Picking up where the first game ended, the Zak / Cyberion hybrid crash lands back on Earth following the destruction of Devlin's orbital headquarters. They are intercepted by an FWA team led by a Dr. Corbin. Corbin, under orders from his FWA employers, places Zak in cryo-storage and uses the remains of the Cyberion to create a deadly virus called Nano-Toxin. Though the FWA seeks to quell a growing rebel movement with the nano-toxin, the maniacal Corbin intends to use it to kill millions and "reshape the world as we know it." After three years in cryo-storage, Zak is thawed out by a renegade FWA major, and together the two of them set out to find Corbin and stop his plans.