On the war-torn, poisoned atmosphere of Nu Earth, Rogue Trooper is a genetic infantryman, one of an elite squad of biologically-engineered clone troops, created to overcome the planet's hostile atmosphere, unhindered in their fight against the enemy, the Nort Republic. After witnessing the betrayal and annihilation of his squad at the Quartz Zone Massacre, Rogue has gone AWOL, determined to hunt down the traitor who sent his brothers-in-arms to their deaths.