In the year 2085, the Earth is now a wasteland ruled by war machines that won an apocalyptic war. Shortly after that battle, mankind left and began new life on Mars. However, Sandy Newman and her comrades are left on Earth. While struggling to survive, the group locates an abandoned nuclear missile launch site. There they must contend with a quasi-religious group called Geo Chris which plans to make the Earth green once more. However to defeat the war machines of the enemy known as the MME, the earth resistance must use the nuclear missiles to attack the MME's citadel, but doing so would carry a heavy price.

On Mars, the viability of the final stages of Operation Exodus is debated, with the Martian military preferring a plan to use a Plasma cannon based on ancient Solnoid technology to destroy the MME citadel and end the war in one strike. The displaced earth resistance members of Operation Exodus and their allies in the Mars military disobey orders and take a ship to earth. On earth, GORN, the leader of the MME, captures Sandy Newman in order to obtain access to Earth's orbital weapons, which it plans to use to prevent the Martian assault. Sandy Newman and GORN must work together to prevent the Mars forces from destroying the earth's chance of survival.

The crew of the Martian vessels sent to Earth in Chapter 2 fight alongside the earth resistance in the final battles of the war with the MME. The main Mars forces have finally arrived as well, and their combined forces finally allow an assault on the MME's Citadel. The war will soon come to an end as Sandy comes face-to-face with GORN, but in doing so the truth behind the entire conflict is revealed