Stealth BioTherapeutics : Investor Presentation - October 2022

Leading

Mitochondrial

Medicine

October 2022

1

Forward-Looking Statements

This presentation and various remarks we make during this presentation contain forward-looking statements within the meaning of The Private Securities Litigation Reform Act of 1995. Such forward-looking statements include those regarding Stealth BioTherapeutics' plans, strategies and expectations for its preclinical and clinical advancement of its drug development programs, including its ongoing clinical trials of elamipretide and planned clinical trial of SBT-272; its expectations regarding regulatory interactions,; the potential benefits of Stealth BioTherapeutics' product candidates; its key milestones for 2022; and its plans regarding future data presentations. Statements that are not historical facts, including statements about Stealth BioTherapeutics' beliefs, plans and expectations, are forward-looking statements. The words "anticipate," "expect," "hope," "plan," "potential," "possible," "will," "believe," "estimate," "intend," "may," "predict," "project," "would" and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. Stealth BioTherapeutics may not actually achieve the plans, intentions or expectations disclosed in these forward-looking statements, and you should not place undue reliance on these forward-looking statements. Actual results or events could differ materially from the plans, intentions and expectations disclosed in the forward-looking statements as a result of known and unknown risks, uncertainties and other important factors, including: Stealth BioTherapeutics' ability to obtain additional funding and to continue as a going concern; the impact of the COVID-19 pandemic; the ability to successfully demonstrate the efficacy and safety of Stealth BioTherapeutics' product candidates and future product candidates; the preclinical and clinical results for Stealth BioTherapeutics' product candidates, which may not support further development and marketing approval; the potential advantages of Stealth BioTherapeutics' product candidates; the content and timing of decisions made by the FDA, the EMA or other regulatory authorities, investigational review boards at clinical trial sites and publication review bodies, which may affect the initiation, timing and progress of preclinical studies and clinical trials of Stealth BioTherapeutics product candidates; the possibility that the FDA will not file the Barth NDA; Stealth BioTherapeutics' ability to obtain and maintain requisite regulatory approvals and to enroll patients in its planned clinical trials; unplanned cash requirements and expenditures; competitive factors; Stealth BioTherapeutics' ability to obtain, maintain and enforce patent and other intellectual property protection for any product candidates it is developing; and general economic and market conditions. These and other risks are described in greater detail under the caption "Risk Factors" included in the Stealth BioTherapeutics' most recent Annual Report on Form 20-F filed with the Securities and Exchange Commission ("SEC"), as well as in any future filings with the SEC. Forward-looking statements represent management's current expectations and are inherently uncertain. Except as required by law, Stealth BioTherapeutics does not undertake any obligation to update forward-looking statements made by us to reflect subsequent events or circumstances.

© 2022 Stealth BioTherapeutics 2

© 2022 Stealth BioTherapeutics 3

Key Messages

Late-stage with Strong Platform Potential and Multiple Near-term Inflection Points

• Significant platform potential in common age-related and rare diseases
• • Strategy is to partner common disease programs and own US rare disease opportunities
  • Late-stageprograms have been de-risked by clinical learnings and enrichment strategies
• Multiple near-term value inflection points with late stage elamipretide development programs
• Deep pipeline of novel compounds supports expansion and growth

Allen et al. Nature Comms Biol 2020

H1 2023

• Barth - NDA & partner-ready
• PMM - P3 enrollment complete
• Dry AMD - partner-ready
• Friedreich's ataxia - IND-ready
• SBT-272 - IND-ready

H2 2023

• Barth - pending approval
• PMM - P3 read-out imminent
• Dry AMD - partnership
• SBT-272 - partner-ready;P2-ready

2024

• Barth - approval, voucher sale & launch
• PMM - NDA submission
• Friedreich's ataxia, DMD - P2 initiation
• SBT-272 - P2 initiation

© 2022 Stealth BioTherapeutics 4

Unlocking Therapeutic Potential in Mitochondrial Disease

Wholly Owned Clinical Programs Targeting Unmet Need in Ophthalmology, Orphan Diseases and Neurology

Elamipretide Demonstrated Evidence of Clinical Activity

• Dry age-related macular degeneration (AMD) with Geographic Atrophy (GA)
• Primary Mitochondrial Myopathy due to nuclear DNA mutations (nPMM)
• Barth syndrome

Product Candidates Granted Multiple Regulatory Designations

• Fast Track Designation:
• • Elamipretide: dry AMD with GA, nPMM, Barth syndrome
• Orphan Drug Designation:
• • Elamipretide: nPMM, Barth syndrome, Friedreich's ataxia, DMD
  • SBT-272:amyotrophic lateral sclerosis (ALS)
• Rare Pediatric Designation:
• • Elamipretide: Barth syndrome

Anticipated Near-Term Milestones

• Define regulatory path in dry
  AMD
• Conduct Barth syndrome natural history analyses to inform post-marketing trial design; potential post- marketing trial initiation H1 2023; potential NDA submission H2 2023
• File IND for SBT-272 for ALS (H1 2023)
• Interim data in Friedreich's ataxia P2a trial to inform IND submission H1 2023

Advancing Next-Generation Compounds for CNS Disease

• Phase 1 data for SBT-272 expected YE 2022
• Plan to initiate Phase 2 study of SBT-272 in ALS in 2024
• Progressing SBT-550 series toward pre-IND enabling studies

© 2022 Stealth BioTherapeutics 5