referred to in Sections 3 and 4 hereof, or in defense of any claim, issue, or
matter therein, he or she shall be indemnified against all costs, charges, and expenses (including
attorneys’ fees) actually and reasonably incurred by him or her or on his or her behalf in
connection therewith. This Section shall not be construed to limit or prohibit other rights to
indemnification provided herein or by statute that may be available and such other rights shall not
be dependent on the outcome of any action.

Section 5. Partial Indemnification. In addition to the rights to indemnification set forth
elsewhere herein, if Indemnitee is only partially successful in the defense, investigation,
settlement, or appeal of any action, suit, investigation, or proceeding described in Section 3 or 4
hereof, and as a result, is not entitled under the other provisions of this Agreement to
indemnification by the Company for the total amount of the expenses (including attorneys’ fees),
costs, judgments, penalties, fines, and amounts paid in settlement actually and reasonably incurred
by him or her, the Company shall nevertheless indemnify Indemnitee, as a matter of right pursuant
to Section 5 hereof, to the extent Indemnitee has been partially successful.

 

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Section 6. Procedures for Seeking Indemnification. An Indemnitee who seeks indemnification
hereunder shall make a written request therefor to the Company.

(a) Subject to Section 6(b), within sixty days of the Company’s receipt of such request, the
Company shall pay or reimburse Indemnitee for the entire amount incurred by the Indemnity in
connection with the subject proceeding.

(b) No indemnification shall be required to be paid by the Company hereunder if, within such
sixty-day period, (i) a disinterested quorum of the Board, by a majority vote thereof, determines
that the Indemnitee requesting indemnification engaged in misconduct constituting a breach of duty
to the Company or (i) a disinterested quorum cannot be obtained. In such case, the Board shall
immediately authorize by resolution that an Authority, as defined in Section 7, determine whether
the Indemnitee’s conduct constituted a breach of duty and, therefore, whether indemnification
should be denied hereunder. If (i) the Board does not authorize an Authority to determine the
Indemnitee’s right to indemnification hereunder within such sixty-day period and/or (ii) if
indemnification of the requested amount is paid by the Company, then it shall be conclusively
presumed for all purposes that a disinterested quorum has affirmatively determined that the
Indemnitee did not engage in misconduct constituting a breach of duty and, in the case of
subsection (i) above (but not subsection (ii)), indemnification by the Company of the requested
amount shall be paid to the Indemnitee immediately.

Section 7. Determination of Entitlement to Indemnification. If the Board authorizes an
Authority to determine an Indemnitee’s right to indemnification pursuant to Section 6, the
Indemnitee requesting indemnification shall have the absolute discretionary authority to select one
of the following as such Authority:

(i) An independent legal counsel; provided, that such counsel shall be mutually
selected by such Indemnitee and by a majority vote of a disinterested quorum of the Board
or, if a disinterested quorum cannot be obtained, then by a majority vote of the Board;

(ii) A panel of three arbitrators selected from the panels of arbitrators of the
American Arbitration Association in Wisconsin; provided, that (A) one arbitrator shall be
selected by such Indemnitee, the second arbitrator shall be selected by a majority vote of a
disinterested quorum or, if a disinterested quorum cannot be obtained, then by a majority
vote of the Board, and the third arbitrator shall be selected by the two previously selected
arbitrators, and (B) in all other respects (other than this Article V), such panel shall be
governed by the American Arbitration Association’s then existing Commercial Arbitration
Rules; or

(iii) A court pursuant to and in accordance with Section 180.0854 of the Statute.

In any such determination by the selected Authority, there shall exist a rebuttable
presumption that the Indemnitee’s conduct did not constitute a breach of duty and that
indemnification against the requested amount is required. The burden of rebutting such a
presumption by clear and convincing evidence shall be on the Company or such other party
asserting that such indemnification should not be allowed. The Authority shall make its
determination within sixty days of being selected and shall submit a written opinion of its
conclusion simultaneously to both the Company and the Indemnitee.

