Document:

EX-10.1

 Exhibit 10.1 

Execution Version 
 STOCK
REPURCHASE AGREEMENT 
 This Stock Repurchase Agreement (this “Agreement”) is made and entered into as of
February 3, 2017, by and between Allison Transmission Holdings, Inc., a Delaware corporation (the “Company”), and ValueAct Capital Master Fund, L.P. (the “Seller”). 

RECITALS 
 A. The
Company previously entered into a Cooperation Agreement, dated December 12, 2014 (the “Cooperation Agreement”) with the Seller, VA Partners I, LLC, ValueAct Capital Management, L.P., ValueAct Capital Management, LLC,
ValueAct Holdings, L.P., ValueAct Holdings GP, LLC and Gregory P. Spivy (collectively, the “ValueAct Group”), whereby the Company agreed, at the ValueAct Group’s election, to appoint Mr. Spivy to the Company’s
Board of Directors. 
 B. Mr. Spivy has served as member of the Company’s Board of Directors since his appointment as a
director on May 14, 2015. 
 C. The Company desires to repurchase from the Seller, and the Seller desires to sell to the Company,
a total of 10,525,204 shares of common stock of the Company (the “Shares”) on the terms and conditions set forth in this Agreement. 

D. The Company is permitted, pursuant to Sections 154, 160 and 244 of the General Corporation Law of the State of Delaware
(“DGCL”), its Second Amended and Restated Certificate of Incorporation, as amended, and its Fifth Amended and Restated Bylaws, to repurchase the Shares on the terms and conditions set forth in this Agreement. 

NOW, THEREFORE, for good and valuable consideration, receipt of which is hereby acknowledged, the parties agree as follows. 

1. Purchase and Sale of Shares. Subject to the terms and conditions of this Agreement, the Company
hereby agrees to purchase, and the Seller hereby agrees to sell to the Company, the Shares for a purchase price of $34.50 per share for an aggregate purchase price of $ 363,119,538 (the “Purchase Price”), as provided herein.
 
 2. Closing. The closing of the purchase and sale of the Shares (the “Closing”) shall
occur on February 8, 2017, or such other date thereafter, as is mutually agreed in writing by the Company and the Seller (the “Closing Date”). At the Closing, the following deliveries will be made: 

(a) By the Company. The Company will deliver to the Seller full payment of the Purchase Price, by wire transfer to the bank account
designated by the Seller in writing at least one business day prior to the Closing; and 
 (b) By the Seller. The Seller will deliver
to the Company, in form reasonably acceptable to the Company, such documents as may be reasonably required in order to effect a transfer of the Shares on the books of American Stock Transfer & Trust Company LLC from the Seller to the
Company. 

  

 3. Representations and Warranties of the Company. The Company hereby represents and
warrants to the Seller as follows: 
 (a) The Company is a corporation validly existing under the laws of Delaware and has full legal right
and corporate power and authority to enter into this Agreement and to consummate the transactions provided for herein. 
 (b) The execution,
delivery and performance by the Company of this Agreement has been duly authorized by all requisite corporate action of the Company, and this Agreement, when executed and delivered by both parties, will be a valid and binding agreement of the
Company enforceable against the Company in accordance with its terms. 
 4. Representations, Warranties and Covenants of the
Seller. The Seller hereby represents, warrants and agrees with the Company as follows: 
 (a) The Seller has full legal authority and
capacity to enter into this Agreement, and to consummate the transactions provided for herein. This Agreement, when executed and delivered by both parties, will be a valid and binding agreement of the Seller, enforceable against the Seller in
accordance with its terms. 
 (b) The Seller acknowledges that its designee, Mr. Spivy, is a director of the Company, and that the
Seller has extensive and substantial knowledge regarding the Company, its financial condition and results of operations, including, without limitation, material, non-public and confidential information about the Company’s financial results for
the quarter and year ended December 31, 2016, scheduled for public release on or about February 6, 2017 (the “Upcoming Earnings Release”). The Seller acknowledges that the Upcoming Earnings Release could cause the
market price of the Company’s common stock to increase or decrease and that the Seller has decided to enter into this repurchase transaction on the date hereof without knowing the effect, if any, of the Upcoming Earnings Release on the market
price of the Company’s common stock. The Seller has asked questions of the Company and has made a full evaluation of the risks and merits of this repurchase transaction. The Seller hereby waives any right to additional consideration with
respect to the Shares. 
 (c) The Seller is and at the Closing will be the sole legal owner of and, will hold valid marketable title to, the
Shares, free and clear of any pledge, lien, security interest, encumbrance, claim or equitable or legal interest (collectively, a “Lien”), and the Seller has not granted any rights to or interest in the Shares to any other
person or entity. The Seller further agrees not to sell, transfer, pledge or encumber the Shares or suffer any lien, security interest, claim or equitable or legal interest to attach to the Shares other than pursuant to this Agreement. 

