Exhibit 2.1 Execution Version Agreement and Plan of Merger

• Date: 24 February 2021
• Section: Merger Agreements

Exhibit 2.1

Execution Version AGREEMENT AND PLAN OF MERGER DATED AS OF FEBRUARY 24, 2021

AMONG MERCK SHARP & DOHME CORP., PANAMA MERGER SUB, INC. AND PANDION

THERAPEUTICS, INC.

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Table of Contents Page ARTICLE 1 DEFINITIONS; INTERPRETATION 2

SECTION 1.1. Definitions 2 SECTION 1.2. Interpretation 14 ARTICLE 2

THE OFFER 15 SECTION 2.1. The Offer 15 SECTION 2.2. Company Action

18 ARTICLE 3 THE MERGER 19 SECTION 3.1. The Merger 19 SECTION

3.2. Effects of the Merger 19 SECTION 3.3. Closing 19 SECTION 3.4.

Effective Time 19 SECTION 3.5. Surviving Corporation 20 ARTICLE 4

CONSIDERATION; EXCHANGE OF CERTIFICATES 20 SECTION 4.1. Conversion of

Merger Sub Capital Stock 20 SECTION 4.2. Conversion of Company Common

Stock 20 SECTION 4.3. Exchange of Certificates 21 SECTION 4.4.

Company Equity Awards and Warrants 23 SECTION 4.5. Employee Stock Purchase

Plan 24 SECTION 4.6. Further Action 25 SECTION 4.7. Adjustments to

Prevent Dilution 25 SECTION 4.8. Withholding Rights 25 SECTION 4.9.

Appraisal Rights 25 ARTICLE 5 REPRESENTATIONS AND WARRANTIES OF THE

COMPANY 26 SECTION 5.1. Organization 26 SECTION 5.2. Capitalization

27 SECTION 5.3. Authorization; No Conflict 28 SECTION 5.4. Subsidiaries

29 SECTION 5.5. SEC Documents 30 SECTION 5.6. Company Financial

Statements 32 SECTION 5.7. Absence of Material Adverse Effect 33

SECTION 5.8. Proceedings 33 SECTION 5.9. Information Supplied 33

SECTION 5.10. Broker’s or Finder’s Fees 34 SECTION 5.11. Employee Plans

34 SECTION 5.12. Employment Matters 37 SECTION 5.13. Opinion of

Financial Advisor 39 -ii-

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SECTION 5.14. Taxes 39 SECTION 5.15. Environmental Matters 42

SECTION 5.16. Compliance 42 SECTION 5.17. Intellectual Property 43

SECTION 5.18. Material Contracts 47 SECTION 5.19. Regulatory Matters

49 SECTION 5.20. Real Property 52 SECTION 5.21. Insurance 52

SECTION 5.22. Affiliate Transactions 53 SECTION 5.23. Takeover

Provisions 53 SECTION 5.24. Assets 53 SECTION 5.25. Books and

Records 53 SECTION 5.26. Anti-Corruption Compliance 54 SECTION 5.27.

Data Protection 54 SECTION 5.28. Sanctions 55 SECTION 5.29. No Other

Representations or Warranties 56 ARTICLE 6 REPRESENTATIONS AND

WARRANTIES OF PARENT AND MERGER SUB 56 SECTION 6.1. Organization 56

SECTION 6.2. Merger Sub 56 SECTION 6.3. Authorization; No Conflict 56

SECTION 6.4. Information Supplied 57 SECTION 6.5. Sufficient Funds 58

SECTION 6.6. Proceedings 58 SECTION 6.7. Ownership of Company Common

Stock 58 SECTION 6.8. Broker’s or Finder’s Fees 58 SECTION 6.9. No

Other Representations or Warranties 58 ARTICLE 7 COVENANTS 59

SECTION 7.1. Conduct of the Company 59 SECTION 7.2. Employee Matters

63 SECTION 7.3. Further Assurances 65 SECTION 7.4. Public Statements

65 SECTION 7.5. Standard of Efforts; Governmental Approvals 66 SECTION

7.6. Notification of Certain Matters; Other Actions 68 SECTION 7.7.

Access to Information; Confidentiality 69 SECTION 7.8. No Solicitation

70 SECTION 7.9. Indemnification and Insurance 74 SECTION 7.10. Section

16 Matters 76 SECTION 7.11. Transaction Litigation 76 SECTION 7.12.

Deregistration; Stock Exchange Delisting 77 SECTION 7.13. Takeover

Provisions 77 SECTION 7.14. Obligations of Merger Sub 77 SECTION 7.15.

