In this paper we propose a distributed real-time fault detection, isolation and mitigation framework for multiagent systems performing cooperative tasks. Various system models and detection schemes with respect to communication and sensing are considered. Two communication protocols for fault detection are introduced first and proved to be effective. Then a scheme based on limited relative state measurements is developed. Furthermore, we propose fault isolation and mitigation steps to guarantee the accomplishment of a global objective. All schemes are distributed in the sense that at each step of the fault detection, isolation and mitigation every agent only uses locally available information. One key feature of the framework is the significant reduction of required computational resource when compared with the fault detection and isolation schemes based on unknown input observers. Later we show that the proposed framework can be applied to the consensus and other cooperative formation problems. Several computer simulations are presented to demonstrate the efficiency of the framework.