  
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 (d) All consents, approvals, authorizations and orders required for the execution and delivery of
this Agreement and the transfer of the Shares under this Agreement by the Seller have been obtained and are in full force and effect. The Seller has full legal right, power and authority to enter into and perform its obligations under this Agreement
and to transfer the Shares under this Agreement. The execution and delivery of this Agreement by the Seller and the transfer of the Shares under this Agreement by the Seller do not require (except for filings pursuant to Section 16 or
Regulation 13D under the Securities Exchange Act of 1934) any filings with, any governmental authority or court, or body or arbitrator having jurisdiction over the Seller. 

(e) The Seller (a) is a sophisticated person familiar with transactions similar to those contemplated by this Agreement, (b) has
adequate information concerning the business and financial condition of the Company to make an informed decision regarding the transfer of the Shares, (c) has independently and without reliance upon the Company, and based on such information
and the advice of such advisors as the Seller has deemed appropriate, made its own analysis and decision to enter into this Agreement. The Seller acknowledges that none of the Company or its affiliates (other than Mr. Spivy) or agents is acting
as a fiduciary or financial or investment adviser to the Seller, and has not given the Seller any investment advice, opinion or other information on whether the transfer of the Shares is prudent. The Seller understands and acknowledges that the
Company is not making, and has not made, any statement, representation or warranty to the Seller concerning: (i) the fairness or adequacy of the Purchase Price; (ii) the current or likely future value of the Shares; (iii) the markets,
business, products, management, technical or marketing capabilities, financial affairs or prospects of the Company; or (iv) any other matter that has been relied upon by the Seller or the Seller’s legal counsel or advisors in assessing the
value of the Shares or determining whether to enter into this Agreement upon the terms and conditions set forth herein. 
 (f) The Seller
acknowledges that (i) the Company or its affiliates or agents currently may have, and later may come into possession of, information with respect to the Company that is not known to the Seller and that may be material to a decision to transfer
the Shares (“Seller Excluded Information”), (ii) the Seller has determined to transfer the Shares notwithstanding its lack of knowledge of the Seller Excluded Information and (iii) none of the Company or its
affiliates or agents shall have any liability to the Seller, and the Seller waives and releases any claims that it might have against the Company or its affiliates or agents whether under applicable securities laws or otherwise, with respect to the
nondisclosure of the Seller Excluded Information in connection with the transfer of the Shares and the transactions contemplated by this Agreement. The Seller understands that the Company and its affiliates and agents will rely on the accuracy and
truth of the foregoing representations, and the Seller hereby consents to such reliance. 
 (g) The Seller has reviewed with its own tax
advisors the federal, state, local and foreign tax consequences of this sale of the Shares and the transactions contemplated by this Agreement. The Seller is relying solely on such advisors and not on any statements or representations of the
Company, the Company’s counsel, auditor, or any of the Company’s agents. The Seller understands that it (and not the Company) shall be solely responsible for its own tax liability that may arise as a result of this sale of the Shares or
the transactions contemplated by this Agreement. 

  
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 (h) The execution and delivery of, and performance by the Seller of the Seller’s obligations
under, this Agreement do not and will not (i) violate or conflict with in any respect, (A) any provision of law, rule or regulation, (B) any order, judgment or decree of any court or other agency or government applicable to the
Seller, (C) any provision of the Seller’s organizational documents, or (D) any note, bond, mortgage, deed, indenture, lien, instrument, contract, agreement, lease or license, whether written or oral, express or implied, to which the
Seller is a party or by which it is bound, or (ii) conflict with, result in a breach of, or constitute (with due notice or lapse of time, or both) a default under, or result in the creation or imposition of any Lien upon any of the property or
assets of the Seller pursuant to any note, bond, mortgage, deed, indenture, lien, instrument, contract, agreement, lease or license, whether written or oral, express or implied, to which the Seller is a party or by which it is bound. 

(i) There is no action, suit, proceeding or investigation pending or, to the Seller’s knowledge, currently threatened that questions the
validity of this Agreement, or the right of the Seller to enter into this Agreement or to consummate the transactions contemplated by this Agreement. There are presently no outstanding judgments, decrees or orders of any court or any governmental or
administrative agency against the Seller, which questions the validity of this Agreement or the right of the Seller to consummate the transactions contemplated by this Agreement. 