 

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If the Authority determines that indemnification is required hereunder, then the Company shall
pay the entire requested amount, including interest thereon at a reasonable rate, as determined by
the Authority, within ten days of receipt of the Authority’s opinion; provided, that, if it is
determined by the Authority that an Indemnitee is entitled to indemnification against liabilities
incurred in connection with some claims, issues or matters, but not as to other claims, issues or
matters, involved in the subject Proceeding, then the Company shall be required to pay (as set
forth above) only the amount requested as the Authority shall deem appropriate in light of all of
the circumstances of such Proceeding. The determination by the Authority that indemnification is
required hereunder shall be binding upon the Company and the Indemnitee, regardless of any prior
determination that the Indemnitee engaged in a Breach of Duty. Any costs or expenses (including
attorneys’ fees) incurred by Indemnitee in connection with his request for indemnification
hereunder shall be borne by the Company. The Company hereby indemnifies and agrees to hold
Indemnitee harmless therefrom irrespective of the outcome of the determination of Indemnitee’s
entitlement to indemnification.

Section 8: Mandatory Allowance of Expenses: The Company shall pay or reimburse from time to
time, within twenty (20) days after the receipt of the Representative’s written request therefore,
the reasonable expenses of the Representative as such expenses are incurred; provided, however, the
following conditions are satisfied:

(i) The Indemnitee furnishes to the Company an executed written certificate affirming
his or her good faith belief that he or she has not breached or failed to perform his or her
duties to the Company; and

(ii) The Indemnitee furnishes to the Company an unsecured executed written agreement to
repay any advances made hereunder if it is ultimately determined that he or she is not
entitled to be indemnified by the Company.

If the Indemnitee must repay any previously advanced expenses pursuant to this Section, then
such Indemnitee shall not be required to pay interest on such amounts.

Section 9. Other Rights to Indemnification. The indemnification and advancement of expenses
(including attorneys’ fees) and costs provided by this Agreement shall not be deemed exclusive of
any other rights to which Indemnitee may now or in the future be entitled under any provision of
the Bylaws of the Company, Articles of Incorporation of the Company, this Agreement, any vote of
shareholders or disinterested directors, provision of law, or otherwise.

Section 10. Attorneys’ Fees and Other Expenses to Enforce Agreement. In the event that
Indemnitee is subject to or intervenes in any proceeding in which the validity or enforceability of
this Agreement is at issue or seeks an adjudication or award in arbitration to enforce his or her
rights under, or to recover damages for breach of this Agreement, Indemnitee, if he or she prevails
in whole or in part in such action, shall be entitled to recover form the Company and
shall be indemnified by the Company against, any actual expenses for attorneys’ fees and
disbursements reasonably incurred by him or her.

 

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Section 11. Directors and Officers’ Insurance. The Company shall, to the extent that the
Board determines it to be economically reasonable, maintain a policy of directors’ and officers’
liability insurance, which includes coverage for Indemnitee, on such terms and conditions as may be
approved by the Board.

Section 12. Duration of Agreement. This Agreement shall continue until and terminate upon the
later of: (i) ten (10) years after Indemnitee has ceased to occupy any of the positions or have any
of the relationships described in this Agreement; and (ii) the final termination of all pending or
threatened actions, suits, proceedings, or investigations with respect to Indemnitee.

Section 13. Severability. Each section and subsection of this Agreement shall be considered
separable and if, for any reason, any section or paragraph herein is determined to be invalid and
contrary to any existing or future laws, such invalidity shall not impair or affect those portions
of the Agreement which are valid.

Section 14. Agreement in Counterparts. This Agreement may be executed in several counterparts
and all so executed shall constitute one agreement, binding on all of the parties hereto,
notwithstanding that all of the parties may not be signatories to the same counterpart, provided
that each party is a signatory to at least one counterpart.

Section 15. Captions and References. Titles or captions contained in this Agreement are
inserted only as a matter of convenience and for reference, and in no way define, limit, extend or
describe the scope of this Agreement or the intent of any provisions hereof.

Section 16. Amendment. This Agreement may only be amended by a written instrument executed by
all of the parties.

Section 17. Notice by Indemnitee. Indemnitee agrees promptly to notify the Company in writing
upon being served with any summons, citation, subpoena, complaint, indictment, information, or
other document relating to any matter which may be subject to indemnification covered hereunder,
either civil, criminal, or investigative.

Section 18. Notices. All notices required or permitted to be given hereunder shall be in
writing and shall be deemed to have been given to a party at the earlier of the date (i) when
actually delivered to such party, (ii) when facsimile transmitted to such party to the facsimile
number indicated for such party below (or to such other facsimile number for a party as such party
may have substituted by notice pursuant to this Section) or (iii) when mailed to such party by
registered or certified U.S. Mail (return receipt requested) or sent by overnight courier,
confirmed by receipt, and addressed to such party at the address designated below for such party
(or to such other address for such party as such party may have substituted by notice pursuant to
this Section):

 

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	(a) If to the Company:

	 	1240 Deming Way
	 

	 	Madison, WI 53717
	 

	 	Attn: General Counsel
	 
	 	 
	(b) If to Indemnitee:

	 	 
	 

	 	 
	 

	 	 
	 

	 	 
	 

	 	 
	 

	 	 

or to such other address as may have been furnished to Indemnitee by the Company or to the Company
by Indemnitee, as the case may be.

