In the opening credits of the film, we see the
Sulaco, the large military ship carrying the survivors from
Aliens. Newt, Hicks, Ripley (
Sigourney Weaver), and the remains of the android Bishop (
Lance Henriksen) are presumably all in hypersleep, but a stowaway alien egg on the ship releases a facehugger. The facehugger explores the cryotubes and breaks into one of them, appearing on the medical scanner as it impregnates one of the sleeping figures. The acid from the facehugger starts an electrical fire, and the ship automatically responds. Unable to contain the fire, the automated systems of the
Sulaco eject all the cryotubes into an escape pod and eject them into outer space. The navigation systems lead the escape vehicle to the nearest planet, which happens to be Fiorina 161, home to nothing more than a penal colony populated by life-sentence prisoners. Unsurprisingly, it is owned and operated by Weyland-Yutani, the omnipresent company that employed Ripley. The EEV crash
lands on the planet, and when the prisoners retreive the EEV, they discover that Ripley is the only survivor. Newt and Hicks are dead, and Bishop now hopelessly smashed beyond repair. As the prisoners tow the EEV wreckage back to the prison unit, a facehugger reveals itself and approaches Spike, a dog belonging to one of the prisoners.
Andrews (
Brian Glover), the warden, announces the news to the prison population, making note that the only survivor is a woman. Dillon (
Charles S. Dutton), the spiritual leader of the prisoners, views the presence of a woman to be dangerous in the all-male population, out of concern for the spiritual well-being of his brothers. Andrews leaves Ripley in the care of the prison doctor, Clemens (
Charles Dance), under orders that she's not to leave the infirmary until a rescue ship arrives for her.
Ripley awakens from hypersleep and is disoriented, but Clemens stabilizes her with an injection. She is distraught to learn of her circumstances, especially the news that her companions are dead. She demands that Clemens take her to the wreckage of the EEV, and she breaks down when she learns that Newt drowned in her cryotube after the ship crashed. Before she can process the information, she sees the acid burn from the facehugger on the side of the cryotube, and immediately suspects the presence of an alien. Ripley wants to examine Newt's body for signs that she had been impregnated by a facehugger, and eventually she insists on an autopsy. Clemens is suspicious but complies, finding nothing but the usual signs that the child drowned. Satisfied that there was no alien, Ripley allows the prisoners to prepare a funeral for her friends; since the prison was used as a lead works at one time, they will use the blast furnace to incinerate the bodies. As Dillon speaks an improvised eulogy for Newt and Hicks, a new alien is born, unseen by anyone; the dog explodes with a chestburster, and an alien that moves on all fours emerges, running off to some distant location inside the maze-like prison complex.
Ripley, whose head is now shaved due to the lice problem on the planet, bathes herself. She has now said goodbye to her new surrogate family, and is once again starting over. Her attempts to connect with the prisoners in the mess hall are met with hostility; Dillon rejects her when she thanks him for his eulogy, and Ripley learns that she is the only woman among a group of rapists and murderers serving life sentences. The prisoners all seem to have found some form of redemption through a fundamentalist Christian religion. In a private moment, Clemens informs Ripley about the history of the prisoners and the penal colony, while the two of them become attracted to one another and share a sexual encounter. Afterwards, Ripley notices a barcode on the back of Clemens' head, but Clemens refuses to talk about it.
Meanwhile, a prisoner named Murphy (
Christopher Fairbank) is working in an isolated tunnel when he finds the embryonic alien finishing its development into an adult. He attracts its attention and it attacks him, spitting acid in his face. Blinded, he falls backwards into a gigantic fan and is immediately shredded to bits. The rest of the prisoners discover the remains, but when Ripley gets the news, she begins to realize that maybe an alien did regenerate itself after all. She gets Clemens to help her recover Bishop's remains, but when he leaves her to meet with Andrews, Ripley is nearly raped by a group of prisoners. Dillon rescues her and properly 'reeducates' his brothers, but not before Ripley punches one of her attackers viciously in the face.
Clemens finds out from Andrews that the installation has received an unprecedented communication from Weyland-Yutani regarding Ripley. The automated communications with the
Sulaco have informed them of Ripley's whereabouts, and they have dispatched a rescue team to remove her. Andrews understands that Ripley must be very important to them, but can't imagine why. After a hostile exchange with Clemens, Andrews grills him about what he might know about Ripley.
Elsewhere, Ripley reconnects what is left of Bishop and has a brief discussion with him. Using Bishop to access the flight recorder from the EEV, Ripley finds out the circumstances of their ejection from the
Sulaco, and Bishop confirms that an alien traveled with them to Fiorina 161. At his wishes, Ripley disconnects him permanently.
Meanwhile, the alien is beginning to attack the prisoners. It attacks a trio of prisoners in another of the prison's many isolated tunnels, allowing one to escape. The survivor, Golic (
Paul McGann), returns to the others and is contained in the infirmary. Andrews and the others dismiss him as insane, and Andrews even refuses to believe Ripley after she confirms his story. Ripley refuses to recount her story to Clemens, in fear of being written off as crazy herself. Instead, she asks Clemens about the barcode on the back of his head. Clemens concedes that he was a former prisoner on Fiorina, after a morphine addiction and a bad medical decision caused several deaths. When the prison was turned into a lead factory, he decided to stay with the inmates, knowing no one else would hire him as a doctor ever again. Happy with his sincerity, Ripley gives her trust to Clemens, but the alien suddenly appears in the infirmary, emerging from a ventilation shaft. It immediately kills Clemens and advances on Ripley, cornering her against a wall. For one terrifying moment, it seems to examine her, pressing itself right up against her cheek, but instead it retreats and takes the body of Clemens with it. Ripley bolts and rushes to the others, where Andrews is snatched through a vent right in front of all the prisoners.