(j) To the knowledge of Seller, no event has occurred that would have a material and adverse effect on the assets, business, prospects,
financial condition, or results of operations of the Company. 
 5. Conditions of the Seller’s Obligations at Closing. The
obligation of the Seller to sell the Shares is subject to the fulfillment, on or before the Closing, of each of the following conditions, unless otherwise waived: 

(a) The representations and warranties contained in Section 3 shall be true and correct in all respects as of the Closing. 

(b) The Company shall have performed and complied with all covenants, agreements, obligations and conditions contained in this Agreement that
are required to be performed or complied with by the Company on or before the Closing. 
 (c) No government, court, tribunal, arbitrator,
administrative agency, commission or other governmental official, authority or instrumentality shall have enacted, issued, promulgated, enforced or entered any statute, rule, regulation, executive order, decree, injunction, order or other legal
restraint (whether temporary, preliminary or permanent) which is in effect and which has the effect of making the sale of the Shares by the Seller illegal or otherwise prohibiting or preventing consummation of the sale of the Shares by the Seller.

  
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 6. Conditions of the Company’s Obligations at Closing. The obligation of the
Company to purchase the Shares is subject to the fulfillment, on or before the Closing, of each of the following conditions, unless otherwise waived: 

(a) The representations and warranties contained in Section 4 shall be true and correct in all respects as of the Closing. 

(b) The Seller shall have performed and complied with all covenants, agreements, obligations and conditions contained in this Agreement that
are required to be performed or complied with by the Seller on or before the Closing. 
 (c) No government, court, tribunal, arbitrator,
administrative agency, commission or other governmental official, authority or instrumentality shall have enacted, issued, promulgated, enforced or entered any statute, rule, regulation, executive order, decree, injunction, order or other legal
restraint (whether temporary, preliminary or permanent) which is in effect and which has the effect of making the purchase of the Shares by the Company illegal or otherwise prohibiting or preventing consummation of the purchase of the Shares by the
Company. 
 7. Termination. This Agreement shall terminate and the term and conditions set forth herein shall be of no further
force or effect (i) upon mutual agreement in writing by the Company and the Seller or (ii) February 15, 2017, provided the Closing has not occurred by such date. 

8. Covenant Against Transfer. Seller covenants that, upon signing this Agreement, it will not take any action to transfer the
Shares to a third party or otherwise take any action to subject the Shares to any Lien. 
 9. Further Assurances. Subject to
the terms and conditions of this Agreement, each party will use its best efforts to take, or cause to be taken, all actions and to do, or cause to be done, all things necessary or desirable under applicable laws and regulations to consummate the
transactions contemplated by this Agreement. 
 10. Legal and Equitable Remedies. The Company has the right to enforce this
Agreement and any of its provisions by injunction, specific performance or other equitable relief without prejudice to any other rights or remedies the Company may have at law or in equity for breach of this Agreement. 

11. Attorneys’ Fees. Each party will pay its own legal and other fees in connection with the negotiation and preparation of
this Agreement; provided that if any action is brought to enforce the terms of this Agreement, the prevailing party will be entitled to recover its reasonable attorneys’ fees, costs and expenses from the other party, in addition to any
other relief to which the prevailing party may be entitled. 

  
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 12. Entire Agreement. This Agreement constitutes the entire agreement between the
Company and the Seller with respect to the subject matter hereof and supersedes all prior negotiations and agreements, whether written or oral, relating to such subject matter. The Seller acknowledges that neither the Company nor its agents or
attorneys have made any promise, representation or warranty whatsoever, either express or implied, written or oral, which is not contained in this Agreement for the purpose of inducing the Seller to execute this Agreement, and the Seller
acknowledges that it has executed this Agreement in reliance only upon such promises as are contained herein. 
 13.
Modification. It is expressly agreed that this Agreement may not be altered, amended, modified or otherwise changed in any respect except by another written agreement that specifically refers to this Agreement, executed by each of the
parties to this Agreement. 
 14. Severability. If any provision of this Agreement, or any part of any such provision, is held
under any circumstances to be invalid or unenforceable in any jurisdiction, then (a) such provision or part thereof shall, with respect to such circumstances and in such jurisdiction, be deemed amended to conform to applicable laws so as to be
valid and enforceable to the fullest possible extent, (b) the invalidity or unenforceability of such provision or part thereof under such circumstances and in such jurisdiction shall not affect the validity or enforceability of such provision
or part thereof under any other circumstances or in any other jurisdiction, and (c) such invalidity or unenforceability of such provision or part thereof shall not affect the validity or enforceability of the remainder of such provision or the
validity or enforceability of any other provision of this Agreement and is separable from every other part of such provision. 
 15.
Governing Law. This Agreement will be governed by the laws of the State of New York without regard to conflicts of laws principles. 