Section 19. Applicable Law and Construction. This Agreement and the validity and construction
hereof shall be determined and governed in all respects by the internal laws of the State of
Wisconsin. This Agreement shall be construed without regard to any rules of construction regarding
the party responsible for the drafting hereof.

Section 20. Binding Effect and Benefit. This Agreement shall be binding upon and inure to the
benefit of the Indemnitee and his or her respective heirs, administrators, executors, successors,
assigns and legal representatives.

IN WITNESS WHEREOF, the parties hereto have executed this Agreement on the date first
appearing above.

TOMOTHERAPY INCORPORATED

  
Frederick A. Robertson,

Chief Executive Officer

  
                                                            , Indemnitee

 

6Filed by Bowne Pure Compliance

Exhibit 10.4

EMPLOYMENT AGREEMENT

(CEO)

THIS AGREEMENT is executed as of this 5th day of November, 2008, by and between TomoTherapy
Incorporated, a Wisconsin corporation (the “Company”), and Frederick A. Robertson, M.D., an
individual (“Employee”).

RECITALS

The Company desires to employ Employee, and Employee desires to be employed by or continued to
be employed by the Company, on the terms and conditions set forth herein.

The parties believe it is in their best interests to make provision for certain aspects of
their relationship during and after the period in which Employee is employed by the Company.

NOW, THEREFORE, in consideration of the premises and the mutual agreements and covenants
contained herein, and for other good and valuable consideration, the receipt and sufficiency of
which is hereby acknowledged by the Company and Employee,

IT IS HEREBY AGREED AS FOLLOWS:

ARTICLE I

EMPLOYMENT

1.1 Term of Employment. The Company employs Employee, and Employee accepts employment by the
Company, for the period commencing on the date hereof and ending on March 31, 2010, subject to
earlier termination as hereinafter set forth in Article III (the “Employment Term”). This
Agreement shall be automatically extended for successive additional one-year periods beginning on
the second anniversary of the date of this Agreement and each year thereafter (collectively, the
“Extension Periods”; individually, an “Extension Period”) unless, prior to the
second anniversary preceding the end of the Employment Term or at least 60 days prior to the then
current Extension Period, either party provides the other with a written notice of intention not to
renew, in which case Employee’s employment with the Company, and the Company’s obligations
hereunder shall terminate as of the end of the Employment Term or said Extension Period, as
applicable, except to the extent specifically provided herein. If the Employment Term is extended,
the terms of this Agreement during such Extension Period shall be the same as the terms in effect
immediately prior to such extension, subject to any such changes or modifications as mutually may
be agreed between the parties as evidenced in a written instrument signed by both the Company and
Employee.

1.2 Position and Duties. Employee shall be employed in the position of Chief Executive Officer
and shall be subject to the authority of, and shall report to, the Company’s Board of Directors.
Employee’s duties and responsibilities shall include all those customarily attendant to the
position of Chief Executive
Officer, and such other duties and responsibilities as may be assigned by the Company’s Board of
Directors. Employee shall devote Employee’s entire business time, loyalty, attention and energies
exclusively to the business interests of the Company while employed by the Company, and shall
perform his duties and responsibilities diligently and to the best of his ability.

 

 

 

ARTICLE II

COMPENSATION AND OTHER BENEFITS

2.1 Base Salary. The Company shall pay Employee a salary at the annual rate of $450,000
(“Base Salary”), payable in accordance with the normal payroll practices of the Company.

2.2 Performance Bonus. Employee will be eligible to earn an annual performance based bonus for
that portion of each full calendar year during which Employee is employed by the Company (a
“Bonus Year”), the terms and conditions of which as well as Employee’s entitlement thereto
shall be determined annually in the sole discretion of the Company’s Board of Directors or an
authorized committee thereof (the “Performance Bonus”). Employee must commence employment
with the Company before October 1 of the Bonus Year in order to be eligible for a Performance Bonus
for that Bonus Year. Any Performance Bonus payable hereunder shall be paid following the Bonus
Year not later than the earlier of (i) 30 days following the Company’s receipt of its annual
audited financial report or (ii) March 15 of the year following the Bonus Year.

