You are on the shuttlecraft Mirata, heading for the Marathon Colony Ship, when one of the ship's Artificial Intelligence Units (AIs), Durandal orders your shuttle to self-destruct. You barely manage to escape, but do find an alien craft in the shuttle bay. You're not sure what is going on, but aliens seem to have taken over Marathon, imprisoning or killing humans and nearly destroying parts of the ship.

One of AIs has been destroyed, one has gone--what appears to be--insane, and the last still seems to be functioning correctly. You must make your way through the ship, killing the aliens and saving the humans, or all your friends and fellow humans will be dead. ~ Lisa Karen Savignano, All Game Guide