Abstract: A protocol-layer governance system is disclosed for controlling execution of autonomous computational processes at the session layer. The system establishes a non-bypassable enforcement sequence in which behavioral qualification, authorization token issuance, directive propagation, and execution reconciliation occur in a fixed, canonical order. A protocol enforcement boundary ensures that execution requests cannot proceed unless derived from a verified protocol session state, and authorization is bound to behavioral qualification rather than identity or policy inference. The system generates immutable execution lineage records and prevents replay, substitution, privilege escalation, reordering, or parallel execution outside the defined sequence.