A fire starts aboard the Colonial Marine spaceship Sulaco. The computer launches an escape pod containing Ellen Ripley, the young girl Newt, Hicks, and the damaged android Bishop; all four are in cryonic stasis. Scans of the crew's cryotubes show an Alien facehugger attached to one of the members. The pod crash-lands on Fiorina "Fury" 161, a foundry facility and penal colony inhabited by male inmates with histories of physical and sexual violence. Inmates recover the pod and its passengers.
Ripley is awakened by Clemens, the prison doctor, who informs her that she is the sole survivor. Ripley is warned by the prison warden, Harold Andrews, that her presence may have disruptive effects. Ripley requests that Clemens perform an autopsy on Newt, he asks what they are looking for in the body of a girl who had obviously drowned. Ripley tells him that they are investigating a possible case of cholera, while secretly fearing that Newt has been impregnated with an alien embryo. Clemens firmly responds by stating that there hasn't been a case of cholera reported for 200 years. The autopsy is conducted and no embryo is found. A funeral is held for Newt and Hicks and their bodies are cremated in the facility furnace. In another section of the prison, an alien bursts out of a prison dog named Spike's chest. The Alien kills several members of the colony and returns outcast prisoner Golic to his deranged state. Ripley re-activates Bishop, who confirms that an Alien came with them to Fiorina in the escape pod. Ripley informs Andrews of her encounters with the Aliens and suggests everyone work together to hunt down and kill it. Andrews does not believe her story, but explains that the facility has no weapons; their only hope is the rescue ship being sent for Ripley by the Weyland-Yutani Corporation.
The Alien surprises Ripley and Clemens in the prison infirmary and kills Clemens. It examines Ripley, but spares her and retreats. Andrews orders Aaron to take her back to the infirmary, but he is ambushed and killed by the Alien. Ripley rallies the inmates and proposes they pour flammable toxic waste into the ventilation system and ignite it to flush out the Alien. However, the Alien's intervention causes an explosion and several inmates are killed. With Aaron's help, Ripley, who has not been feeling well this whole time, scans herself using the escape pod's medical equipment and discovers the embryo of an Alien Queen growing inside her. She also discovers that Weyland-Yutani hopes to turn the Queen embryo and the adult Alien into biological weapon.
Deducing that the Alien will not kill her because of the embryo she carries, Ripley begs Dillon to kill her; he agrees only if she helps the inmates kill the adult creature first. They form a plan to lure the creature into the foundry's molding facility, trap it via a series of closing doors, and drown it in molten lead. The bait-and-chase plan results in the death of every prisoner except Morse and Dillon. Dillon remains in the mold to distract the Alien, allowing it to tear him apart as Morse pours the molten lead onto them. The Alien is covered in molten metal but escapes the mold; Ripley activates the fire sprinklers, causing the Alien's exoskeleton to cool rapidly and shatter, killing it.
The WeylandâYutani commando team arrives, including a man who looks identical to Bishop and explains that he is Bishop's creator. He tries to persuade Ripley to undergo surgery to remove the Queen embryo, which he claims will be destroyed. Knowing he is lying, Ripley refuses and steps back onto a mobile platform, which Morse positions over the furnace. The WeylandâYutani team shoot Morse in the leg in a late effort to stop him; Aaron strikes the man with a wrench and is shot dead. The commando team begs Ripley to let them have the "magnificent specimen" with no success. Ripley throws herself into the furnace, just as the baby Alien Queen begins to erupt from her chest. Ripley grabs it to prevent it from escaping as they both fall into the furnace to their deaths. The facility is closed and the only surviving inmate, Morse, is led away.
Who woke Ripley?
Clemens