Document:

PROMISSORY NOTE DATED DECEMBER 1, 2008

Exhibit 10.39

Confidential treatment has been requested for portions of this exhibit. The copy filed herewith
omits the information subject to the confidentiality request. Omissions are designated as [ * ].
A complete version of this exhibit has been filed separately with the Securities and Exchange
Commission.

*[ * ]-095512012008*

PROMISSORY NOTE

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Principal	 	Loan Date	 	Maturity	 	Loan No	 	Call / Coll	 	Account	 	Officer	 	Initials
	$50,000,000.00
	 	 	12-01-2008	 	 	 	11-30-2009	 	 	 	[ * ]	 	 	 	 	 	 	 	[ * ]	 	 	 	11485	 	 	 	 	 

References in the boxes above are for Lender’s use only and do not limit the applicability of this document to any particular loan or item.

Any item above containing “***” has been omitted due to text length limitations.

	 	 	 	 	 	 	 	 	 
	Borrower:

	 	Tomotherapy Incorporated
	 	 	 	Lender:
	 	M&I Marshall & Ilsley Bank
	 

	 	1240 Deming Way
	 	 	 	 	 	Capitol Square — Commercial
	 

	 	Madison, WI 53717-1954
	 	 	 	 	 	One W Main Street
	 

	 	 	 	 	 	 	 	Madison, WI 53703

			
	Principal Amount: $50,000,000.00
	 	Date of Note: December 1, 2008

PROMISE TO PAY. Tomotherapy Incorporated (“Borrower”) promises to pay to M&I Marshall &
Ilsley Bank (“Lender”), or order, in lawful money of the United States of America, the
principal amount of Fifty Million & 00/100 Dollars ($50,000,000.00) or so much as may be
outstanding, together with interest on the unpaid outstanding principal balance of each
advance. Interest shall be calculated from the date of each advance until repayment of each
advance.

PAYMENT. Borrower will pay this loan in one payment of all outstanding principal plus all
accrued unpaid interest on November 30, 2009. In addition, Borrower will pay regular
monthly payments of all accrued unpaid interest due as of each payment date, beginning
December 31, 2008, with all subsequent interest payments to be due on the last day of each
month after that. Unless otherwise agreed or required by applicable law, payments will be
applied to Accrued Interest, Principal, Late Charges, and Escrow. Borrower will pay Lender
at Lender’s address shown above or at such other place as Lender may designate in writing.

VARIABLE INTEREST RATE. The interest rate on this Note is subject to change from time to
time based on changes in an independent index which is the one month British Bankers
Association (BBA) LIBOR and reported by a major news service selected by Lender (such as
Reuters, Bloomberg or Moneyline Telerate). If BBA LIBOR for the one month period is not
provided or reported on the first day of a month because, for example, it is a weekend or
holiday or for another reason, the One Month LIBOR Rate shall be established as of the
preceding day on which a BBA LIBOR rate is provided for the one month period and reported by
the selected news service (the “Index”). The Index is not necessarily the lowest rate
charged by Lender on its loans. If the Index becomes unavailable during the term of this
loan, Lender may designate a substitute index after notifying Borrower. Lender will tell
Borrower the current Index rate upon Borrower’s request. The interest rate change will not
occur more often than each first day of each calendar month and will become effective
without notice to the Borrower. Borrower understands that Lender may make loans based on
other rates as well. The Index currently is 4.003% per annum. The interest rate to be
applied to the unpaid principal balance of this Note will be calculated as described in the
“INTEREST CALCULATION METHOD” paragraph using a rate of 1.750 percentage points over the
Index, resulting in an initial rate of 5.753% per annum based on a year of 360 days.
NOTICE: Under no circumstances will the interest rate on this Note be more than the maximum
rate allowed by applicable law.

INTEREST CALCULATION METHOD. Interest on this Note is computed on a 365/360 basis; that is,
by applying the ratio of the interest rate over a year of 360 days, multiplied by the
outstanding principal balance, multiplied by the actual number of days the principal balance
is outstanding. All interest payable under this Note is computed using this method. This
calculation method results in a higher effective interest rate than the numeric interest
rate stated in this Note.

