Complex underwater missions involving heterogeneous groups of AUVs and other types of vehicles require a number of steps from defining and planning the mission, orchestration during the mission execution, recovery of the vehicles, and finally post-mission data analysis. In this work the Mission Management Tool (MMT), a software solution for addressing the above-mentioned services is proposed. As demonstrated in the real-world tests the MMT is able to support the mission operators. The MMT hides the complex system consisting of software solutions, hardware, and vehicles from the user, and allows intuitive interaction with the vehicles involved in a mission. The tool can adapt to a wide spectrum of missions assuming different types of robotic systems and mission objectives.