An apparatus and method of a hardware isolated secure element protecting a plurality of mission critical subsystems are provided. The method includes performing an actuation operation received across an unsecure path that modifies the state of a mission critical subsystem, performing a diagnostic operation received across the unsecure path that requests state information of the mission critical subsystem, storing information used to determine which of the diagnostic operation and the actuation operation received across the unsecure path are performed, and flashing an execution image of an electronic control unit when the execution image of the electronic control unit is received across the unsecure path.