10-K/A

 UNITED STATES

 SECURITIES AND EXCHANGE COMMISSION

 Washington, D.C. 20549

 FORM 10-K/A

 (Amendment No. 2)

 (Mark One)

 ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

 For the fiscal year ended December 31, 2023

 or

 TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

 For the transition period from to

 Commission File No. 000-30319

 INNOVIVA, INC.

 (Exact name of registrant as specified in its charter)

 Delaware
(State or other jurisdiction of
incorporation or organization)

 94-3265960
(I.R.S. Employer
Identification No.)

 1350 Old Bayshore Highway, Suite 400
 Burlingame, CA
(Address of principal executive offices)

 94010
(Zip Code)

 Registrant's telephone number, including area code: ( 650) 238-9600

 Title of Each Class

 Trading Symbol(s)

 Name of Each Exchange On Which Registered

 Common Stock $0.01 Par Value

 INVA

 The Nasdaq Stock Market LLC

 SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT: NONE

 Indicate by check mark if the registrant is a well known seasoned issuer, as defined in Rule 405 of the Securities Act. Yes No

 Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act. Yes No

 Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes No

 Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§ 232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes No

 Indicate by check mark whether registrant is a large accelerated filer, an accelerated filer or a non-accelerated filer. See definition of "accelerated filer and large accelerated filer" in Rule 12b-2 of the Exchange Act (Check One):

 Large accelerated filer

 Accelerated filer

 Non accelerated filer

 Smaller reporting company

 Emerging growth company

 If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act.

 Indicate by check mark whether the registrant has filed a report on and attestation to its management's assessment of the effectiveness of its internal control over financial reporting under Section 404(b) of the Sarbanes-Oxley Act (15 U.S.C. 7262(b)) by the registered public accounting firm that prepared or issued its audit report.

 If securities are registered pursuant to Section 12(b) of the Act, indicate by check mark whether the financial statements of the registrant included in the filing reflect the correction of an error to previously issued financial statements.

 Indicate by check mark whether any of those error corrections are restatements that required a recovery analysis of incentive-based compensation received by any of the registrant's executive officers during the relevant recovery period pursuant to §240.10D-1(b).

 Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b 2 of the Exchange Act). Yes No

 The aggregate market value of the voting and non-voting common equity held by non-affiliates of the registrant based upon the closing price of the registrant's Common Stock on The Nasdaq Global Select Market on June 30, 2023 was $ 731,926,690. This calculation does not reflect a determination that persons are affiliates for any other purpose.

 On February 14, 2024, there were 63,227,333 shares of the registrant's Common Stock outstanding.

 DOCUMENTS INCORPORATED BY REFERENCE

 Specified portions of the registrant's definitive Proxy Statement to be issued in conjunction with the registrant's 2023 Annual Meeting of Stockholders, which is expected to be filed not later than 120 days after the registrant's fiscal year ended December 31, 2023, are incorporated by reference into Part III of this Annual Report. Except as expressly incorporated by reference, the registrant's Proxy Statement shall not be deemed to be a part of this Annual Report on Form 10-K.

 EXPLANATORY NOTE

 This Amendment No. 2 on Form 10-K/A (the "Amendment") amends the Annual Report on Form 10-K of Innoviva, Inc. (the "Company") for the year ended December 31, 2023, originally filed on February 29, 2024 (the "Original Filing") and amended on March 4, 2024 on form 10-K/A ("Amendment No.1"), is being filed pursuant to and in compliance with the time requirements of Rule 3-09 of Regulation S-X, to amend Item 15, Exhibits and Financial Statement Schedules, to include the Audited Consolidated Financial Statements of Armata Pharmaceuticals, Inc. ("Armata") at December 31, 2023 and 2022 and for the years then ended and the Consent of Ernst & Young LLP Independent Registered Public Accounting Firm of Armata as Exhibit 99.1 and Exhibit 23.3, respectively. These exhibits were not available at the time of the Original Filing and the Amendment No.1. Additional information on the Audited Consolidated Financial Statements of Armata for the year ended December 31, 2021 can be found in the Company's Amendment No. 1 on Form 10-K/A for the year ended December 31, 2022, filed on March 20, 2023, and is incorporated herein by reference.

