Arm yourself! The 20-year wait is over as the first true sequel to the classic 1988 Nintendo Entertainment System original, Bionic Commando, sees the return of the bionically-enhanced Nathan "Rad" Spencer. Time has not been kind to Spencer. Ten years after his heroic defeat of the Imperials, he is betrayed by the government, and sentenced to death for crimes he didn't commit.

But then, terrorists detonate a massive experimental weapon in Ascension City, unleashing an intense earthquake that turns the city into rubble, wipes out the population, and results in the city's air defense grid in the control of a massive terrorist force. There is only one option left, a behind-the-lines assault by a Bionic Commando.