G.I. Rogue is part of a bilogically-engineered clone troop that goes rogue after seeing his whole infantry get betrayed and annihilated at the Quartz Zone Massacre when they were sent there on a mission. Rogue goes AWOL and hunts down the general w3hop betrayed him and his fellow troopers armed with the latest in experimental weaponry. He uses a gun, a helmet and his backpack that are all encoded with bio-chips containing the digitised personalities and knowledge of his comrades that died in battle.

Rogue Trooper can be played online by up to four players with split-screen modes.