The advantages of UAVs in the aviation arena have led to extensive research activities on autonomous technology of UAVs to achieve specific mission objectives. This thesis mainly focuses on the development of a mission-based guidance system. Among various missions expected of UAVs for future needs, autonomous formation flight (AFF) and obstacle avoidance within safe operation limits are investigated. In the design of an adaptive guidance system for AFF, the leader information except position is assumed to be unknown to a follower. Thus, the only measured information related to the leader is the line-of-sight range and angle. Adding an adaptive element with neural networks into the guidance system provides a capability to effectively handle leader's velocity changes. Therefore, this method can be applied to the AFF control systems that use passive sensing methods. The simulation and flight test results clearly show that the adaptive guidance control system is a promising solution for autonomous formation flight of UAVs. The successful flight evaluations using the GTMax rotary wing UAV also demonstrate unique maneuvering aspects associated with rotary wing UAVs in formation flight. In the design of an autonomous obstacle avoidance system, an integrated approach is proposed to resolve the conflict between aggressive maneuvering needed for obstacle avoidance and the constrained maneuvering needed for envelope protection. A time-optimal problem with obstacle and envelope constraints is used for an integrated approach for obstacle avoidance and envelope protection. The Nonlinear trajectory generator (NTG) is used as a real-time optimization solver. The computational complexity arising from the obstacle constraints is reduced by converting the obstacle constraints into a safe waypoint constraint along with an implicit requirement that the horizontal velocity during the avoidance maneuver must be non-negative. The issue of when to initiate a time-optimal avoidance maneuver is addressed by including a requirement that the vehicle must maintain its original flight path to the maximum extent possible. The simulation results using a rotary wing UAV demonstrate the feasibility of the proposed approach for obstacle avoidance with envelope protection.