The AFTC controls both the engine itself as well as the variable exhaust nozzles controlling the engine exhaust gases. Additionally, the AICS (Air Inlet Control System) helps by controlling the engine airflow for an even subsonic airflow to the engine inlets. This is done through the variable geometry intakes, more precisely the variable ramps in the intakes.
All this is achieved by the AFTC and AICS using appropriate sensor inputs which then control engine operations according to programmed schedules.
In addition both engines also drive separate fuel, hydraulic and electric generators to create redundancy.
In case of a failure in the AFTC the MEC (Main engine control) is capable of assuming control of the engines to provide a fall-back, mechanical control. The normal mode, AFTC, is the primary mode (PRI) and called as such while the fall-back MEC is the secondary (SEC) mode. The selection of primary or secondary is automatic in case of a failure in the AFTC but can also be manually selected. Of note is that in secondary mode the engine nozzles are fully closed and disabled in addition to the afterburners being disabled with a corresponding loss of engine performance.