 In accordance with applicable Securities and Exchange Commission ("SEC") rules and as required by Rule 12b-15 under the Securities Exchange Act of 1934, as amended, this Amendment includes new certifications from the Company's Principal Executive Officer and Principal Financial Officer dated as of the date of filing of this Amendment.

 This Amendment consists solely of the preceding cover page, this explanatory note, Part IV., Item 15., "Exhibits and Financial Statement Schedules," in its entirety, the Exhibits, the signature page and the new certifications of the Company's Principal Executive Officer and Principal Financial Officer.

 This Amendment does not reflect events occurring after the date of the Original Filing and does not amend or update in any way the disclosures made in the Original Filing, except as described above. In particular, the information included in this Amendment under Part II, Item 8 is identical in all respects to the information included under such caption in the Original Filing and the Amendment No. 1. This Amendment should be read in conjunction with the Original Filing and with the Company's subsequent filings with the SEC.

 ITEM 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES

 (a) The following documents are filed as part of this Amendment No. 2 on Form 10 K/A:

 1. Financial Statements:

 The following financial statements, supplementary data and reports of independent public accountants appear in Part II, Item 8 of the Original Filing and the Amendment No. 1 are incorporated herein by reference:

 Consolidated Balance Sheets as of December 31, 2023 and 2022

 Consolidated Statements of Income for each of the three years in the period ended December 31, 2023

 Consolidated Statements of Comprehensive Income for each of the three years in the period ended December 31, 2023

 Consolidated Statements of Stockholders' Equity for each of the three years in the period ended December 31, 2023

 Consolidated Statements of Cash Flows for each of the three years in the period ended December 31, 2023

 Notes to the Consolidated Financial Statements

 Reports of Independent Registered Public Accounting Firm (PCAOB ID 34), Deloitte & Touche LLP, San Jose, CA

 Report of Independent Registered Public Accounting Firm (PCAOB ID 248)

 2. Financial Statement Schedules:

 All schedules have been omitted because of the absence of conditions under which they are required or because the required information, where material, is shown in the financial statements, financial notes or supplementary financial information.

 (b) Exhibits required by Item 601 of Regulation S K:

 The information required by this Item is set forth on the exhibit index that follows the signature page of this report.

 Exhibits

 Incorporated by Reference

 Filed Herewith

 Exhibit
Number

 Description

 Form

 Exhibit

 Filing
Date/Period
End Date

 2.1

 Agreement and Plan of Merger, dated as of May 23, 2022, by and among Innoviva, Inc., Innoviva Merger Sub, Inc. and Entasis Therapeutics

 2.1

 5/24/2022

 2.2

 Agreement and Plan of Merger, dated as of July 10, 2022, by and among Innoviva, Inc., Innoviva Acquisition Sub, Inc. and La Jolla Pharmaceutical Company

 2.1

 7/11/2022

 3.1

 Amended and Restated Certificate of Incorporation

 8 K

 99.2

 4/28/2016

 3.2

 Amended and Restated Bylaws, amended and restated as of January 1, 2023

 8 K

 3.1

 1/4/2023

 4.1

 Specimen certificate representing the common stock of the registrant

 10 K

 4.1

 12/31/2006

 4.2

 Indenture, dated as of January 24, 2013 by and between Theravance, Inc. and The Bank of New York Mellon Trust Company, N.A., as trustee

 8 K

 4.1

 1/25/2013

 4.3

 Form of 2.125% Convertible Subordinated Note Due 2023 (included in Exhibit 4.4)

 4.2

 1/25/2013

 4.4

 Indenture (including form of Note) with respect to Innoviva's 2.50% Convertible Senior Notes due 2025, dated as of August 7, 2017, between Innoviva and The Bank of New York Mellon Trust Company, N.A., as trustee

 8 K

 4.1

 8/7/2017

 4.5

 Description of Registrant's Securities Registered Pursuant to Section 12 of the Securities Exchange Act of 1934

 4.9

 2/19/2020

 4.6

 Indenture (including form of Note) with respect to Innoviva's 2.125% Convertible Senior Notes due 2028, dated as of March 7, 2022, between Innoviva, Inc. and The Bank of New York Mellon Trust Company, N.A., as trustee

 4.1

 3/8/2022

 10.2

 Collaboration Agreement between the registrant and Glaxo Group Limited, dated as of November 14, 2002

