The main protagonist is Conrad Hart who, in Flashback, destroyed the planet of hostile aliens called the Morphs and went into suspended animation in a spaceship that floats aimlessly through outer space. In the year 2190 (50 years later), he is found by the Morphs and imprisoned in the Lunar prison of New Alcatraz. There, he is rescued by a man who introduces himself as John O'Conner, who tells him that the Morphs beat him to Conrad's ship, and leaves Conrad a few items "of interest" (a PDA and a handgun), before destroying the camera. On the PDA is a message from John, who tells Conrad to sneak around the base. Mandragore agents left a radar scrambler there. Conrad soon makes it to John's ship. As they blast off, Morph ships start attacking them. They teleport to Mandragore base Shadow just as the ship is destroyed.
They meet Sarah Smith, the leader of the Mandragore resistance. Later, in a meeting with Mandragore commander Hank, she tells Conrad that while he was in suspended animation the Morphs attacked Earth with superior forces, which made the governments surrender. The Mandragore has far fewer people, but they refuse to give up. Agents then call Sarah and tell her that they have found the location of Professor Bergstein: Morph asteroid base D321. Sarah sends Conrad and John there to rescue him. Conrad eventually finds Bergstein, who tells him that the base must be destroyed because it contains the Morph's new mind-manipulating weapon. He gives him a datacube (similar to the holocube that is in Flashback), which he explains contains a virus that he programmed in. The virus will blow up the base when the datacube is connected to the core. They connect the virus to the core and escape the base with John as it blows up, along with the asteroid itself.