Three years have passed since Anubis suffered defeat at the hand of Mike Anderson. A new age of prosperity has begun to emerge and along with it, the rebirth of some of earth's great cities. But just as quickly as he disappeared following his defeat, Anubis has reappeared to resume his tyranny. Again the player must join Mike and attempt to crush the iron rule of Anubis before he can once more throw the earth back into the darkest of ages. Afterwards, Anubis reveals that he is only a small portion of a much larger threat. A race of aliens called the Eltorians have come to conquer Earth, and the Solar System must be defended from their advancing forces. Near the end of the plot an enormous spaceship called "Eltoria" emerges where Mike must go to battle Anubis.