 10 Q

 10.1

 6/30/2014

 10.3

 Amended and Restated Investors' Rights Agreement by and among the registrant and the parties listed therein, dated as of May 11, 2004

 S 1

 10.13

 6/10/2004

 10.4*

 Strategic Alliance Agreement between the registrant and Glaxo Group Limited, dated as of March 30, 2004

 10 K

 10.13

 12/31/2013

 10.5+

 Description of Cash Bonus Program, as amended

 10 K

 10.22

 12/31/2009

 10.6+

 Amendment to Change in Control Severance Plan effective December 16, 2009

 10 K

 10.47

 12/31/2009

 10.7+

 2009 Change in Control Severance Plan adopted December 16, 2009

 10 K

 10.48

 12/31/2009

 10.8

 Second Amendment to Amended and Restated Governance Agreement among the registrant, Glaxo Group Limited, GlaxoSmithKline plc and GlaxoSmithKline LLC, dated as of November 29, 2010

 8 K

 10.2

 11/29/2010

 10.9

 Amendment to Strategic Alliance Agreement, dated October 3, 2011

 10 K

 10.34

 12/31/2011

 10.10+

 2012 Equity Incentive Plan, as approved by the board of directors February 8, 2012 and approved by stockholders May 16, 2012 and forms of equity award

 10 Q

 10.38

 6/30/2012

 10.11

 Base Capped Call Transaction, dated January 17, 2013

 8 K

 10.1

 1/23/2013

 10.12

 Additional Capped Call Transaction, dated January 18, 2013

 8 K

 10.2

 1/23/2013

 10.13

 Master Agreement by and among Theravance, Inc., Theravance Biopharma, Inc. and Glaxo Group Limited, dated March 3, 2014

 8 K/A

 10.1

 3/6/2014

 10.14*

 Collaboration Agreement Amendment by and between Theravance, Inc. and Glaxo Group Limited, dated March 3, 2014

 8 K/A

 10.2

 3/6/2014

 10.15*

 Strategic Alliance Agreement Amendment by and between Theravance, Inc. and Glaxo Group Limited, dated March 3, 2014

 8 K/A

 10.3

 3/6/2014

 10.16

 Transition Services Agreement between Theravance and Theravance Biopharma, dated June 2, 2014

 8 K

 10.2

 6/5/2014

 10.17

 Tax Matters Agreement between Theravance and Theravance Biopharma, dated June 2, 2014

 8 K

 10.3

 6/5/2014

 10.18

 Employee Matters Agreement between Theravance and Theravance Biopharma, dated June 1, 2014

 8 K

 10.4

 6/5/2014

 10.19

 Theravance Respiratory Company, LLC Limited Liability Company Agreement between Theravance and Theravance Biopharma, dated May 31, 2014

 8 K

 10.5

 6/5/2014

 10.20

 Amendment/Clarification to Transition Services Agreement between Theravance and Theravance Biopharma, dated March 2, 2015

 10 Q

 10.64

 3/31/2015

 10.21+

 First Amendment to 2009 Change In Control Severance Plan (Renamed 2009 Severance Plan)

 8 K

 10.2

 7/29/2015

 10.22

 Form of Notice of Performance Based Restricted Stock Award and Restricted Stock Award Agreement under 2012 Equity Incentive Plan (director form)

 10 K

 10.76

 2/23/2018

 10.23+

 Second Amendment to 2009 Severance Plan

 10 Q

 10.81

 7/26/2018

 10.24+

 Offer Letter with Marianne Zhen, dated September 7, 2018

 8 K

 10.1

 9/11/2018

 10.25+

 Offer Letter between Innoviva, Inc. and Pavel Raifeld, dated May 20, 2020

 8 K

 10.1

 5/26/2020

 10.26+

 Offer Letter between Innoviva, Inc. and Pavel Raifeld, dated April 29, 2022

 10.1

 5/2/2022

 10.27

 Strategic Advisory Agreement, dated as of December 11, 2020, by and between Sarissa Capital Management LP and Innoviva, Inc.