Now that there can be no question about whether or not they are in danger, the prisoners attempt to deal with their situation. The successor of Andrews is Aaron (
Ralph Brown), who is held in poor regard by all the prisoners due to his obvious low intelligence (the prisoners claim his IQ is only 85), and nobody takes him seriously. Leadership of the survivors reverts to Ripley after Dillon begs off.
Ripley informs the prisoners what she knows about the alien, and eventually they come up with a plan; they will use a highly combustible material left behind in the colony to burn the alien out of the tunnels, at which point they will force it into a toxic waste containment unit and trap it indefinitely. The inmates start making preparations, but the plan backfires when the alien attacks before they can finish, and the explosion happens too soon. The prisoners are trapped in the burning tunnels and their numbers are drastically reduced.
After the catastrophe, Ripley suffers pains in her chest and suspects internal bleeding. But when she uses the scanner in the wrecked EEV, she finds something worse: she was the one who was impregnated by the facehugger in the
Sulaco, and she is carrying an alien embryo. Even worse, the embryo is a queen, and therefore capable of replicating the entire alien colony.
Ripley suspects that Weyland-Yutani knows about the alien embryo already, and her suspicions are confirmed when she uses Aaron to send a message to the Company about the alien they have. She pretends that they've trapped it, but the Company forbids them to kill it. Aaron won't allow her to ward the Company off, and Ripley knows they will arrive and take the alien for their own purposes just like they've always wanted to do. Even worse, they could get ahold of the queen she is carrying. Knowing that she herself is doomed, Ripley seeks out the alien and confronts it, hoping it will kill her, but it refuses to harm her; it can somehow sense that she is carrying the queen, which is why it did not kill her in the infirmary earlier.
Ripley asks Dillon to kill her, but Dillon refuses, wanting instead to use Ripley to kill the adult alien that has murdered his men. Ripley promises that if Dillon agrees to kill her afterwards, she will help him kill the creature. Their plan is to fire up the blast furnace and lure the alien into the mold and drown it in hot lead. The prisoners act as bait, rushing down the corridors of the lead works, closing off all the entranceways until the alien is forced into the mold. Initially, the plan is not met with much enthusiasm; some prisoners, and Aaron, still believe that the Company plans to rescue them by killing the alien for them. Ripley tells them about the two previous encounters with the alien, and how the Company relentlessly sacrificed its crew to obtain the creature. Dillon finally convinces the others that it is better to go down trying to do something good, than die begging on ones knees. Aaron still dismisses the plan as foolish, and returns to the top floor to wait for the Company crew.
Ripley's plan works, although at high costs: the alien manages to kill all of the prisoners except for Dillon, and Morse (
Danny Webb), who is manning the boiling lead. When Dillon sacrifices himself by wrestling with the alien in the mold, so that Ripley can climb out, Morse dumps the lead on Ripley's command, completely burying the alien in molten metal. However, the lead fails to kill the alien and it bursts out of the mold, now enraged. It makes for Ripley, who climbs a series of chains to get away from it, but it begins to scramble up after her. Suddenly Morse shouts to Ripley and reminds her of the sprinkler system hanging above her. Ripley triggers it and dumps cold water over the alien. The sudden cooling immediately causes cracks and breaks to appear over the Alien, until it finally explodes.
Ripley climbs up onto Morse's platform, which hovers somewhere above the furnace. When she looks up, she is confronted by aaron who brought the Company medics and soldiers, who have arrived to remove her. A man moves to the front, and Ripley recognizes him as Bishop. He speaks soothingly to her and tells her that he is not the Bishop android, but rather its designer, sent by the Company to ensure Ripley's safe return. He tells her that the medic team is there to remove the embryo from her in a simple surgical procedure that will save her life. Ripley asks him what they intend to do with the alien embryo once it is removed, and Bishop II promises her that they will destroy it. Ripley, however, will be unconscious so she will have to trust them. Ripley wants to believe that she has a chance, but she knows that the Company really doesn't care about her. Throughout her experiences with the alien (in the last two films), Weyland-Yutani has only been concerned with the creature and have considered human beings expendable. As long as she allows them to remove the queen from her body, the alien creature will continue to regenerate and threaten all humanity. Ripley closes the fence that separates Morse and herself from the rest of them. Morse moves the platform away from the others and one of the soldiers immediately shoots him in the leg. In response, Aaron hits Bishop II in the back with a lead pipe and the soldiers kill Aaron. Bishop II, wounded and dazed, begs Ripley not to ruin his chances for studying the alien: "It's a magnificent specimen! You must let me have it!" he shouts at her. Ripley asks Morse to help her one more time, and he moves the platform out over the boiling blast furnace. Walking to the edge, she summons up her strength and deliberately falls backwards into the furnace, taking her own life. On the way down, the queen alien erupts from her chest, but Ripley holds tightly onto it, dragging it with her into the furnace where both she and it are incinerated.
With nothing left to do, and no alien to take back, the Company medics bandage Morse's wound and take him along with them when they leave, abandoning the penal colony on Fiorina 161. During a final pass by the crashed EEV, we hear the radio picking up Ripley's final transmission from the end of the first movie, decades before: "This is Ripley, last survivor of the Nostromo, signing off."