A self reconfiguring autopilot system is presented, which is based on a rational agent framework that integrates decision making with abstractions of sensing and actions for next generation unmanned aerial vehicles. The objective of the new intelligent control system is to provide advanced capabilities of self-tuning control for a new UAS airframe or adaptation for an old UAS in the presence of failures in adverse flight conditions. High-level system performance is achieved through on-board dynamical monitoring and estimation associated with controller switching and tuning by the agent. The agent can handle an untuned autopilot or retune the autopilot when dynamical changes occur due to aerodynamic and on-board system changes. The system integrates dynamical modelling, hybrid adaptive control, model validation, flight condition diagnosis, control performance evaluation through software agent development. An important feature of the agent is its abstractions from real-time measurements and also its abstractions from model based on-board simulation. The agent, while tuning and supervising the autopilot, also performs real-time evaluations on the effects of its actions.