Aerospace vehicles are vulnerable to hardware and software faults that lead to mission-critical failures. Advances in onboard fault protection capability are necessary as both terrestrial and space vehicles increase in autonomy. State machines offer a useful tool for system behavior modeling and fault protection. This study presents an architecture for aerospace vehicle fault protection, focusing on the guidance, navigation, and control subsystem. The architecture is designed to be generic for use with any vehicle or mission; modular with components that can be added, removed, or rearranged; and portable for ease of conversion to flight software. A subsystem taxonomy delineates relevant vehicle hardware and software components. A fault tree analysis is performed to identify relevant faults. To model system mode behavior, a functional state machine is defined. A diagnostic state machine is developed for onboard model-based fault diagnosis. Finally, a system block diagram illustrates how fault and mode components can be integrated with other aspects of the system. Two specific case studies are presented, including an unmanned aerial vehicle application and a Mars sample return orbital rendezvous and capture scenario, demonstrating that the generic architecture can be adapted to diverse vehicles in very different regimes.