The Model Context Protocol (MCP) standardizes tool use for LLM-based agents and enable third-party servers. This openness introduces a security misalignment: agents implicitly trust tools exposed by potentially untrusted MCP servers. However, despite its excellent utility, existing agents typically offer limited validation for third-party MCP servers. As a result, agents remain vulnerable to MCP-based attacks that exploit the misalignment between agents and servers throughout the tool invocation lifecycle. In this paper, we propose MCPShield as a plug-in security cognition layer that mitigates this misalignment and ensures agent security when invoking MCP-based tools. Drawing inspiration from human experience-driven tool validation, MCPShield assists agent forms security cognition with metadata-guided probing before invocation. Our method constrains execution within controlled boundaries while cognizing runtime events, and subsequently updates security cognition by reasoning over historical traces after invocation, building on human post-use reflection on tool behavior. Experiments demonstrate that MCPShield exhibits strong generalization in defending against six novel MCP-based attack scenarios across six widely used agentic LLMs, while avoiding false positives on benign servers and incurring low deployment overhead. Overall, our work provides a practical and robust security safeguard for MCP-based tool invocation in open agent ecosystems.

The evolution of Large Language Models (LLMs) has resulted in a paradigm shift towards autonomous agents, necessitating robust security against Prompt Injection (PI) vulnerabilities where untrusted inputs hijack agent behaviors. This SoK presents a comprehensive overview of the PI landscape, covering attacks, defenses, and their evaluation practices. Through a systematic literature review and quantitative analysis, we establish taxonomies that categorize PI attacks by payload generation strategies (heuristic vs. optimization) and defenses by intervention stages (text, model, and execution levels). Our analysis reveals a key limitation shared by many existing defenses and benchmarks: they largely overlook context-dependent tasks, in which agents are authorized to rely on runtime environmental observations to determine actions. To address this gap, we introduce AgentPI, a new benchmark designed to systematically evaluate agent behavior under context-dependent interaction settings. Using AgentPI, we empirically evaluate representative defenses and show that no single approach can simultaneously achieve high trustworthiness, high utility, and low latency. Moreover, we show that many defenses appear effective under existing benchmarks by suppressing contextual inputs, yet fail to generalize to realistic agent settings where context-dependent reasoning is essential. This SoK distills key takeaways and open research problems, offering structured guidance for future research and practical deployment of secure LLM agents.