In the year 2198, on the moon of Lethe, the USS
Otago prepares for a shakedown. Meanwhile, at Pioneer Station, a shuttle, the
Bentonville, drops off cargo. A mysterious infiltrator releases its contents: deadly
Xenomorph aliens, which begin to massacre the crew. Noticing ''Bentonville's
cargo weight discrepancy,
Deputy Administrator Maeko Hayes recommends the ship be detained but her supervisor McDonald refuses. Hayes encounters the aliens in the docking bay, trying to weld the doors shut. As the shuttle leaves, McDonald and the control staff are attacked and impregnated by Facehuggers. Narrowly escaping, Hayes realizes more Xenomorphs are in Bentonville's
remaining cargo and reluctantly activates the Cerberus Protocol, a Weyland-Yutani planetary quarantine procedure using armed satellites. Bentonville
and a freighter, Baldrin
, are destroyed with all hands while the Otago
is crippled. Hayes is extracted by Sgt. Jonas Harper and his squad of Colonial Marines to the crash-landed Otago'', where he takes command and deputizes Hayes as his Intelligence officer. The Marines enter the Dead Hills settlement, killing a Xenomorph Queen under the colony. After scouting the Berkley's Docks spaceport for parts to repair the
Otago, the Marines encounter the
Darwin Era, an anti-Weyland-Yutani cult who revere the Xenomorphs as a higher stage of evolution. Upon returning, Hayes admits to Harper that she activated Cerberus; despite this, they continue to work together. Hayes also works with
chief medical officer Bookard, Weyland-Yutani xenobiologist Becker,
chief engineer Corrigan, ship
psychologist Kabiri, and armory head Sgt. Martinez to find materials and personnel in the field to bring to
Otago. Harper traces the origin of the Xenomorph containers to Olduvai, Lethe's main Trimonite refinery. In its mines, they encounter Guardians: modified cultists containing
Chestbursters in their bodies who are ignored by the Xenomorphs along with discovering the cult is taking people to the Cassandra Project. Harper briefly reminces on this "Cassandra", before Joseph Marlow, Darwin Era's leader and a former Weyland-Yutani scientist, addresses the Marines directly, implying that Cassandra is working with him. Hayes, originally planning to use the ''Otago's
last escape pod as a beacon to send out a distress call, instead uses it as an improvised missile to rescue the Marines just before they are overrun. Returning to the Otago
, Harper discloses to Hayes that Cassandra is his daughter from his time on Lethe, as he was born on the planet. The Otago'' is directly attacked by Xenomorphs, but the Marines fight them off; Harper, who gets painful flashes and visions when Xenomorphs are nearby, begins to fall ill. Director Barbara Pryce, Weyland-Yutani's head of operations on Lethe, contacts the Marines and informs them that Cerberus is entering Phase 2: full nuclear sterilization of Lethe. The Marines storm Pioneer to try to stop Cerberus and kill another Queen, but it is too late to stop Cerberus. With little time, the Marines rush to repair ''Otago's'' hull, hypersleep chambers, and boost power to its energy shield to break the blockade. Pryce offers an atmospheric processor's power core, as well as looking for Cassandra and rescuing her from Marlow, in exchange for being allowed access to
Otago. The Marines raid the processor, stealing its core, killing another Queen, and recovering an APC, but Harper steadily weakens. The Marines then salvage a hypersleep gas-mixer chip from the USCSS
Monterro, an old M-class vessel used during a prior rebellion against Weyland-Yutani for which Harper was present. A Guardian sneaks onboard
Otago to persuade Harper to join Darwin Era, revealing that Marlow is using Cassandra for a project allowing communication with the Xenomorphs using her innate telepathic connection to the alien's hivemind, a trait that Harper shares with her and is the cause of his visions and failing health, before the Chestburster erupts from him and kills him. Harper confronts Pryce, who has dispatched men to find Cassandra, led by former Marine Theo Stern, in the Tantalus underground laboratory but Pryce had lost contact with them. The Marines infiltrate the lab and recover Stern, who joins the Marines, but they find from old footage that Cassandra has already been moved elsewhere to a new location and they narrowly escape the lab's self-destruct. During the escape, they capture Marlow who divulges that Pryce is playing them; she destroyed Tantalus and left Stern to die to tie up loose ends. Unable to get Cassandra's location from Marlow, Harper kills him after discovering that it is a Synth recreation of the real Marlow, before falling unconscious. Meanwhile, back on
Otago, Becker, working with Pryce to erase his debts to the company, cripples the ship's defenses and releases a Xenomorph Warrior that emerged from the captured Guardian, which kills Bookard while Weyland-Yutani commandos arrive to capture the ship. Hayes narrowly fends off the mercenaries with the ARC, though it is ruined by the commandos gunship; Becker gets the drop on her and holds her at gunpoint, but is killed by the Xenomorph. Hayes manages to lure the Xenomorph into the ship's reactor when it restarts, frying it and securing the ship. With Harper in critical condition and Kabiri unable to effectively treat him without Bookard, Stern and Hayes storm Pharos Spire, Weyland-Yutani's headquarters on Lethe, to extract Marlow's location from Pryce. She divulges that Marlow had set up in an ancient alien city under Olduvai, which is where he is keeping Cassandra prisoner and desperately tries to bribe Hayes to take her with them. Disgusted, Hayes renounces Pryce as less human than a Synth and leaves her to die. As Pryce furiously states she is human, Xenomorphs begin to swarm the facility. As Cerberus prepares to launch Phase 2, Hayes, determined to atone for serving Weyland-Yutani, decides to raid Marlow's city and save Cassandra. The now-repaired
Otago takes to the air and the Marines launch an all-out assault on the mine, killing a Queen and many cultists. Hayes, Martinez, and Stern descend to and enter the underground city, which contains mummified remains of a giant, wormlike alien species and large Xenomorph eggs. They also discover the corpse of the real Marlow, who had died from a chestburster long ago, and countless non-hostile Marlow Synths he had created to continue his work on the Cassandra Project. Finding Cassandra and freeing her, a gargantuan Xenomorph made from one of the ancient aliens wakes up, killing Stern and Martinez. The women are cornered, but Harper uses the last of his strength to briefly immobilize the Xenomorph, allowing them to escape at the cost of his own life. The remaining Marines stay behind to hold off the endless swarming Xenomorphs while Hayes and Cassandra extract to
Otago as the nuclear missiles start to fall. ''Otago's'' shields hold; the ship breaks the blockade and leaves Lethe's orbit. After mourning Harper, Hayes, Cassandra, and the remaining crew enter hypersleep as the
Otago enters deep space. ==Development==