The full plot follows a breakout on the Auriga, a journey through a ship that is slowly falling apart, and a final confrontation with a creature that the scientists never planned for.
The scientists clone Ripley and remove the alien queen growing inside her, which leaves a clone with alien traits. The Betty crew delivers its frozen humans, who become hosts for new aliens. The creatures break out of their enclosures and kill many of the crew, including General Perez and Elgyn. Dr. Wren then reveals that the ship's automatic course is Earth, which would let the creatures loose on the planet.
Ripley 8 and the survivors head for the Betty, planning to escape and destroy the Auriga. On the way, Ripley finds a lab holding the ruined remains of earlier failed clones, and she burns it. A flooded kitchen section costs the group Hillard and Christie, who blinds himself to save the others.
Wren betrays them and shoots Call, which reveals that Call is an android. She links to the ship's systems and sets it to crash into Earth. Ripley is captured and taken to the nest, where the queen, now able to give live birth, produces a pale, human looking hybrid. The hybrid kills the queen and Gediman, and it treats Ripley as its mother.
Ripley reaches the Betty, but the hybrid follows and kills Distephano. She makes a hole in a window with her acidic blood, and the hybrid is sucked out into space. The Auriga hits Earth as the survivors escape in the Betty.