Following the United Nations attack upon the newly established machine civilization of Zero One, a global nuclear war between both factions began for control of the Earth. After several desperate plans to halt the never-ending waves of robot-soldiers, the human leaders realized that the Machines had a good chance of winning. The human leaders began the construction of an entirely underground city, called Zion, that was built for the purpose of preserving the human species.

When the war ended in the Machines' favor, the remnants of humanity were left struggling to survive on the cold, dangerous, and desolate surface. The captured survivors were imprisoned and put into the newly constructed bio-electric towers with their minds placed in the Matrix to keep them docile. Twenty-three prisoners were freed by a mysterious Matrix-controlling figure referred to as "The One" and led to the unfinished Zion where they worked to complete it.

After making the city operational and regaining technological usage from geothermal energy from the Earth's core, the One taught the humans to continue building and maintaining a war effort, and to fight inside and outside the Matrix. After the One's death, the humans learned to survive on their own and began waging a partial-guerrilla war from Zion against the Machines, and at the same time trying to free the Matrix's population from their virtual "prison".

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