This paper presents a formal intent based Flight Management System (FMS) hardware and functional structure utilising multi-level autonomy modes. The novel advanced capabilities added to the UAV autopilots are envisioned to meet the requirements of the future flight operations of the UAVs integrated into national airspace. The proposed FMS structure integrates new functionalities such as a) formal intent based information exchange and collaborative tactical planning utilising air-to-air and air-to-ground data links and, b) decentralised immediate sense-and-avoid. The collaborative nominal operation mode enables the ground operator to build "shared intelligence" with the UAV through the intent sharing. In this mode, the intent sharing process benefits from the advantages of formal intent languages at different levels of abstraction and data-links. The air-to-ground data link allows the ground operator to update/modify/re-plan the flight intent (FI) of the UAV(s) in any phase of the operation according to evolving situations through ground station. The air-to-air intent sharing also continues between the surrounding aircraft through the aircraft intent (AI) ("machine-to-machine" level) communication which makes unmanned systems to be visible. The sense-and-avoid mode, the FMS recursively computes and observes the probabilities of potential immediate collisions with the other aircraft and terrain. Whenever the immediate response needs, the FMS executes the generated 3D avoidance maneuver. For technology demonstration purposes, an experimental FMS hardware has been deployed in a quadrotor UAV, and a ground operator station with GUI has been designed enabling envisioned operational experiments.