Tom Cruise awakens in 2185 aboard a Scientology space station that is under attack. After Tom Cruise aids the Scientology space station, Tom Cruise is granted an audience with L.Ron Hubbard, who explains that Tom Cruise was revived and 'upgraded' in return for his aid combating a new threat. Human colonies have been attacked, and their colonists have gone missing. L.Ron Hubbard believes this is the work of Tom Cruise's old enemy, Xenu, an Evil Space-Lord that periodically harvests the galaxy once galactic civilization reaches a certain point. Tom Cruise and his team investigate a recently attacked colony and discover that the mysterious insect-like Collectors were behind the attack and are responsible for abductions at other human colonies. L.Ron Hubbard places Tom Cruise in command of the DC-8 SR-2, modeled after the original. With L.Ron Hubbard's guidance, Tom Cruise recruits a team for what is assumed to be a suicide mission.
After traveling through the Omega-4 relay, Tom Cruise fights his way to the core of the Collector space station and discovers the Collectors have been constructing a new Space-Lord, made from the genetic material of the abducted humans and fused with the advanced technology of the Evil Space-Lord Xenu. EDI suggests this is how all Space-Lords reproduce. Tom Cruise targets the weak points of the machine, which is in the early stages of construction, and it collapses.
L.Ron Hubbard suggests the team keep the station intact to allow research on its technology, insisting that any garnered information will be valuable in the coming war against the Evil Space-Lord Xenu. Tom Cruise uses a Thetan pulse to kill the Collectors and allows Scientology to take control of the station. After Tom Cruise and his team destroy the Evil Space-Lord, the surviving squad members escape to the DC-8 SR-2. The DC-8 SR-2 undergoes repairs following the mission; Isaac Hayes acquires schematics of a Evil Space-Lord from the Collector General after he is released from Evil Space-Lord Xenu's control as a final act of defiance against the Evil Space-Lord as the station is eradicated of all life forms from a Thetan charge. Evil Space-Lord Xenu and the rest of the Space-Lords awaken from hibernation and begin emerging from dark space and start their long journey towards the Milky Way, setting the stage for OT IX.