This chapter presents a distributed architecture for unmanned aircraft systems that provides full integration of both low autonomy and high autonomy. The architecture has been instantiated and used in a rotorbased aerial vehicle, but is not limited to use in particular aircraft systems. Various generic functionalities essential to the integration of both low autonomy and high autonomy in a single system are isolated and described. The architecture has also been extended for use with multi-platform systems. The chapter covers the full spectrum of functionalities required for operation in missions requiring high autonomy. A control kernel is presented with diverse flight modes integrated with a navigation subsystem. Specific interfaces and languages are introduced which provide seamless transition between deliberative and reactive capability and reactive and control capability. Hierarchical Concurrent State Machines are introduced as a real-time mechanism for specifying and executing low-level reactive control. Task Specification Trees are introduced as both a declarative and procedural mechanism for specification of high-level tasks. Task planners and motion planners are described which are tightly integrated into the architecture. Generic middleware capability for specifying data and knowledge flow within the architecture based on a stream abstraction is also described. The use of temporal logic is prevalent and is used both as a specification language and as an integral part of an execution monitoring mechanism. Emphasis is placed on the robust integration and interaction between these diverse functionalities using a principled architectural framework. The architecture has been empirically tested in several complex missions, some of which are described in the chapter.