Alien 3 start with the spaceship Sulaco catching fire. To save themselves, Ellen Ripley, a young girl named Newt, Corporal Hicks and the android Bishop escape using a space pod. In cryonic stasis, they leave the burning space vessel. A scan of one of the pod’s passengers show an Alien facehugger, a kind parasite that infects its host with its embryos. The pod lands on Fiorina “Fury” 161, a prison for male convicts accused with cases of physical and sexual violence. After the prisoners have recovered the passengers of the pod, a facehugger comes out and heads for the prison dog.
Ripley wakes up and is greeted by Clemens, the prison doctor. He informs her that she’s the only one who survived among her crew. She also meet Dillon, the leader of a religious group of inmates, and Harold Andrews, the warden who warns her that she might bring trouble to the inmates. At Ripley’s request, Clemens performs an autopsy on Newt. To Ripley’s relief, nothing is found on the girl’s body. The warden and his assistant now start having doubts regarding Ripley’s behavior.
The dead bodies are cremated. In one corner of the facility, an alien bursts out from the body of the prison dog. The alien immediately kills some of the prisoners. Surprise by this event, Ripley re-activates the android to confirm that an alien indeed came with in the pod. Ripley relays information to Andrews regarding the aliens and she proposes that they must take action right to get rid of the creature. The wardens does not believe any word she says but goes to inform her that there aren’t any weapons inside the facility. The only thing that they can do is to wait for the ship sent by Weyland-Yutani that will be coming for Ripley.
The alien makes a surprise attack on Ripley and Clemens. Clemens is killed but the alien spares Ripley. Because of this, Andrews orders his assistant to take Ripley back to the infirmary. However, the alien kills the warden on their way to the infirmary. Ripley then asks the inmates for help. She persuades them to discharge toxic wastes into the ventilation and set it on fire to flush out the alien. The alien thwarts their plan by causing an explosion that kills several prisoners. Wondering why the alien has spared her, Ripley scans herself and she finds out that she’s carrying an embryo of an alien queen. She also learns that Weyland-Yutani plans on using the queen embryo and the alien as biological weapons.
Because she knows that the alien will not kill her, Ripley asks Dillon to kill her. In exchange, Dillon demands that she helps them in killing the alien. They make a plan to lure the alien and kill it by dropping it on molten lead. As they try to execute the plan, the prisoners are killed one by one except for Dillon and another prisoner named Morse. Dillon then works on distracting and luring the alien to a mold. When the Dillon and the alien are inside the mold, Morse set on pouring the molten lead on them. Unfortunately, the alien escapes even though its entire body is covered with molten metal. As the alien tries to recover, Ripley turns on the sprinklers and the alien’s body is cooled rapidly. The sudden drop in temperature causes the exoskeleton of the alien to shatter.
After the incident, the rescue team arrives with the man who created the android, Bishop. The man tries to convince Ripley to go with them and have the queen embryo removed from her. Ripley strongly declines and steps into a platform. Morse operates the platform and positions it over a furnace. The rescue team shoots Morse in the leg and kills the warden’s assistant when he tries to fight. As the people from Weyland-Yutani beg Ripley to surrender to them, Ripley jumps into the furnace. As she falls down, the queen embryo bursts out from her but she clings on to it and both of them die at the end. The movie concludes with Morse being taken away from the facility where he’s the only one left alive.