PREPAYMENT. Borrower may pay without penalty all or a portion of the amount owed earlier
than it is due. Early payments will not, unless agreed to by Lender in writing, relieve
Borrower of Borrower’s obligation to continue to make payments of accrued unpaid interest.
Rather, early payments will reduce the principal balance due. Borrower agrees not to send
Lender payments marked “paid in full”, “without recourse”, or similar language. If Borrower
sends such a payment, Lender may accept it without losing any of Lender’s rights under this
Note, and Borrower will remain obligated to pay any further amount owed to Lender. All
written communications concerning disputed amounts, including any check or other payment
instrument that indicates that the payment constitutes “payment in full” of the amount owed
or that is tendered with other conditions or limitations or as full satisfaction of a
disputed amount must be mailed or delivered to: M&I Marshall & Ilsley Bank, P.O. 3114
Milwaukee, WI 53201-3114.

LATE CHARGE. If a payment is not made on or before the 10th day after its due date,
Borrower will be charged 5.000% of the unpaid portion of the regularly scheduled payment.

INTEREST AFTER DEFAULT. Upon default, including failure to pay upon final maturity, the
interest rate on this Note shall be increased by adding a 3.000 percentage point margin
(“Default Rate Margin”). The Default Rate Margin shall also apply to each succeeding
interest rate change that would have applied had there been no default. However, in no
event will the interest rate exceed the maximum interest rate limitations under applicable
law.

DEFAULT. Each of the following shall constitute an event of default (“Event of Default”)
under this Note:

Payment Default. Borrower fails to make any payment when due under this Note.

Other Defaults. Borrower fails to comply with or to perform any other term, obligation,
covenant or condition contained in this Note or in any of the related documents or to
comply with or to perform any term, obligation, covenant or condition contained in any
other agreement between Lender and Borrower.

 

 

Default in Favor of Third Parties. Borrower or any Grantor defaults under any loan,
extension of credit, security agreement, purchase or sales agreement, or any other
agreement, in favor of any other creditor or person that may materially affect any of
Borrower’s property or Borrower’s ability to repay this Note or perform Borrower’s
obligations under this Note or any of the related documents.

False Statements. Any warranty, representation or statement made or furnished to Lender
by Borrower or on Borrower’s behalf under this Note or the related documents is false or
misleading in any material respect, either now or at the time made or furnished or
becomes false or misleading at any time thereafter.

Insolvency. The dissolution or termination of Borrower’s existence as a going business,
the insolvency of Borrower, the appointment of a receiver for any part of Borrower’s
property, any assignment for the benefit of creditors, any type of creditor workout, or
the commencement of any proceeding under any bankruptcy or insolvency laws by or against
Borrower.

Creditor or Forfeiture Proceedings. Commencement of foreclosure or forfeiture
proceedings, whether by judicial proceeding, self-help, repossession or any other method,
by any creditor of Borrower or by any governmental agency against any collateral securing
the loan. This includes a garnishment of any of Borrower’s accounts, including deposit
accounts, with Lender. However, this Event of Default shall not apply if there is a good
faith dispute by Borrower as to the validity or reasonableness of the claim which is the
basis of the creditor or forfeiture proceeding and if Borrower gives Lender written
notice of the creditor or forfeiture proceeding and deposits with Lender monies or a
surety bond for the creditor or forfeiture proceeding, in an amount determined by Lender,
in its sole discretion, as being an adequate reserve or bond for the dispute.

Events Affecting Guarantor. Any of the preceding events occurs with respect to any
guarantor, endorser, surety, or accommodation party of any of the indebtedness or any
guarantor, endorser, surety, or accommodation party dies or becomes incompetent, or
revokes or disputes the validity of, or liability under, any guaranty of the indebtedness
evidenced by this Note.

Adverse Change. A material adverse change occurs in Borrower’s financial condition, or
Lender believes the prospect of payment or performance of this Note is impaired.

Insecurity. Lender in good faith believes itself insecure.

LENDER’S RIGHTS. Upon default, Lender may declare the entire unpaid principal balance under
this Note and all accrued unpaid interest immediately due, and then Borrower will pay that
amount.