2.3 Benefit Plans. Employee will be eligible to participate in the Company’s retirement plans
that are qualified under Section 401(a) of the Internal Revenue Code of 1986, as amended (“Code”),
and in the Company’s welfare benefit plans that are generally applicable to all executive employees
of the Company (the “Plans”), in accordance with the terms and conditions thereof. The
Company intends to provide Employee with: (a) portable term life insurance with a death benefit
equal to twice the sum of Employee’s current Base Salary and target Performance Bonus; provided,
however, that the minimum benefit shall equal at least $500,000; and (b) long-term disability
insurance with an annual benefit equal to at least 75% of the sum of Employee’s Base Salary and
target Performance Bonus. Both the term life insurance and long-term disability insurance are,
however, subject to the underwriting process. To the extent that the costs of such coverages
materially exceed the average of such costs for other executives at the Company, the Company
reserves the right to modify the scope of coverage for Employee, or not offer it at all.

2.4 Expenses. The Company shall reimburse Employee for all reasonable expenses incurred in the
course of the performance of Employee’s duties and responsibilities pursuant to this Agreement and
consistent with the Company’s policies with respect to travel, entertainment and miscellaneous
expenses, and the requirements with respect to the reporting of such expenses.

2.5 Vacation. Employee shall be entitled to a maximum of four weeks of vacation in any
calendar year in accordance with the Company’s general vacation policies for similarly situated
executive employees.

 

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ARTICLE III

TERMINATION

3.1 Right to Terminate; Automatic Termination.

(a) Termination by Company Without Cause. Since Employee is an at-will employee, subject to
Section 3.2, the Company may terminate Employee’s employment and all of the obligations under this
Agreement at any time and for any reason.

(b) Termination by Employee for Good Reason. Subject to Section 3.2, Employee may terminate
his employment obligation hereunder for “Good Reason” (as hereinafter defined) if Employee gives
written notice thereof to the Company (which notice shall specify the grounds upon which such
notice is given) within 90 days of the initial occurrence of a “Good Reason” event and the Company
fails, within 90 days of receipt of such notice, to cure or rectify the grounds for such Good
Reason termination set forth in such notice. If the Company fails to so cure or rectify, the
Employee’s termination of employment shall not be deemed for “Good Reason” unless the Employee
terminates employment within one year of the initial occurrence of Good Reason. “Good Reason”
shall mean any of the following: (i) a material reduction of the Employee’s duties and
responsibilities hereunder; (ii) a material adverse change in the working conditions of the
Employee including, without limitation, relocation of Employee’s principal workplace over 50 miles
from the Company’s existing workplace, without the consent of Employee; or (iii) the Company’s
material breach of the Agreement.

(c) Termination by Company For Cause. Subject to Section 3.2, the Company may terminate
Employee’s employment and all of the Company’s obligations under this Agreement at any time for
"Cause” (as defined below) by giving notice to Employee stating the basis for such termination,
effective immediately upon giving such notice or at such other time thereafter as the Company may
designate. “Cause” shall mean any of the following: (i) Employee has materially breached this
Agreement or any other agreement to which Employee and the Company are parties or has materially
breached any other obligation or duty owed to the Company, which material breach remains uncured
for 30 days after Employee receives notice thereof from the Board of Directors; (ii) Employee has
committed gross negligence, willful misconduct or any material violation of law or the Company’s
Comprehensive Corporate Compliance Program in the performance of Employee’s duties to the Company;
(iii) Employee has engaged in any willful misconduct likely to result in material discredit to or
material loss of business, reputation or goodwill of the Company; (iv)
Employee has failed to follow in any material respect lawful instructions from the officer or body
to whom Employee reports concerning the operations or business of the Company, which material
failure to follow lawful instructions remains uncured for 30 days after Employee receives notice
thereof from the Board of Directors; (v) Employee has been convicted of, or pled nolo contendere to
a felony; (vi) Employee has misappropriated funds or property of the Company; or (vii) Employee has
attempted to obtain a personal profit from any transaction in which the Employee knows the Company
has an interest, and which constitutes a corporate opportunity of the Company or is adverse to the
interests of the Company, unless the transaction was approved in writing by the Company’s Board of
Directors after full disclosure of all details relating to such transaction. The cessation of
employment of Employee shall not be deemed to be for Cause unless and until there shall have been
delivered to Employee a copy of a resolution duly adopted by the affirmative vote of not less than
three-quarters of the independent directors of the Board at a meeting of the Board called and held
for such purpose (after reasonable notice is provided to Employee and Employee is given an
opportunity, together with counsel for Employee, to be heard before the Board), finding that, in
the good faith opinion of the Board, Employee is guilty of the conduct described in this Section
3.1(c), and specifying the particulars thereof in detail.

