Bionic Commando features Nathan Spencer (voiced by former lead singer of Faith No More, Mike Patton), as a government operative who, after distinguishing himself in a fierce conflict against the Imperials, is betrayed and falsely imprisoned by the very people he unquestioningly served.

Five years later, on the day he is due to be executed for his supposed crimes, an experimental weapon detonates in Ascension City, unleashing an immensely powerful earthquake coupled with a radiation shockwave that leaves the city in ruins, wiping out its populace. Military intelligence suggests that a large terrorist search force has moved in and occupied Ascension City, but as yet their motives remain unclear. With the terrain in ruins and the terrorists in control of Ascension City’s air defences the FSA has only one option open to them – the reactivation of Nathan Spencer.