This paper proposes MI9, a runtime governance framework for the safe and responsible deployment of agent-based AI systems, which exhibit unpredictable behavior during execution, unlike existing AI models. MI9 provides real-time control through six integrated components: an agency risk index, agent semantic telemetry collection, continuous permission monitoring, an FSM-based compliance engine, target-conditional deviation detection, and a progressive isolation strategy. Through analysis of various scenarios, we demonstrate the systematic application of MI9 to governance challenges that existing approaches fail to address.