ATTORNEYS’ FEES; EXPENSES. Lender may hire or pay someone else to help collect this Note if
Borrower does not pay. Borrower will pay Lender that amount. This includes, subject to any
limits under applicable law, Lender’s attorneys’ fees and Lender’s legal expenses, whether
or not there is a lawsuit, including attorneys’ fees, expenses for bankruptcy proceedings
(including efforts to modify or vacate any automatic stay or injunction), and appeals. If
not prohibited by applicable law, Borrower also will pay any court costs, in addition to all
other sums provided by law.

JURY WAIVER. Lender and Borrower hereby waive the right to any jury trial in any action,
proceeding, or counterclaim brought by either Lender or Borrower against the other.

GOVERNING LAW. This Note will be governed by federal law applicable to Lender and, to the
extent not preempted by federal law, the laws of the State of Wisconsin without regard to
its conflicts of law provisions. This Note has been accepted by Lender in the State of
Wisconsin.

CHOICE OF VENUE. If there is a lawsuit, Borrower agrees upon Lender’s request to submit to
the jurisdiction of the courts of Dane County, State of Wisconsin.

DISHONORED ITEM FEE. Borrower will pay a fee to Lender of $15.00 if Borrower makes a
payment on Borrower’s loan and the check or preauthorized charge with which Borrower pays is
later dishonored.

RIGHT OF SETOFF. To the extent permitted by applicable law, Lender reserves a right of
setoff in all Borrower’s accounts with Lender (whether checking, savings, or some other
account). This includes all accounts Borrower holds jointly with someone else and all
accounts Borrower may open in the future. However, this does not include any IRA or Keogh
accounts, or any trust accounts for which setoff would be prohibited by law. Borrower
authorizes Lender, to the extent permitted by applicable law, to charge or setoff all sums
owing on the debt against any and all such accounts, and, at Lender’s option, to
administratively freeze all such accounts to allow Lender to protect Lender’s charge and
setoff rights provided in this paragraph.

LINE OF CREDIT. This Note evidences a revolving line of credit. Advances under this Note,
as well as directions for payment from Borrower’s accounts, may be requested orally or in
writing by Borrower or by an authorized person. Lender may, but need not, require that all
oral requests be confirmed in writing. Borrower agrees to be liable for all sums either:
(A) advanced in accordance with the instructions of an authorized person or (B) credited
to any of Borrower’s accounts with Lender. The unpaid principal balance owing on this Note
at any time may be evidenced by endorsements on this Note or by Lender’s internal records,
including daily computer print-outs. Lender will have no obligation to advance funds under
this Note if: (A) Borrower or any guarantor is in default under the terms of this Note or
any agreement that Borrower or any guarantor has with Lender, including any agreement made
in connection with the signing of this Note; (B) Borrower or any guarantor ceases doing
business or is insolvent; (C) any guarantor seeks, claims or otherwise attempts to limit,
modify or revoke such guarantor’s guarantee of this Note or any other loan with Lender; (D)
Borrower has applied funds provided pursuant to this Note for purposes other than those
authorized by Lender; or (E) Lender in good faith believes itself insecure.

HEDGING INSTRUMENTS. Obligations and Indebtedness includes, without limitation all
obligations, indebtedness and liabilities arising pursuant to or in connection with any
interest rate swap transaction, basis swap, forward rate transaction, interest rate option,
price risk hedging transaction or any similar transaction between the Borrower and Lender.

UNUSED COMMITMENT FEE:. Borrower shall pay a commitment fee in an amount equal to .05% per
year. The commitment fee shall be calculated on the average daily unused portion of the
Principal Amount from the date of this Promissory Note until the Maturity Date, which shall
be payable at the time interest is payable on the yearly anniversary date of the Promissory
Note.

SUCCESSOR INTERESTS. The terms of this Note shall be binding upon Borrower, and upon
Borrower’s heirs, personal representatives, successors and assigns, and shall inure to the
benefit of Lender and its successors and assigns.

