Document:

EX-4.1

 Exhibit 4.1 

SECOND SUPPLEMENTAL INDENTURE 

(TO FIRST LIEN INDENTURE) 

THIS SECOND SUPPLEMENTAL INDENTURE (this “Second Supplemental Indenture”) is dated as of January 29, 2013, and
has been entered into by and between Horizon Lines, LLC, a Delaware limited liability company, having its principal office at 4046 Colony Road, Suite 200, Charlotte, North Carolina 28211 (the “Company”), the guarantors listed on the
signature pages hereto (the “Guarantors”) and U.S. Bank National Association, as trustee (the “Trustee”) and collateral agent. 

RECITALS 
 WHEREAS,
the Company, the Guarantors and the Trustee previously entered into that certain indenture dated as of October 5, 2011 (as supplemented by that certain first supplemental indenture dated as of April 9, 2012, the
“Indenture”), providing for the issuance of the Company’s 11.00% First Lien Senior Secured Notes due 2016 (the “Notes”);  

WHEREAS, Section 11.01 of the Indenture provides that the Company may (a) cure any ambiguity, omission, defect or
inconsistency that does not adversely affect Holders in any material respect or (b) make any change that would provide any additional rights or benefits to the Holders of Notes or that does not adversely affect the legal rights under the
Indenture of any such Holder in any material respect without the consent of the Noteholders; 
 WHEREAS, the Company desires
to amend certain provisions of the Indenture, as set forth in Article I of this Second Supplemental Indenture; and 
 WHEREAS,
all acts and requirements necessary to make this Second Supplemental Indenture the legal, valid and binding obligation of the Company and the Guarantors have been done. 

AGREEMENT 
 NOW,
THEREFORE, in consideration of the premises and the covenants and agreements contained herein, and for other good and valuable consideration the receipt of which is hereby acknowledged, and for the equal and proportionate benefit of the
Holders of the Notes, the Company and the Trustee hereby agree as follows: 
 ARTICLE I 

AMENDMENTS TO INDENTURE 

Section 1.01 Amendment to Section 4.12 of the Indenture. The second sentence of clause (e) of
Section 4.12 of the Indenture is hereby amended and restated in its entirety to read as follows: 
 In
addition, any Net Proceeds received by Parent or its Restricted Subsidiaries in excess of $60.0 million in the aggregate after the Issue Date that are not applied under clause (iv) of Section 4.12(b) (in the case of Net Proceeds in respect
of Notes Priority Collateral) or under clause (i) of Section 4.12(c) (in the case of other Net Proceeds) shall be deemed to be Excess Proceeds, to the extent not applied to such permanent repayment, prepayment, repurchase or other
retirement for value within 60 days after receipt thereof (which time period shall be extended during the pendency of any offers using such Net Proceeds that are required to be conducted by the “Asset Sale” or similar provisions of any
Senior Lien Debt or an ABL Facility). 

 ARTICLE II 

MISCELLANEOUS 

Section 2.01 Instruments To Be Read Together. This Second Supplemental Indenture is executed as and shall constitute an
indenture supplemental to and in implementation of the Indenture, and the Indenture and this Second Supplemental Indenture shall henceforth be read together. This Second Supplemental Indenture shall form a part of the Indenture for all purposes, and
every Holder of Notes shall be bound hereby and thereby. 
 Section 2.02 Confirmation. The Indenture as amended
and supplemented by this Second Supplemental Indenture is in all respects confirmed and preserved. 
 Section 2.03
Terms Defined. Capitalized terms used in this Second Supplemental Indenture and not otherwise defined herein shall have the meanings assigned to such terms in the Indenture. 

Section 2.04 Trust Indenture Act Controls. If any provision of this Second Supplemental Indenture limits, qualifies or
conflicts with another provision that is required to be included in this Second Supplemental Indenture or the Indenture by the Trust Indenture Act of 1939, as amended, as in force at the date that this Second Supplemental Indenture is executed, the
provisions required by the Trust Indenture Act of 1939 shall control. 
 Section 2.05 Headings. The headings of
the Articles and Sections of this Second Supplemental Indenture have been inserted for convenience of reference only, and are not to be considered a part hereof and shall in no way modify or restrict any of the terms and provisions hereof.

 Section 2.06 Governing Law. The internal law of the State of New York shall govern this Second Supplemental
Indenture without giving effect to applicable principles of conflicts of law to the extent that the application of the laws of another jurisdiction would be required thereby. 

Section 2.07 Counterparts. This Second Supplemental Indenture may be executed in any number of counterparts, each of which
so executed shall be deemed to be an original, but all such counterparts shall together constitute but one and the same instrument. 

