Long ago the evil Vaxxian Empire overran the galaxy. Most of humanity was enslaved and abducted to the Vaxxian homeworld. A few humans, who were scientists, managed to escape. At the current moment (according to the timeline of the game), the Empire has since collapsed. However, numerous Vaxxian space stations, all blindly controlled and defended by robots, still remain in the galaxy, mindlessly pursuing their original orders.
The small band of scientists who initially escaped managed to clone the great human hero Major Havoc, in order to fly his Catastrofighter through a wormhole in space, so that he may lead a clone army against the dreaded Vaxxian robots, and to liberate the remnants of humanity by destroying the enemy reactors. The player controls Major Havoc, the leader of this very band of clones.