16. Counterparts. This Agreement may be executed in any number of counterparts, each of which will be an original, but all of
which together will constitute one instrument. 
 17. Headings. The headings contained in this Agreement are included for
purposes of convenience only, and do not affect the meaning or interpretation of this Agreement. 
 [Remainder of Page Intentionally Left
Blank] 

  
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 IN WITNESS WHEREOF, the parties have executed this Stock Repurchase Agreement as of the date
first written above. 
  

			
	COMPANY:
	
	ALLISON TRANSMISSION HOLDINGS, INC.
		
	By:	 	 /s/ Eric C. Scroggins

	Name:	 	Eric C. Scroggins
	Title:	 	Vice President, General Counsel & Secretary
	
	SELLER:
	
	 VALUEACT CAPITAL MASTER FUND L.P.

  

by VA Partners I, LLC, its General Partner

		
	By:	 	 /s/ Bradley E. Singer

	Name:	 	Bradley E. Singer
	Title:	 	Chief Operating OfficerExhibit 10.1

 

AMENDMENT TO WARRANT AGREEMENT

 

ONCOBIOLOGICS, INC.

 

AND

 

AMERICAN STOCK TRANSFER & TRUST COMPANY,
LLC, AS WARRANT AGENT

 

THIS AMENDMENT, dated
February 6, 2017 (“Amendment”), to the Warrant Agreement, dated as of May 18, 2016 (the “Warrant
Agreement”), by and between Oncobiologics, Inc., a Delaware corporation (the “Company”),
and American Stock Transfer & Trust Company, LLC, a New York limited liability trust company, as Warrant Agent (the “Warrant
Agent”).

 

WHEREAS, the Company
and the Warrant Agent entered into that certain Warrant Agreement relating to, among other things, the issuance of Series A warrants
to purchase shares of the Company’s common stock at an exercise price of $6.60 per share (the “Series A Warrants”);
and

 

WHEREAS, pursuant to
Section 8.9 of the Warrant Agreement, the Company and the Warrant Agent have agreed to amend the Warrant Agreement to extend the
period for exercising the Warrants from February 18, 2017 to February 18, 2018.

 

NOW, THEREFORE, in
consideration of the mutual agreements herein contained, the Company and the Warrant Agent agree as follows:

 

		1.	Amendments.

 

		a.	Section 3.3.1 of the Warrant Agreement is amended and restated as follows:

 

		“3.3.1	Series A Warrants. Each Series A Warrant may be exercised, in whole or in part, at any time during the period commencing
on the Detachment Date and ending at 5:00pm New York City time on February 18, 2018.”

 

		b.	The first sentence of Section 3.3.3 of the Warrant Agreement is amended and restated as follows:

 

“For purposes of this
Agreement, the term “Expiration Date” means February 18, 2018 with respect to the Series A Warrants and May 18, 2018
with respect to the Series B Warrants and the term “Exercise Period” means the period during which the Series A Warrant
or Series B Warrant, as the case may be, is exercisable, as described in subsection 3.1, 3.3.1 or 3.3.2 hereof.”

 

		2.	Counterparts. This Amendment may be executed in any number of original or facsimile counterparts
and each of such counterparts shall for all purposes be deemed to be an original, and all such counterparts shall together constitute
but one and the same instrument.

 

[Signature page follows]

 

     

     

    

 

IN WITNESS WHEREOF, the parties hereto have
caused this Amendment to be duly executed as of the date first above written.

 

	 	COMPANY:
	 	 
	 	Oncobiologics, Inc.
	 	 	 
	 	By:	 /s/ Pankaj Mohan, Ph.D.
	 	 	Name: Pankaj Mohan, Ph.D.
	 	 	Title: President and Chief Executive Officer
	 	 
	 	WARRANT AGENT:
	 	 
	 	American Stock Transfer & Trust Company, LLC
	 	 	 
	 	By:	/s/ Jennifer Donovan
	 	 	Name: Jennifer Donovan
	 	 	Title: Senior Vice President Relationship Management

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