This paper presents a Flight Management System (FMS) with multi-level autonomy modes that meet the requirements of future flight operations for unmanned aerial systems (UAS). It is envisioned that the future of airspace will become highly heterogeneous and integrate non-standardized aerial systems. In that case, only ground systems will be able to predict future trajectories based on performance models (stored in huge parametric databases). Meanwhile, airborne systems are required to share information. The proposed FMS structure integrates new functionalities such as (1) formal intent and information exchange and collaboration in tactical planning utilizing air-to-air and air-to-ground data links and (2) decentralized, short-term collision detection and avoidance. The air-to-ground data link enables intent sharing and allows field operators (i.e., flight operators or air traffic controllers) to interpret, modify, or re-plan UAS flight intent. The onboard FMS persistently monitors the airspace, tracks potential collisions with the other aircraft and the terrain, and requests re-planning when it detects a possible issue. When an immediate response is needed, the onboard FMS generates a 3D evasive maneuver and executes it autonomously. Flight traffic information is obtained from ADS-B/In transponders and air-to-air data links. ADS-B-In/Out implementations make the unmanned systems more visible to the systems in 3D. In addition, the air-to-air data links enable intent sharing between airborne systems and are traceable in four dimensions (i.e., space and time). The experimental FMS was deployed in quadrotor UASs and a ground station and GUI was designed to perform demonstrations and field experiments for the issues introduced in the paper.