Bionic Commando sees the return of the bionically-enhanced Nathan "R.A.D." Spencer. Time has not been kind to Spencer: Five years after his heroic defeat of the Imperials, he has been betrayed by the government he swore to serve, imprisoned for crimes he didn't commit, and sentenced to death. On the very day of Spencer's execution, terrorists detonate a massive experimental weapon in Ascension City, unleashing an intense earthquake that has turned the city into rubble and wiped out its population. With the terrain in ruins and the city's air defense grid now in the control of a massive terrorist force whose goal remains unclear, the FSA have only one option left - a behind-the-lines assault.