Section 2.08 Effectiveness; Termination. The provisions of this Second Supplemental Indenture will become effective
immediately upon its execution by the Trustee in accordance with the provisions of Section 11.03 of the Indenture; provided, that the amendments to the Indenture set forth in Section 1.01 of this Second Supplemental Indenture shall become
operative as specified in Section 1.01 hereof.  
 Section 2.09 Acceptance by Trustee. The Trustee accepts
the amendments to the Indenture effected by this Second Supplemental Indenture and agrees to execute the trusts created by the Indenture as hereby amended, but only upon the terms and conditions set forth in the Indenture. 

Section 2.10 Responsibility of Trustee. The recitals contained herein shall be taken as the statements of the Company, and the
Trustee assumes no responsibility for their correctness. The Trustee makes no representations as to the validity or sufficiency of this Second Supplemental Indenture. 

  
 2 

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

			
	HORIZON LINES, LLC
		
	By:	 	 /s/ Michael F. Zendan II

	Name:	 	Michael F. Zendan II
	Title:	 	Secretary
	
	HORIZON LINES, Inc.
	HORIZON LINES HOLDING CORP.
	HAWAII STEVEDORES, INC.
	HORIZON LINES OF PUERTO RICO, INC.
	HORIZON LINES OF ALASKA, LLC
	HORIZON LINES OF GUAM, LLC
	HORIZON LINES VESSELS, LLC
	H-L DISTRIBUTION SERVICE, LLC
	HORIZON LOGISTICS, LLC
	AERO LOGISTICS, LLC
	SEA-LOGIX, LLC
	HORIZON SERVICES GROUP, LLC
		
	By:	 	 /s/ Michael F. Zendan II

	Name:	 	Michael F. Zendan II
	Title:	 	Secretary

 [Signature Page to Second Supplemental Indenture (First Lien Indenture)] 

 
			
	U.S. BANK NATIONAL ASSOCIATION,
	as Trustee and Collateral Agent
		
	By:	 	 /s/ K. Wendy Kumar

		
	Name:	 	 K. Wendy Kumar

		
	Title:	 	 Vice President

 [Signature Page to Second Supplemental Indenture (First Lien Indenture)]EX-4.2

 Exhibit 4.2 

THIRD SUPPLEMENTAL INDENTURE 

(TO SECOND LIEN INDENTURE) 

THIS THIRD SUPPLEMENTAL INDENTURE (this “Third Supplemental Indenture”) is dated as of January 29, 2013, and has
been entered into by and between Horizon Lines, LLC, a Delaware limited liability company, having its principal office at 4046 Colony Road, Suite 200, Charlotte, North Carolina 28211 (the “Company”), the guarantors listed on the
signature pages hereto (the “Guarantors”) and U.S. Bank National Association, as trustee (the “Trustee”) and collateral agent. 

RECITALS 
 WHEREAS,
the Company, the Guarantors and the Trustee previously entered into that certain indenture dated as of October 5, 2011 (as supplemented by that certain first supplemental indenture dated as of April 9, 2012, and that certain second
supplemental indenture dated as of July 17, 2012, the “Indenture”), providing for the issuance of the Company’s Second Lien Senior Secured Notes due 2016 (the “Notes”);  

WHEREAS, Section 11.01 of the Indenture provides that the Company may (a) cure any ambiguity, omission, defect or
inconsistency that does not adversely affect Holders in any material respect or (b) make any change that would provide any additional rights or benefits to the Holders of Notes or that does not adversely affect the legal rights under the
Indenture of any such Holder in any material respect without the consent of the Noteholders; 
 WHEREAS, the Company desires
to amend certain provisions of the Indenture, as set forth in Article I of this Third Supplemental Indenture; and 
 WHEREAS,
all acts and requirements necessary to make this Third Supplemental Indenture the legal, valid and binding obligation of the Company and the Guarantors have been done. 

AGREEMENT 
 NOW,
THEREFORE, in consideration of the premises and the covenants and agreements contained herein, and for other good and valuable consideration the receipt of which is hereby acknowledged, and for the equal and proportionate benefit of the
Holders of the Notes, the Company and the Trustee hereby agree as follows: 
 ARTICLE I 

AMENDMENTS TO INDENTURE 

Section 1.01 Amendment to Section 4.12 of the Indenture. The second sentence of clause (e) of
Section 4.12 of the Indenture is hereby amended and restated in its entirety to read as follows: 
 In
addition, any Net Proceeds received by Parent or its Restricted Subsidiaries in excess of $60.0 million in the aggregate after the Issue Date that are not applied under clause (iv) of Section 4.12(b) (in the case of Net Proceeds in respect
of Notes Priority Collateral) or under clause (i) of Section 4.12(c) (in the case of other Net Proceeds) shall be deemed to be Excess Proceeds, to the extent not applied to such permanent repayment, prepayment, repurchase or other
retirement for value within 60 days after receipt thereof (which time period shall be extended during the pendency of any offers using such Net Proceeds that are required to be conducted by the “Asset Sale” or similar provisions of any
Senior Lien Debt or an ABL Facility). 

