The story is set on the planet Nu-Earth, which is caught in the gravitational forces of two suns and a black hole (used by Southers to warp into their space station high command), where a perpetual war between the Norts and Southers is being fought, in which millions have been killed. During the war all forms of chemical and biological weapons have been used, poisoning the planet, and the troops of both sides must live in enclosed cities and only venture into the outside if wearing protective gear known as a "bio-suit". The Southers have, through genetic engineering (done by the so-called "gene genies"), developed a race of warriors who are immune to the deadly atmosphere and will therefore be superior troops, the Genetic Infantry. All of the G.I.s were made immune to all toxins, diseases, and acids (except for one). The Souther High Command deploy their secret weapon in an airborne assault, but a traitor has betrayed the secret of the G.I.s to the Norts and they are massacred during the drop. This is known as the Quartz Zone Massacre.

Rogue, apparently the only surviving G.I. (until he meets Venus Bluegenes), goes AWOL in order to track down the Traitor General responsible and avenge the rest of the G.I.s. Along the way he thwarts numerous Nort schemes, destroys some of Nort-land's highest personnel, such as Grand Admiral Hoffa and Sergeant-Kaptain Natashov.

All G.I.s possess a biochip implanted inside of the skull that contains their personality traits, memories and consciousness. After a G.I. dies his biochip can be inserted in a slot in another G.I's equipment or weapon, enabling him to control it. The biochip can later be placed into a new body, allowing the fallen G.I. to be reborn. One quotation is "we're genetic infantry – even when we're dead we don't escape from war."