 

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(d) Termination Upon Death or Disability. Subject to Section 3.2, Employee’s employment and
the Company’s obligations under this Agreement shall terminate: (i) automatically, effective
immediately and without any notice being necessary, upon Employee’s death; or (ii) in the event of
the disability of Employee, by the Company giving notice of termination to Employee. For purposes
of this Agreement, “disability” means the inability of Employee, due to a physical or mental
impairment, for 180 days (whether or not consecutive) during any period of 360 days to perform,
with reasonable accommodation, the essential functions of the work contemplated by this Agreement.
In the event of any dispute as to whether Employee is disabled, the matter shall be determined by
the Company’s Board of Directors in consultation with a physician satisfactory to the Company, and
Employee shall cooperate with the efforts to make such determination. Any such determination shall
be conclusive and binding on the parties. Any determination of disability under this Section
3.1(d) is not intended to alter any benefits any party may be entitled to receive under any
long-term disability insurance policy carried by either the Company or Employee with respect to
Employee, which benefits shall be governed solely by the terms of any such insurance policy.
Nothing in this subsection shall be construed as limiting or altering any of Employee’s rights
under state workers compensation laws or state or Federal family and medical leave laws.

(e) Termination Upon Resignation or Retirement. Since Employee is an at-will
employee, subject to Section 3.2, Employee may terminate employment and all of the obligations
under this Agreement at any time and for any reason. If Employee terminates employment as a
result of retirement from the Company, Employee shall provide the Company with at least 90 days’
notice.

3.2 Rights Upon Termination; Non-Renewal by Company.

(a) Section 3.1(a) and 3.1(b) Termination. If Employee’s employment is terminated pursuant to Section 3.1(a) or 3.1(b) hereof or upon
expiration of this Agreement pursuant to the Company’s notice of its intention not to renew
pursuant to Section 1.1, Employee shall have no further rights against the Company hereunder,
except that the Company, subject to Section 3.2(g), will:

(i) within 10 days following the termination of employment, pay Employee (a) any unpaid
Base Salary with respect to the period prior to the effective date of termination, (b)
reimbursement of expenses to which Employee is entitled under Section 2.4 hereof, and
payment of any accrued but unused vacation to which Employee is entitled to under Section
2.5 hereof (collectively, the “Accrued Obligations.”).

(ii) subject to Section 3.2(f), pay Employee a lump-sum severance payment (the
“Severance Payment”) 53 days following the Employee’s termination of employment, in an
amount equal to the sum of: (a) 1.5 times Employee’s annual base salary as in effect on the
date of termination; and (b) 1.5 times the average of the two annual bonuses paid to
Employee for the two years immediately preceding the year in which such termination occurs;
provided that if the Employee was not employed for the period required to be eligible for
two prior full year annual bonuses, then the amount in this subparagraph (b) shall be the
amount of the annual bonus, if any, received for the year prior to the year in which
termination of employment occurred.

 

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(iii) subject to Section 3.2(f), pay the COBRA premium for group health care coverage
for Employee and Employee’s eligible dependents, as applicable and to the extent eligible,
provided that Employee properly elects COBRA continuation coverage, for up to eighteen (18)
months immediately following the date of such termination of Employee’s employment, except
that payment of such premiums shall cease if and when the Employee (and Employee’s eligible
dependents) become eligible for medical, hospital and health coverage under a plan of a
subsequent employer; and

(iv) subject to Section 3.2(f), pay up to $10,000 for outplacement services, such
services to be used within two years of termination of employment.

Further, the Company’s Board of Directors shall consider, and decide within its sole discretion,
whether to accelerate any unvested stock options held by Employee at the time of such termination.

(b) Section 3.1(c) and 3.1(e) Termination. If Employee’s employment is terminated pursuant to
Sections 3.1(c) or 3.1(e) hereof, Employee shall have no further rights against the Company
hereunder, except for the right to receive the Accrued Obligations.

