It has been ten years since Nathan "RAD" Spencer managed to defeat the Imperials and destroy the Albatross in Bionic Commando. Hailed as heroes he and his comrade Joseph "Super Joe" Gibson became responsible for the training of new recruits under the flag of the TASC. But when Spencer disobeyed an order from Gibson during Operation Blackout, which lead to the death of several TASC agents, Spencer was court-martialed and sentenced to death while through his actions the public changed its opinion about bionic technology leading to the cancellation of the program and the "Bionic Purge". During the purge all TASC personnel were ordered to turn in their bionics or have them forcibly removed. Some fled, others obeyed but in the end bionic technology was effectively removed from the nation - at least until terrorists from BioReign detonate an atomic bomb in Ascension City. With no military unit returning from Ground Zero once gone in, Nathan is spared his fate for now and is instead send in to deal with the situation under the promise to get new information about the where-abouts of his missing wife Emily.
