We are interested in providing an agent infrastructure for truly distributed control. Requirements include multiple language implementations, so that this agent host environment can exist in both real-time controllers and contain the ability to operate with external agent systems. Our first infrastructure, the Autonomous Cooperative System (ACS), accomplished these goals, but presented other issues. Although ACS has been successfully deployed on commercial controllers, new releases of controllers will cause complications in the evolution of the software and adoption of future functionality. We need to establish a formal integration procedure of the agent functionality with the controllers and to transform the underlying system into a fully integrated and open heterogeneous system. We use a shipboard automation example to demonstrate the use of the agent virtual machine. With this system, the shipboard automation system is designed as a distributed and survivable environment, thereby spreading intelligence throughout the controllers and not in central locations.