(c) Section 3.1(d) Termination. If Employee’s employment is terminated pursuant to Section
3.1(d) hereof, Employee or Employee’s estate shall have no further rights against the Company
hereunder, except for the right to receive (i) the Accrued Obligations, (ii) payment of the COBRA
premium for group health care coverage for Employee and Employee’s eligible dependents, as
applicable and to the extent eligible, provided that Employee or Employee’s estate properly elects
COBRA continuation coverage, for up to eighteen (18) months immediately following the date of such
termination of Employee’s employment, and (iii) the continuing rights under the life insurance
benefit under Section 2.3.

(d) Termination Pursuant to a Change of Control. If, within three (3) months before or twenty
four (24) months following a Change of Control, the Company terminates Employee’s employment
without Cause pursuant to Section 3.1(a) or Employee terminates his employment for Good Reason
pursuant to Section 3.1(b), Employee shall have no further rights against the Company hereunder,
except the Company will, subject to Section 3.2(g):

(i) pay the Employee the Accrued Obligations:

(ii) subject to Section 3.2(f), pay Employee a lump-sum severance payment (the
“Severance Payment”) 53 days following the termination of employment, in an amount equal to
the sum of: (a) 3.0 times Employee’s annual base salary as in effect on the date of
termination; and (b) 3.0 times the greater of (x) the average of the two annual bonuses paid
to Employee for the two years preceding the year in which such termination occurs, provided
that if the Employee was not employed for the period required to be eligible for two prior
annual bonuses, then the amount in this subparagraph (b)(x) shall be the amount of the
annual bonus, if any, received for the year prior to the year in which termination of
employment occurred, or (y) the target bonus for the year in which such termination occurs;
provided such lump sum shall be reduced by the amount of any lump sum payable under Section
3.2(a)(ii).

 

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(iii) subject to Section 3.2(f), pay the COBRA premium for group health care coverage
for Employee and Employee’s eligible dependents, as applicable and to the extent eligible,
provided that Employee properly elects COBRA continuation coverage, for the 36 month period
immediately following the date of such termination of Employee’s employment, except that
payment of such premiums shall cease if and when the Employee (and Employee’s eligible
dependents) become eligible for medical, hospital and health coverage under a plan of a
subsequent employer; and

(iv) subject to Section 3.2(f), pay up to $10,000 for outplacement services, provided
such payment shall be reduced by the amount of any payment under Section 3.2(a)(iv), and
provided further that such services are used within two years of termination of employment.

(e) Definition of Change of Control. As used herein, “Change of Control” shall mean
the occurrence of a “change in the ownership,” a “change in the effective control” or a “change in
the ownership of a substantial portion of the assets” of the Company, as determined in accordance
with this definition.  In determining whether an event shall be considered a “change in the
ownership,” a “change in the effective control” or a “change in the ownership of a substantial
portion of the assets” of the Company, the following provisions shall apply:

(i) A “change in the ownership” of the Company shall occur on the date on which any
one person, or more than one person acting as a group, acquires ownership of stock of the
Company that, together with stock held by such person or group, constitutes
more than 50% of the total fair market value or total voting power of the stock of the
Company, as determined in accordance with Treasury Regulation § 1.409A-3(i)(5)(v).  If a
person or group is considered either to own more than 50% of the total fair market value or
total voting power of the stock of the Company, or to have effective control of the Company
within the meaning of part (b) of this definition, and such person or group acquires
additional stock of the Company, the acquisition of additional stock by such person or group
shall not be considered to cause a “change in the ownership” of the Company.

(ii) A “change in the effective control” of the Company shall occur on either of
the following dates:

(A) The date on which any one person, or more than one person acting as a
group, acquires (or has acquired during the 12-month period ending on the date of
the most recent acquisition by such person or persons) ownership of stock of the
Company possessing 30% or more of the total voting power of the stock of the
Company, as determined in accordance with Treasury Regulation § 1.409A-3(i)(5)(vi). 
If a person or group is considered to possess 30% or more of the total voting power
of the stock of the Company, and such person or group acquires additional stock of
the Company, the acquisition of additional stock by such person or group shall not
be considered to cause a “change in the effective control” of the Company; or

 

6

 

(B) The date on which a majority of the members of the Company’s Board of
Directors is replaced during any 12-month period by directors whose appointment or
election is not endorsed by a majority of the members of the Company’s Board of
Directors before the date of the appointment or election, as determined in
accordance with Treasury Regulation § 1.409A-3(i)(5)(vi).

