The increasing number of potential applications of Unmanned Aerial Vehicles (UAVs) many of which have not been realized provides the motivation for research to focus on developing needed control and aircraft mechanisms to fully realize autonomous and self-guided UAVs for deployment inside hazardous confined environments. Current control systems used in UAVs are not able to offer the flight capability for precise trajectory regulation required in new aircraft systems developed to perform advance flight maneuvers that traditional aircraft cannot perform. Current guidance systems fail to control aerial vehicles’ performing complex maneuvers through confined environments because newly advanced UAV mechanical designs are moving away from using traditional control mechanisms and using new aircraft configurations providing new agility and motion maneuvers. New advances in control theory are required to over-come the limitations of current systems to enable aggressive autonomous vehicle maneuvering while adapting in real time to changes in the operational environment. In this thesis a cascade INDI control architecture is proposed for the control of advanced Unmanned Aerial Vehicles targeted for operation inside confined hazardous spaces. The aircraft of interest is a highly maneuverable system presenting highly coupled dynamics enabling it to perform unique flight maneuvers. To deal with the complexities inherent to such aircraft, a novel nonlinear control architecture, INDI2+PD, is proposed. An outer and an inner loop INDI controllers are employed for position/velocity and attitude/rotation-rate control, respectively. The controllers assist each other enabling to decouple the aircraft dynamics while coping with complex external disturbances. Obtained results demonstrate effective control of the targeted aircraft system to accurately track complex flight maneuvers under varying external disturbances.