This paper presents a comprehensive framework for the cooperative guidance of a fleet of autonomous vehicles, relying on Model Predictive Control (MPC). Solutions are provided for many common problems in cooperative control, namely collision and obstacle avoidance, formation flying and area exploration. Cost functions of the MPC strategy are defined to ensure a safe collaboration between the vehicles for these missions. An efficient way to select the optimal cost with limited computation time is also provided. The performance of the proposed approach is illustrated by simulation results.