GENERAL PROVISIONS. This Note benefits Lender and its successors and assigns, and binds
Borrower and Borrower’s heirs, successors, assigns, and representatives. If any part of
this Note cannot be enforced, this fact will not affect the rest of the Note. Lender may
delay or forgo enforcing any of its rights or remedies under this Note without losing them.
Borrower and any other person who signs, guarantees or endorses this Note, to the extent
allowed by law, waive presentment, demand for payment, and notice of dishonor. Upon any
change in the terms of this Note, and unless otherwise

 

 

expressly stated in writing, no party who signs this Note, whether as maker, guarantor,
accommodation maker or endorser, shall be released from liability. All such parties agree
that Lender may renew or extend (repeatedly and for any length of time) this loan or release
any party or guarantor or collateral; or impair, fail to realize upon or perfect Lender’s
security interest in the collateral; and take any other action deemed necessary by Lender
without the consent of or notice to anyone. All such parties also agree that Lender may
modify this loan without the consent of or notice to anyone other than the party with whom
the modification is made. The obligations under this Note are joint and several.

PRIOR TO SIGNING THIS NOTE, BORROWER READ AND UNDERSTOOD ALL THE PROVISIONS OF THIS NOTE,
INCLUDING THE VARIABLE INTEREST RATE PROVISIONS. BORROWER AGREES TO THE TERMS OF THE NOTE.

BORROWER ACKNOWLEDGES RECEIPT OF A COMPLETED COPY OF THIS PROMISSORY NOTE.

BORROWER:

	 	 	 	 	 	 	 
	 	 	TOMOTHERAPY INCORPORATED	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Frederick A. Robertson, MD
 

	 	 
	 	 	Frederick A. Robertson, MD,	 	 
	 	 	Chief Executive Officer of Tomotherapy	 	 
	 	 	IncorporatedFIRST AMENDMENT TO EMPLOYMENT AGREEMENT

EXHIBIT 10.40

FIRST AMENDMENT TO EMPLOYMENT AGREEMENT

     This First Amendment to Employment Agreement (“First Amendment”) is executed as of this 12th
day of March, 2009, by and between TomoTherapy Incorporated, a Wisconsin corporation (the
“Company”), and Stephen C. Hathaway, an individual (“Employee”).

RECITALS

     The Employee had previously announced his intention to retire effective March 31, 2009, with
the Employment Agreement entered into between the parties on November 5, 2008 (“Employment
Agreement”) expiring by its terms on that same date.

     The parties now desire to continue Employee’s employment beyond March 31, 2009, until such
time as Employee’s successor is appointed, on the terms and conditions set forth herein.

     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:

	 	1.	 	Article 1.1 of the Employment Agreement is deleted in its entirety and the
following is inserted in its place:
	 
	 	 	 	The Company employs Employee, and Employee accepts employment by the Company, for the
period commencing on the date hereof and continuing on a month-to-month basis, subject
to earlier termination as hereinafter set forth in Article III (the “Employment
Term”). Upon agreement of the parties, or upon thirty days’ prior written notice
of intention by one party to the other of an intention to terminate the Employment
Term, Employee’s employment with the Company, and the Company’s obligations hereunder
shall terminate. In any event, the termination of employment shall be considered a
Termination upon Retirement as set forth in Article 3.1(e), and the requirement of 90
days notice of retirement as required by Article 3.1(e) is not valid.
	 
	 	2.	 	Article 2.2 of the Employment Agreement is deleted in its entirety and the
following is inserted in its place:
	 
	 	 	 	Should Employee’s employment be terminated by agreement of the parties or at the
request of the Company, Employee will be entitled to receive a stay bonus equal to
$140,000 pro-rated by the number of days Employee is employed in calendar year 2009.
Such bonus shall be a lump sum payment

 

 

	 	 	 	made within thirty days of Employee’s last day of work, and shall be paid less any
applicable required payroll deductions. Employee will not be entitled to any bonus if
he terminates employment earlier than agreed to by the Company.

All other provisions of the Employment Agreement are not altered by this First Amendment and remain
in full force and effect.

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

	 	 	 
	EMPLOYEE:

	 	COMPANY:
	Stephen C. Hathaway

	 	TomoTherapy Incorporated
	/s/ Stephen C. Hathaway

	 	By: /s/ Frederick A. Robertson, M.D.
	 

	 	 
	 

	 	Frederick A. Robertson, M.D.
	 

	 	Chief Executive Officer

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