This thesis presents the initial components of an integrated guidance, navigation, and control system for vertical take-off and landing (VTOL) autonomous unmanned aerial vehicles (UAVs) such that they may map complex environments that may be hostile. The first part of this thesis presents an autonomous guidance system. For goal selection, the map is partitioned around the presence of obstacles and whether that area has been explored. To perform this partitioning, the Octree algorithm is implemented. In this thesis, we test this algorithm to find a parameter set that optimizes this algorithm. Having selected goal points, we perform a comparison of the LPA* and A* path planning algorithms with a custom heuristic that enables reckless or tactical maneuvers as the UAV maps the environment. For trajectory planning, the fMPC algorithm is applied to the feedback-linearized equations of motion of a quadcopter. For collision avoidance, standalone versions of 4 different constraint generation algorithms are evaluated to compare their resulting computation times, accuracy, and computed volume on a voxel map that simulates a 2-story house along with fixed paths that vary in length at fixed intervals as basis of tests. The second part of this thesis presents the theory of Model Reference Adaptive Control(MRAC) along with augmentation for output signal tracking and switched-dynamic systems. We then detail the development of longitudinal and lateral controllers a Quad-Rotor Tailsitter(QRBP) style UAV. In order to successfully implement the proposed controller on the QRBP, significant effort was placed upon physical design and testing apparatus. / Master of Science / For an autonomously operated, Unmanned Aerial Vehicle (UAV), to operate, it requires a guidance system to determine where and how to go, and a control system to effectively actuate the guidance system's commands. In this thesis, we detail the characterization and optimization of the algorithms comprising the guidance system. We then delve into the theory of MRAC and apply it toward a control system for a QRBP. We then detail additional tools developed to support the testing of the QRBP.