The commercial space tug Nostromo is returning to Earth with a seven-member crew in stasis: Captain Dallas, Executive Officer Kane, Warrant Officer Ripley, Navigator Lambert, Science Officer Ash, and two engineers, Parker and Brett. Detecting a transmission, the ship's computer, Mother, awakens the crew. Per company policy requiring any potential distress signal be investigated, they land on the moon despite Parker's protests, sustaining damage from its atmosphere and rocky landscape in the process. The engineers stay on board to effect repairs while Dallas, Kane, and Lambert head out to investigate. They discover the signal originates from a derelict alien ship and enter it, losing communication with the Nostromo. Ripley deciphers part of the transmission, determining it to be a warning, but cannot relay this information to those on the derelict ship.

Meanwhile, Kane discovers a chamber containing hundreds of large, egg-like objects. When he touches one, a creature springs out, breaks through his helmet, and attaches itself to his face. Dallas and Lambert carry the unconscious Kane back to the Nostromo. As acting senior officer, Ripley refuses to let them aboard, citing quarantine regulations, but Ash overrides her decision and lets them inside. Ash attempts to remove the creature from Kane's face, but stops when he discovers that its blood is an extremely corrosive acid. It later detaches of its own accord and is found dead. The ship is partially repaired, and the crew continue their journey back to Earth. Kane awakens with some memory loss, but seems to be otherwise unharmed. During a final crew meal before returning to stasis, he suddenly chokes and convulses. A small alien creature bursts from Kane's chest, killing him, and escapes into the ship, with Ash dissuading the rest from killing it.

The crew attempts to locate it with tracking devices and capture it with nets, electric prods, and flamethrowers. Brett follows the crew's cat Jones into a landing leg compartment, where the now-fully-grown alien attacks Brett and disappears with his body. After a heated discussion, the crew decide the creature must be in the air ducts. Dallas enters the ducts, intending to force the monster into an airlock, but it ambushes and kills him. Lambert, realizing that the alien intends to aggressively kill the crew one by one, implores the others to abandon ship and escape in its small shuttle, but Ripley, now in command, explains it will not support four people and insists on continuing with Dallas' plan of flushing out the alien.

Accessing Mother, Ripley discovers Ash has been secretly ordered by the company to bring the alien back, with the crew considered expendable. She confronts Ash, who tries to choke her to death. Parker intervenes and clubs Ash, knocking his head loose and revealing him as an android. Ash's head is reactivated, and they learn he was assigned to ensure the creature's survival. He expresses admiration for the creature's psychology, unhindered by conscience or morality, and taunts them about their chances of survival. Ripley cuts off his power; as they leave, Parker incinerates him.

The remaining crew decides to self-destruct the Nostromo and escape in the shuttle. However, Parker and Lambert are ambushed and killed by the creature while gathering life-support supplies. Ripley initiates the self-destruct sequence, but finds the alien blocking her path to the shuttle. She retreats and attempts unsuccessfully to abort the self-destruct. With no further options, she makes her way to the shuttle and barely escapes as the Nostromo explodes.

As Ripley prepares for stasis, she discovers that the alien is aboard, having wedged itself into a narrow space. She puts on a spacesuit and uses gas to flush the creature out. It approaches Ripley, but before it can attack, she opens an airlock door, almost blasting the creature into space. It manages to hang on by gripping the frame. Ripley shoots it with a grappling hook, but the gun catches as the airlock door closes, tethering the alien to the shuttle. It pulls itself into an engine exhaust but Ripley fires the engines, blasting the creature away into the depths of space. After recording the final log entry, she places Jones and herself into stasis for the trip back to Earth.

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