When the Agent Becomes the Kernel: A Systematization of Security on the Path to AI-Native Operating Systems

Large language model agents are now privileged principals that take consequential actions: editing code repositories, operating inboxes, completing purchases. Their authority is kernel-grade, but it comes without what classical systems security requires: a trusted mediator interposed on every access. Operating-system vendors are now rebuilding the platform around this de-facto agent kernel, inheriting complete mediation as a design problem. We systematize the security of such systems around a single distinction: a crossing mediated over provenance admits a deterministic check, while one over content semantics does not. A trust-boundary taxonomy locates where mediation must occur and isolates the central mediation gap at two kinds of semantic judgment: distinguishing data from instruction in untrusted input, and an authorized action from an unauthorized one. We argue that this gap leaves an irreducible residual of undetected attacks wherever inputs and actions are not restricted in advance to an enumerated set. The same distinction makes attack-success statistics actionable, placing each number on a spectrum from deployment debt (a sound deterministic mediator left unused) to a structural gap (no such mediator known). We systematize defenses across runtime monitoring, architectural separation, and authorization, and show that current evaluations tend to overstate deployed security through evaluation-validity failures. Finally, we carry that analysis forward beyond the de-facto kernel, to an architecture in which the model itself becomes the arbitration core, and derive the design constraints, open challenges, and research agenda for a security-first AI-native OS.