In 2118, 99.9% of humanity was wiped out by an invading alien force known as the Draktor. The survivors' memories are wiped before resuming life in fortified shelters. Humanity mounts an attack to take back the planet using giant robots known as Megaton-class Rogues. Yamato Ichidaiji is called to pilot one of the Rogues, just as memories of the invasion return and dangerous questions arise.