In 2137, 15 years after the events of the original Alien film, Amanda Ripley, daughter of Ellen Ripley, learns that the flight recorder of her mother’s ship, the Nostromo, has been located. The flight recorder was retrieved by salvage ship Anesidora, and is being held aboard Sevastopol, a Seegson Corporation space station orbiting gas giant KG-348. Christopher Samuels, a Weyland-Yutani android, offers Ripley a place on the retrieval team so that she can have closure regarding the fate of her missing mother.
Ripley, Samuels, and Weyland-Yutani executive Nina Taylor travel to Sevastopol via the Torrens, a courier ship, finding that the station is damaged and external communications are offline. They attempt to spacewalk into Sevastopol, but their EVA line is severed by debris, separating Ripley from the others. While exploring the station, Ripley finds the flight recorder of the Nostromo, but the data has been corrupted. She also discovers that the station is out of control due to a single, deadly Alien creature lurking aboard. After regrouping with Samuels and Taylor, Ripley meets the station’s Marshal, Waits, and his deputy, Ricardo. Waits explains that the alien was brought onto the station by Anesidora captain Henry Marlow. After recovering the Nostromo’s flight recorder while salvaging its remains in space, the crew was able to backtrack the Nostromo’s path to LV-426 and locate the derelict ship, containing within a nest of alien eggs. Marlow’s wife was attacked by a Facehugger, and was then brought aboard Sevastopol for emergency medical treatment, but died after a Chestburster hatched from her. Waits convinces Ripley to contain the Alien inside a remote module of the station, and then eject it into space. Although Ripley is successful, Waits ejects the module with her still inside. Careening into KG-348, Ripley space-jumps back to Sevastopol using a space suit.
Ripley makes her way back to confront Waits, but Ricardo reveals that the station’s service androids abruptly started slaughtering the remaining crew, including Waits. Samuels attempts to interface with the station’s artificial intelligence, APOLLO, to cease the rampage. However, the systems’s defensive countermeasures kill him shortly after he opens a path for Ripley into APOLLO’s control core. There, Ripley discovers that Seegson had been trying to sell off Sevastopol to Weyland-Yutani, who instructed APOLLO to protect the alien at all costs. Ripley tells APOLLO that the creature is no longer aboard the station and demands to cease all activity, but the system refuses, stating that “scheduled reactor scans are unverified”. At the reactor, Ripley discovers a nest with hundreds of Aliens, and initiates a reactor purge to destroy it.
Ripley learns that Taylor was secretly sent to retrieve the Alien from Sevastopol, and that she freed Marlow in exchange for the location of LV-426. However, Marlow double-crossed her and took her hostage aboard the Anesidora. There, Ripley finally discovers the Nostromo’s flight recorder, containing Ellen Ripley’s monologue from the end of Alien. Meanwhile, Marlow attempts to overload the fusion reactor of the Anesidora to destroy Sevastopol and ensure that no alien creatures survive; Taylor kills him in an attempt to stop him, but she herself is killed by electric discharge, forcing Ripley to escape shortly before the Anesidora explodes. The explosion destroys Sevastopol’s orbital stabilisers, causing the station to slowly drift into KG-348’s atmosphere. Ripley and Ricardo contact the Torrens for extraction, but a facehugger latches on to Ricardo, forcing Ripley to leave him. After making her way outside to help the Torrens detach from the station, Ripley is surrounded by Alien creatures and ultimately thrown into the ship by a blast. Aboard the Torrens, Ripley discovers that another Alien has boarded the ship. When Ripley is cornered in the airlock, she ejects herself and the Alien into space. Adrift in her space suit, Ripley is awakened by a searchlight.