From Tool Connection to Execution Control: Benchmarking Security Invariants in MCP-Style Agent Runtimes

AI agents increasingly call external tools (file system, network, APIs) through the Model Context Protocol (MCP). These tool calls are the agent's syscalls: privileged operations with side effects on shared state, yet today's safety enforcement lives entirely in userspace, where a 10-line script can bypass it. I propose Governed MCP, a kernel-resident tool governance gateway built on a logit-based safety primitive (ProbeLogits). The gateway interposes on every MCP tool call in a 6-layer pipeline: schema validation, trust tier, rate limit, adversarial pre-filter, a ProbeLogits semantic gate (the load-bearing check), and constitutional policy match, with a Blake3-hashed audit chain. I implement Governed MCP in Anima OS, a bare-metal x86-64 kernel in ~286,000 lines of Rust. The five non-inference layers plus the audit append cost a measured 11.3 us per call; the ProbeLogits gate (one probe-prompt prefill plus a single logit read) costs 332-556 ms per classification across Qwen2.5-7B, Llama-3-8B, and Mistral-7B, 2.4-3.4x faster than a Llama Guard 3 pass on the same hardware. A silicon-measured ablation shows that removing the ProbeLogits layer collapses F1 from 0.789 to 0.357 (delta-F1 = -0.432): hand-rule firewalling alone is insufficient. Every WASM-to-system host function and every registered MCP tool is mediated by the kernel gateway, so the 10-line userspace bypass that defeats existing guardrail libraries is structurally impossible; a disclosed set of ring-3 syscall paths remains ungated pending future work. Multi-model validation across three architectures (HarmBench 98-99% non-copyright block, XSTest 98.5-100% unsafe recall, ToxicChat parity with Llama Guard 3) shows the underlying primitive is architecture-agnostic. Governed MCP demonstrates that tool-call governance is feasible as an OS primitive, not just an application-layer concern.

The Model Context Protocol (MCP) standardizes how a large-language-model (LLM) agent and an external tool server exchange messages, but not trust: a host reads a server's self-declared tool list and dispatches calls, with no notion of which servers it may use, at what sensitivity, or which of a server's tools are in bounds. This work grew out of a concrete need -- letting the Enclawed agent use Google's externally-operated MCP servers (Gmail, Calendar, Drive) safely, admitting the server and bounding the tools it may drive, without changing MCP or Enclawed's own tool application-programming interface (API). The mechanism we built, mcp-attested (shipped in both the open enclawed-oss distribution and the enclaved flavor), generalizes: the gap that makes an unmediated third-party connection unsafe for one user makes a regulated deployment impossible to accredit. We close it with three additive mechanisms: (1) a small, offline-signed clearance assertion a server publishes at a well-known Uniform Resource Identifier (URI) and a host verifies against a pinned trust root before any tool dispatch; (2) a deny-by-default per-server tool allowlist, so admitting a server is not trusting its every tool; and (3) a flavor-gated enforcement mode that turns the checks from warnings into hard denials, with every decision written to a tamper-evident audit log. We give the wire format, the verification algorithm, a security analysis, and an LLM-driven adversarial evaluation; we then state the design in normative Request-for-Comments (RFC 2119) form -- schema, verification rules, error registry, well-known registration, and machine-checkable conformance vectors -- so it can be adopted as an MCP addendum rather than reinvented. An unextended host ignores the well-known document and behaves exactly as today.

The Model Context Protocol (MCP) is an open-source standard that allows AI agents to connect to external tools, databases, and services. While this connectivity enables powerful agent capabilities, it also introduces multi-step attacks that existing per-call defenses cannot reliably detect. Attackers can compose individually benign tool invocations into malicious sequences that evade isolated inspection. This paper presents ChainWatch, a sequential detection framework for identifying multi-step attacks in MCP-based AI agent systems. ChainWatch models attack progression using a six-stage kill chain and applies a Hidden Markov Model (HMM) to classify tool-call sequences. Detection rules are triggered when a session exhibits suspicious progression across multiple stages. The framework is supported by a structured threat model covering direct sequential attacks, indirect prompt injection chains, and hybrid multi-stage attacks. A 20-dimensional feature extraction schema captures behavioral signals from tool interactions. We demonstrate the approach using five representative attack scenarios from the security literature, showing how ChainWatch detects attack chains that evade traditional per-call security mechanisms.