This paper presents an Integrated Mission Management System for Unmanned Aircraft Systems (UAS). The system consists in a number of mission and flight software modules that control the UAS path and the operation of its on-board payload in a coordinated manner. The overall system is called UAS Service Architecture Layer (USAL). An important requirement of the system is that it should be highly adaptable to perform a broad range of civil missions. To achieve this goal the flight plan and mission specifications are separated from the modules that perform its execution. The flight plan is described using a formalism speci fically designed for UAS civil applications. State Chart XML is used to provide a state based model for the UAS behavior during the mission. USAL o ers additional capabilities oriented to the automated reaction to contingencies. This paper describes the alternative aifi eld specifi cation mechanism and the contingency management architecture employed in the USAL.