Certain limitations exist in autonomous software and guidance, navigation, and control architectures developed for extraterrestrial planetary exploration rovers in regard to fault tolerance, changes in environment, and changes in rover capabilities. To address these limitations, this paper outlines a self-reconfiguring guidance, navigation, and control architecture, using an ontology-based rational agent to enable autonomous reconfiguration of mission goals, software architecture, software components, and the control of hardware components during the run time. This new architecture was evaluated through implementation onboard a rover and tested in challenging, Mars-like environments, both simulated and real world, and was found to be highly reliable, fault tolerant, and adaptable