 8 K

 10.1

 12/14/2020

 10.28

 Amended and Restated Limited Partnership Agreement of ISP Fund LP, dated as of December 11, 2020, by and among ISP Fund LP, Sarissa Capital Fund GP LP, Innoviva Strategic Partners LLC and the other parties named therein

 8 K

 10.2

 12/14/2020

 10.29

 Share Repurchase Agreement, dated as of May 2021, by and between Innoviva, Inc. and Glaxo Group Limited

 10.1

 5/20/2021

 10.30

 Letter Agreement, dated as of May 20, 2021, by and among Innoviva Strategic Partners LLC, ISP Fund LP and Sarissa Capital Fung GP LP

 10.2

 5/20/2021

 10.31

 Capped Call Confirmation dated March 2, 2022, by and among Innoviva, Inc., Bank of America, N.A., Goldman Sachs & Co. LLC and Deutsche Bank AG, London Branch

 10.1

 3/8/2022

 10.32

 Amendment No. 1 to the Investor Rights Agreement, dated May 23, 2022, by and among Innoviva, Inc. and Entasis Therapeutics Holdings Inc.

 10.1

 5/24/2022

 10.33

 Support Agreement, dated July 10, 2022, by and among Innoviva, Inc., Innoviva Acquisition Sub, Inc., Tang Capital Partners, LP and Kevin C. Tang Foundation

 10.1

 7/11/2022

 10.34

 Equity Purchase Agreement, dated July 13, 2022, by and among Innoviva, Inc., Innoviva TRC Holdings LLC and Royalty Pharma Investments 2019 ICAV

 10.1

 7/13/2022

 10.35

 Third Amendment to Collaboration Agreement, dated July 13, 2022, by and among Innoviva, Inc., Glaxo Group Limited, and Theravance Respiratory Company, LLC.

 10.2

 7/13/2022

 10.36+

 Transition Agreement between Larry Edwards and Innoviva Specialty Therapeutics, Inc., dated February 23, 2023, and Release of Claims form signed by Larry Edwards, dated April 5, 2023

 10.1

 5/9/2023

 10.37

 2023 Employee Stock Purchase Plan

 DEF 14A

 4/28/2023

 10.38+

 Offer Letter between Innoviva, Inc. and Stephen Basso dated July 28, 2023

 10.1

 8/25/2023

 21.1

 List of Subsidiaries

 X**

 23.1

 Consent of Deloitte & Touche LLP, Independent Registered Public Accounting Firm

 X***

 23.2

 Consent of Grant Thornton LLC, Independent Registered Public Accounting Firm

 X**

 23.3

 Consent of Ernst & Young LLP, Independent Registered Public Accounting Firm of Armata Pharmaceuticals, Inc.

 X

 24.1

 Power of Attorney (see signature page to this Annual Report on Form 10 K)

 X**

 31.1

 Certification of Principal Executive Officer Pursuant to Rule 13a 14 under the Securities Exchange Act of 1934

 X

 31.2

 Certification of Principal Financial Officer Pursuant to Rule 13a 14 under the Securities Exchange Act of 1934

 X

 32#

 Certifications Pursuant to 18 U.S.C. Section 1350

 Innoviva Clawback Policy (effective as of October 2, 2023)

 X**

 99.1

 Audited Consolidated Financial Statements of Armata Pharmaceuticals, Inc. at December 31, 2023 and 2022 and for the two years ended December 31, 2023

 X

 99.2

 Amendment No.1 on Form 10-K/A for Innoviva, Inc. for the year ended December 31, 2022, filed on March 20, 2023

 10-K/A

 99.1

 3/20/2023

 101.INS

 X

 101.SCH

 X

 101.CAL

 X

 101.DEF

 X

 101.LAB

 X

 101.PRE

 X

 X

 + Management contract or compensatory plan or arrangement required to be filed pursuant to Item 15(b) of Form 10 K.

 * Confidential treatment has been granted for certain portions which are omitted in the copy of the exhibit electronically filed with the Securities and Exchange Commission. The omitted information has been filed separately with the Securities and Exchange Commission pursuant to Innoviva, Inc.'s application for confidential treatment.

 ** Previously filed with the Original Filing on February 29, 2024

 *** Previously filed with the Amendment No. 1 on March 4, 2024

 # Furnished herewith.

 SIGNATURES

 Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the Registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

 INNOVIVA, INC.

 Date: March 22, 2024

 By:

 /s/ PAVEL RAIFELD
 Pavel Raifeld
Chief Executive Officer