In the future, a computer intelligence known as SkyNet uses its access to the GDI Ion-Cannon network to rain judgement down upon mankind. The survivors fight to live each day. Hunted by merciless machines, GDI and the Resistance fight a desperate holding action. Hoping and praying that the machines can be beaten. But all is not lost, for hope may come from unlikely places.

In an desprate attempt to release the world from the threat of the machines, Einstein builds the ultimate doomsday device. The result throws them into a war they never expected.