The overall goal of this project is to develop an onboard, autonomous Multi-spacecraft Supervisory Engine (MSE) for formation-flying guidance, navigation and control (FF-GNC), suitable for a wide range of formation flying topologies and distributed, multi-spacecraft missions. MSE will be developed in the context of specific NASA formation flying missions, using Terrestrial Planet Finder (TPF) as the target FF-GNC system architecture. Other missions, such as the Stellar Imager and/or MAXIM will also be studied. It will be developed using the concepts of Intelligent Systems, Formal Methods for Finite-State Automata modeling and Hybrid Model Predictive Optimization. Specific problems to be addressed include: formation initialization and calibration maneuver planning/control, formation reconfiguration (including conflict/constraint resolution), FF-GNC resource allocation and optimal resource management, and FF-GNC health maintenance and reconfiguration. In collaboration with the relevant technology teams at NASA-JPL, we propose co-development of MSE technology in parallel with (and interfaced to) NASA-JPL's FF mission and GNC analysis testbeds (ie. Formation Algorithms and Simulation Testbed, FAST and Formation Control Testbed, FCT). The Phase II project will deliver MSE system designs, prototype software, analysis tools and techniques. A Technology Infusion Roadmap for MSE technology will also be provided for NASA Program Office planning purposes.