Ten years have passed since the Imperials and the Federation clashed in the events of the original Bionic Commando. After defeating the fascistic Imperials and their Albatross war machine, Nathan "Rad" Spencer became responsible for training a new generation of "bionic commandos". Under the supervision of TASC director "Super" Joe Gibson, bionics became the foremost weapon of war in the Federal States of America (FSA) - but the new technology was not welcomed by all. Some feared that it was the first step into a new arms race; others wondered what it would mean to be a normal human in a world of super-powered bionics.