 ARTICLE II 

MISCELLANEOUS 

Section 2.01 Instruments To Be Read Together. This Third Supplemental Indenture is executed as and shall constitute an
indenture supplemental to and in implementation of the Indenture, and the Indenture and this Third Supplemental Indenture shall henceforth be read together. This Third Supplemental Indenture shall form a part of the Indenture for all purposes, and
every Holder of Notes shall be bound hereby and thereby. 
 Section 2.02 Confirmation. The Indenture as amended
and supplemented by this Third Supplemental Indenture is in all respects confirmed and preserved. 
 Section 2.03
Terms Defined. Capitalized terms used in this Third Supplemental Indenture and not otherwise defined herein shall have the meanings assigned to such terms in the Indenture. 

Section 2.04 Trust Indenture Act Controls. If any provision of this Third Supplemental Indenture limits, qualifies or
conflicts with another provision that is required to be included in this Third Supplemental Indenture or the Indenture by the Trust Indenture Act of 1939, as amended, as in force at the date that this Third Supplemental Indenture is executed, the
provisions required by the Trust Indenture Act of 1939 shall control. 
 Section 2.05 Headings. The headings of
the Articles and Sections of this Third Supplemental Indenture have been inserted for convenience of reference only, and are not to be considered a part hereof and shall in no way modify or restrict any of the terms and provisions hereof.

 Section 2.06 Governing Law. The internal law of the State of New York shall govern this Third Supplemental
Indenture without giving effect to applicable principles of conflicts of law to the extent that the application of the laws of another jurisdiction would be required thereby. 

Section 2.07 Counterparts. This Third Supplemental Indenture may be executed in any number of counterparts, each of which
so executed shall be deemed to be an original, but all such counterparts shall together constitute but one and the same instrument. 

Section 2.08 Effectiveness; Termination. The provisions of this Third Supplemental Indenture will become effective
immediately upon its execution by the Trustee in accordance with the provisions of Section 11.03 of the Indenture; provided, that the amendments to the Indenture set forth in Section 1.01 of this Third Supplemental Indenture shall become
operative as specified in Section 1.01 hereof.  
 Section 2.09 Acceptance by Trustee. The Trustee accepts
the amendments to the Indenture effected by this Third Supplemental Indenture and agrees to execute the trusts created by the Indenture as hereby amended, but only upon the terms and conditions set forth in the Indenture. 

Section 2.10 Responsibility of Trustee. The recitals contained herein shall be taken as the statements of the Company, and the
Trustee assumes no responsibility for their correctness. The Trustee makes no representations as to the validity or sufficiency of this Third Supplemental Indenture. 

  
 2 

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

			
	HORIZON LINES, LLC
		
	By:	 	 /s/ Michael F. Zendan II

	Name:	 	Michael F. Zendan II
	Title:	 	Secretary
	
	HORIZON LINES, Inc.
	HORIZON LINES HOLDING CORP.
	HAWAII STEVEDORES, INC.
	HORIZON LINES OF PUERTO RICO, INC.
	HORIZON LINES OF ALASKA, LLC
	HORIZON LINES OF GUAM, LLC
	HORIZON LINES VESSELS, LLC
	H-L DISTRIBUTION SERVICE, LLC
	HORIZON LOGISTICS, LLC
	AERO LOGISTICS, LLC
	SEA-LOGIX, LLC
	HORIZON SERVICES GROUP, LLC
		
	By:	 	 /s/ Michael F. Zendan II

	Name:	 	Michael F. Zendan II
	Title:	 	Secretary

 [Signature Page to Third Supplemental Indenture (Second Lien Indenture)] 

 
			
	U.S. BANK NATIONAL ASSOCIATION,
	as Trustee and Collateral Agent
		
	By:	 	 /s/ K. Wendy Kumar

		
	Name:	 	 K. Wendy Kumar

		
	Title:	 	 Vice President

 [Signature Page to Third Supplemental Indenture (Second Lien Indenture)]

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