# Governed MCP: Kernel-Level Tool Governance for AI Agents via Logit-Based Safety Primitives

arXiv: https://arxiv.org/abs/2604.16870 · HTML: https://mlsanity.com/paper/2604.16870/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Placed in Agent threats, guardrails and governance, one of 16 directions in LLM agents and tool use.
- Builds on 11 of its 28 references that are in the map.
- First posted on arXiv 18 Apr 2026.

## Placed in

- LLM agents and tool use / [Agent threats, guardrails and governance](https://mlsanity.com/agents/agent-threats-guardrails-and-governance/)

## Builds on (most cited first, 11 of 11)

- [Not what you've signed up for: Compromising Real-World LLM-Integrated Applications with Indirect Prompt Injection](https://mlsanity.com/paper/2302.12173/) (2023)
- [HarmBench: A Standardized Evaluation Framework for Automated Red Teaming and Robust Refusal](https://mlsanity.com/paper/2402.04249/) (2024)
- [Llama Guard: LLM-based Input-Output Safeguard for Human-AI Conversations](https://mlsanity.com/paper/2312.06674/) (2023)
- [XSTest: A Test Suite for Identifying Exaggerated Safety Behaviours in Large Language Models](https://mlsanity.com/paper/2308.01263/) (2023)
- [WildGuard: Open One-Stop Moderation Tools for Safety Risks, Jailbreaks, and Refusals of LLMs](https://mlsanity.com/paper/2406.18495/) (2024)
- [NeMo Guardrails: A Toolkit for Controllable and Safe LLM Applications with Programmable Rails](https://mlsanity.com/paper/2310.10501/) (2023)
- [ToxicChat: Unveiling Hidden Challenges of Toxicity Detection in Real-World User-AI Conversation](https://mlsanity.com/paper/2310.17389/) (2023)
- [Efficient Guided Generation for Large Language Models](https://mlsanity.com/paper/2307.09702/) (2023)
- [AIOS: LLM Agent Operating System](https://mlsanity.com/paper/2403.16971/) (2024)
- [ProbeLogits: Kernel-Level LLM Inference Primitives for AI-Native Operating Systems](https://mlsanity.com/paper/2604.11943/) (2026)
- [Guillotine: Hypervisors for Isolating Malicious AIs](https://mlsanity.com/paper/2504.15499/) (2025)

## Built on by (most cited first, 1 of 1)

- [Elastic Gang: Per-Token Membership Change for a Hard-Barriered LLM Inference Gang Co-Scheduled with OS Processes](https://mlsanity.com/paper/2607.04668/) (2026)

## Abstract (arXiv)

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.