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

 

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      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