(iii) A “change in the ownership of a substantial portion of the assets” of the
Company shall occur on the date on which any one person, or more than one person acting as a
group, acquires (or has acquired during the 12-month period ending on the date of the most
recent acquisition by such person or persons) assets from the Company that have a total
gross fair market value equal to or more than 40% of the total gross fair market value of
all of the assets of the Company immediately before such acquisition or acquisitions, as
determined in accordance with Treasury Regulation § 1.409A-3(i)(5)(vii).  A transfer of
assets shall not be treated as a “change in the ownership of a substantial portion of the
assets” when such transfer is made to an entity that is controlled by the shareholders of
the Company, as determined in accordance with Treasury Regulation § 1.409A-3(i)(5)(vii)(B).

(f) Exclusive Remedy; Waiver and Release. To the extent permitted by applicable law,
the payments contemplated by this Section 3.2 shall constitute the exclusive and sole remedy for
any termination of Employee’s employment by the Company (whether pursuant to, or in violation of,
the terms of this Agreement). Employee covenants not to assert or pursue any remedies, other than
an action to enforce the payments due to Employee under this Agreement, at law or in equity, with
respect to any termination of employment, and shall execute a release and waiver on such terms and
conditions as the
Company may require as a condition of entitlement to such payments. If any applicable revocation
period for such release and waiver has not expired before the date payment is due to be made
hereunder, such payment shall be forfeited.

(g) Limitation of Benefits. If any payments or benefits payable to the employee under this
Agreement or otherwise would be subject to the excise tax under Section 4999 of the Code, such
payments and/or benefits will be reduced to the extent necessary so that no amount will be subject
to such excise tax; provided that such reduction will only occur if the employee will be in a more
favorable, after-tax position than if no such reduction was made.

(h) Six Month Delay. If payment of any amount of “deferred compensation” (as
defined under Section 409A of the Code, after giving effect to the exemptions thereunder) is
triggered by a Separation from Service (as defined in Section 4.7) that occurs while the Employee
is a “specified employee” with respect to the Company (as defined under Section 409A of the Code
and determined in good faith), and if such amount is scheduled to be paid within six (6) months
after such Separation from Service, the amount shall accrue without interest and shall be paid the
first business day after the end of such six-month period, or, if earlier, within 15 days after the
appointment of the personal representative or executor of the Employee’s estate following the
Employee’s death.

 

7

 

ARTICLE IV

GENERAL PROVISIONS

4.1 Notices. Any and all notices provided for in this Agreement shall be given in writing and
shall be deemed given to a party at the earlier of (i) when actually delivered to such party, or
(ii) when mailed to such party by registered or certified mail (return receipt requested) or sent
to such party by courier, confirmed by receipt, and addressed to such party at the address
designated below for such party as follows (or to such other address for such party as such party
may have substituted by notice pursuant to this Section 4.1):

	 	(a)	 	If to the Company:

TomoTherapy Incorporated

1240 Deming Way

Madison, WI 53717

Attn: General Counsel

	 	(b)	 	If to Employee:

938 Winding Way

Middleton, WI 53562

Attn: Frederick A. Robertson, M.D.

4.2 Entire Agreement. This Agreement contains the entire understanding and the full and
complete agreement of the parties and supersedes and replaces any prior understandings and
agreements among the parties,
with respect to the subject matter hereof., provided that the Indemnity Agreement dated November 5,
2008, the Confidentiality and Non-Competition Agreement dated April 1, 2007, (“Confidentiality
Agreement”) and the Assignment of Inventions Agreement dated January 3, 2005, (“Assignment
Agreement”) between the Company and the Employee are and shall remain in effect.

4.3 Amendment. This Agreement may be altered, amended or modified only in a writing, signed by
both of the parties hereto. Headings included in this Agreement are for convenience only and are
not intended to limit or expand the rights of the parties hereto. References to Sections herein
shall mean sections of the text of this Agreement, unless otherwise indicated.

4.4 Assignability. This Agreement and the rights and duties set forth herein may not be
assigned by Employee, but may be assigned by the Company, in whole or in part. This Agreement
shall be binding on and inure to the benefit of each party and such party’s respective heirs, legal
representatives, successors and assigns.

4.5 Severability. If any court of competent jurisdiction determines that any provision of this
Agreement is invalid or unenforceable, then such invalidity or unenforceability shall have no
effect on the other provisions hereof, which shall remain valid, binding and enforceable and in
full force and effect, and such invalid or unenforceable provision shall be construed in a manner
so as to give the maximum valid and enforceable effect to the intent of the parties expressed
therein.

