Large-scale systems refer to systems that consist of many interdependent local systems. Conventional centralized control schemes are not suitable for such large-scale systems due to global dynamic behavior complexity and computational difficulties. This paper introduces a general framework of agent based federated control motivated by the political structure where partially self-governing states are united by a federal government. Likewise, a multi-agent based federated control system is composed of local autonomous subsystems that cooperate to provide an overall system behavior. Formation stability and trajectory tracking control of a group of autonomous agents is designed based on this concept. Decentralized cooperative federated controllers are developed for each individual agent. Simulations show that the overall system is globally asymptotically stable to track a time-varying trajectory with a pre-designated formation for a group of nonlinear dynamic agents.