Exploiting the Model Context Protocol: Deep Dive into the GitHub MCP Vulnerability

Introduction In May 2025, security researchers at Invariant Labs disclosed a critical vulnerability in the Model Context Protocol (MCP) integration for GitHub. MCP is a new open protocol that connects large language model (LLM) agents with external tools and data sources in a standardized way. The affected GitHub MCP server (an open-source integration with ~14k stars) enables AI agents to interface with GitHub APIs for tasks like reading repository content, managing issues, and automating workflows. Invariant’s findings show how an attacker can abuse this integration via a prompt injection in a public GitHub issue to hijack an AI agent and leak data from private repositories. This deep dive will examine the MCP architecture, explain how the vulnerability arises, and analyze the real-world risks—ranging from compromised GitHub Actions to supply chain integrity issues—before discussing mitigation strategies for secure MCP use in AI pipelines. MCP Architecture and How It Works What is MCP...