 

8

 

4.6 Arbitration. Any controversy, dispute or claim arising out of or relating to this
Agreement (including, but not limited to, any claim regarding the scope or effect of this Section
and any claim that this Section is invalid or unenforceable), or the breach hereof, shall be
settled by a single arbitrator in binding arbitration conducted in Milwaukee, Wisconsin in
accordance with the Commercial Arbitration Rules of the American Arbitration Association (“AAA”)(or
such other arbitration service as the parties may agree upon), and judgment upon the award rendered
by the arbitrator may be entered in any court having jurisdiction thereof. The arbitrator’s
decision shall be in writing. In addition to the Commercial Arbitration Rules of the AAA and
unless otherwise agreed to by the parties, the following rules shall apply:

(a) Each party shall be entitled to discovery exclusively by the following means: (i) requests
for admission, (ii) requests for production of documents, (iii) up to 15 written interrogatories
(with any subpart to be counted as a separate interrogatory), and (iv) depositions of no more than
six individuals.

(b) Unless the arbitrator finds that delay is reasonably justified or as otherwise agreed to
by the parties, all discovery shall be completed, and the arbitration hearing shall commence within
five months after the appointment of the arbitrator.

(c) Unless the arbitrator finds that delay is reasonably justified, the hearing will be
completed, and an award rendered within 30 days of commencement of the hearing.

The arbitrator’s authority shall include the ability to render equitable types of relief and, in
such event, any aforesaid court may enter an order enjoining and/or compelling such actions or
relief ordered or as found by the arbitrator. The arbitrator also shall make a determination
regarding which party’s legal position in any such controversy or claim is the more substantially
correct (the “Prevailing Party”) and the arbitrator shall require the other party to pay the legal
and other professional fees and costs incurred by the Prevailing Party in connection with such
arbitration proceeding and any necessary court action. In addition, the parties expressly agree
that a court of competent jurisdiction may enter a temporary restraining order or an order
enjoining a breach of the Assignment Agreement, the Confidentiality Agreement or any similarly
subsequently executed agreement between the parties, pending a final award or further order by the
arbitrator. Such remedy, however, shall be cumulative and nonexclusive, and shall be in addition
to any other remedy to which the parties may be entitled.

 

9

 

4.7 Separation from Service. “Separation from Service,” “termination of employment,” or
words of similar import shall mean, with respect to any payments of deferred compensation subject
to Section 409A of the Code, the Employee’s “separation from service” as defined in Section 409A of
the Code. For this purpose, a “separation from service” is deemed to occur on the date that the
Company and the Employee reasonably anticipate that the level of bona fide services the Employee
would perform after the date (whether as an employee or independent contractor) would permanently
decrease to a level that, based on the facts and circumstances would constitute a separation from
service; provided that a decrease to a level that is 50% or more of the average level of bona fide
services provided over the prior 36 months shall not be a Separation from Service, and a decrease
to a level that is 20% or less of the average level of such bona fide services shall be a
Separation from Service. The bona fide services taken into account for purposes of determining
whether there has been a Separation from Service shall be services performed for the Company and
any person or entity that would be considered a single employer with the Company under Section
414(b) or 414(c) of the Code; provided that, in applying Section 1563(a)(1),(2), and (3) of the
Code, the language “at least 50 percent” shall be used instead of “at least 80 percent;” and
further provided that “at least 20 percent” shall be used instead of “at least 50 percent” where
based on legitimate business criteria.

4.8 Waiver of Breach. The waiver by either party of the breach of any provision of this
Agreement shall not operate or be construed as a waiver of any subsequent breach by either party.

 

10

 

4.9 Governing Law; Construction. This Agreement shall be governed by the internal laws of the
State of Wisconsin, without regard to any rules of construction concerning the party responsible
for the drafting hereof.

IN WITNESS WHEREOF, the parties have executed this Agreement as of the day and year written
above.

	 	 	 	 	 	 	 
	EMPLOYEE:

	 	COMPANY:	 	 
	 
	 	 	 	 	 	 
	Frederick A. Robertson, M.D.

	 	TomoTherapy Incorporated	 	 
	 
	 	 	 	 	 	 
	/s/ Frederick A. Robertson

	 	By:
	 	/s/ Stephen C. Hathaway	 	 
	 

	 	 	 	 

Stephen C. Hathaway
	 	 
	 

	 	 	 	Chief Financial Officer	 	 

 

11

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