Rule 14d-10 Matters 77 SECTION 7.16. Tax Matters 78 -iii-

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SECTION 7.17. Merger Sub Stockholder Consent 78 ARTICLE 8 CONDITIONS

78 SECTION 8.1. Conditions to Each Party’s Obligation To Effect the Merger

78 ARTICLE 9 TERMINATION 79 SECTION 9.1. Termination 79 SECTION

9.2. Effect of Termination 81 SECTION 9.3. Termination Fee and Expenses

81 ARTICLE 10 GENERAL PROVISIONS 83 SECTION 10.1. Notices 83

SECTION 10.2. Amendments and Waivers 84 SECTION 10.3. Representations

and Warranties 84 SECTION 10.4. Governing Law; Jurisdiction 85 SECTION

10.5. WAIVER OF JURY TRIAL 85 SECTION 10.6. Counterparts; Effectiveness

85 SECTION 10.7. Assignment; Third Party Beneficiaries 85 SECTION 10.8.

Severability 86 SECTION 10.9. Entire Agreement; No Reliance 86 SECTION

10.10. Enforcement 86 SECTION 10.11. Remedies 87 Annex I Offer

Conditions Exhibit A Form of Support Agreement Exhibit B Form of Certificate

of Incorporation of the Surviving Corporation Schedule I Individuals for

Retention Agreements -iv-

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AGREEMENT AND PLAN OF MERGER (this “Agreement”), dated as of February 24, 2021,

among MERCK SHARP & DOHME CORP., a New Jersey corporation (“Parent”), PANAMA

MERGER SUB, INC., a Delaware corporation and a wholly owned subsidiary of Parent

(“Merger Sub”), and PANDION THERAPEUTICS, INC., a Delaware corporation (the

“Company”).

INTRODUCTION

WHEREAS, the respective boards of directors of the Company, Parent and Merger

Sub have approved the acquisition of the Company by Parent on the terms and

subject to the conditions set forth in this Agreement;

WHEREAS, on the terms and subject to the conditions set forth herein, Parent has

agreed to cause Merger Sub to commence a cash tender offer (as it may be

extended, amended and supplemented from time to time as permitted by this

Agreement, the “Offer”) to purchase all of the issued and outstanding shares of

common stock, par value $0.001 per share, of the Company (collectively, the

“Company Common Stock”), other than the Excluded Shares, at a price per share

equal to $60.00 net to the seller in cash, without interest (such amount or any

greater amount per share paid pursuant to the Offer, the “Offer Price”);

WHEREAS, following the consummation of the Offer, the parties intend that Merger

Sub will be merged (the “Merger”) with and into the Company on the terms and

subject to the conditions set forth in this Agreement (with the Merger being

governed by Section 251(h) of the General Corporation Law of the State of

Delaware (the “DGCL”));

WHEREAS, as a condition and inducement to the willingness of Parent and Merger

Sub to enter into this Agreement, certain Stockholders are entering into tender

and support agreements with Parent in substantially the form of Exhibit A

attached hereto (the “Support Agreements”) simultaneously with the execution and

delivery of this Agreement;

WHEREAS, simultaneously with the execution and delivery of this Agreement, the

Company is entering into retention agreements in a form agreed to by Parent with

each of the individuals listed on Schedule I (collectively, the “Retention

Agreements”), the effectiveness of which is contingent upon the Closing; and

WHEREAS, the Company Board has unanimously (i) determined that the Transactions,

including the Offer and the Merger, are advisable, fair to and in the best

interests of the Company and the stockholders of the Company (the

“Stockholders”), (ii) adopted, approved and declared advisable this Agreement

and the Transactions, including the Offer and the Merger, in accordance with the

DGCL, and approved the execution, delivery and performance of the Agreement and

the Transactions, (iii) resolved that the Merger shall be effected pursuant to

Section 251(h) of the DGCL and that the Merger shall be effected as soon as

practicable following the Acceptance Time, and (iv) resolved to recommend that

the Stockholders accept the Offer and tender their shares of Company Common

Stock to Merger Sub in the Offer (the “Company Recommendation”).

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NOW, THEREFORE, in consideration of the foregoing and of the representations,

warranties, covenants and agreements set forth in this Agreement, the parties

agree as follows:

ARTICLE 1 DEFINITIONS; INTERPRETATION

SECTION 1.1. Definitions.

(a) As used in this Agreement, the following terms have the respective meanings