A fuel cell system control system includes a fuel cell system and a controller. The controller includes a display and a processor configured to execute a program for managing an operation of a fuel cell state machine having a plurality of states and capable of executing logic to execute state transitions, and a fuel cell failure detection and correction program, configured to detect one or more fuel cell system failures and correct each detected failure while the fuel cell system continues to operate. The control process includes the steps of representing an operation of a fuel cell control system as a state machine having one or more states, controlling the operation of the fuel cell system using the state machine, executing one or more states of the state machine, and correcting operational errors in the fuel cell control system while the fuel cell system continues to operate.