The Colonial Marine spaceship Sulaco; crewmembers in stasis: A hatched Alien egg somewhere on the Sulaco can be seen in the opening credits. A facehugger is shown creeping onto a crew's cryo-tube.
The ship's medical scans show an Alien facehugger attached to one of the crewmembers. Alien acid drops and melts through to the subflooring, causing an electrical short.
Computer Voice: Stasis interrupted. Fire in cryogenic compartment. Repeat, fire in cryogenic compartment. All personnel report to emergency escape vehicle launch pod. Deep-space flight will commence in T-minus twenty seconds.
A gulf of flames spreads through the ship. Through automation, the cryotubes containing Ellen Ripley along with Newt, Hicks, and the damaged android Bishop, are moved to the escape pod.
The Sulaco launches the pod and it plunges in the ocean on Fiorina.
On Fiorina is a foundry facility and penal colony inhabited by all-male inmates with histories of physical and sexual violence. Many of the inmates have elected to remain at the site permanently for religious reasons.
Some inmates recover the pod and its passengers. Inmate Frank enters the pod just before the prison dog startles him.
Frank: That stupid dog of yours. Get it out of here! . . . Wait! One of them is still alive.
Ripley is taken in and treated by Clemens.
As she is being treated we see computer identity profiles of the crew displayed on a screen. Hoisted by a crane, inmates transport the pod to the facility. Along for the ride is the prison dog, who is at the opening, barking at an Alien facehugger creeping over a metal brace.
The prison's Superintendant, Harold Andrews has ordered the prisoners to gather so he can inform them of what they found.
Andrews: This is Rumor Control. Here are the facts. As some of you know, a 337 model E.E.V. crash landed here at 0600 on the morning watch. There wass one survivor, two dead, and an android that was smashed hopelessly beyond repair. The survivor is a woman.
The inmates react with an uproar and protests.
Morse: I just want to say I have taken a vow of celibacy. We've all taken a vow!
Andrews: We are well aware of your feelings on this matter. You will be pleased to know that I have requested a rescue team. Hopefully, they will arrive here inside of a week and evacuate her A.S.A.P. . . [to Clemens] What's her medical status?
Andrews: Gentlemen, we should stick to our set routine and not get unduly agitated. Correct? All right. Thank you, gentlemen.
Later, Murphy discovers burn marks on the dog.
Murphy: What kind of animal would do this to a dog?
Ripley wakes up and interrupts Clemens giving her a shot.
Ripley: What's that?
Clemens: It's just a little cocktail of my own mix. Sort of eye-opener.
Ripley: You the doctor?
Clemens: My name is Clemens. I'm the chief medical officer here.
Clemens: Fury 161. It's one of Weyland Yutani's backwater prisons, it grieves me to say. Do you mind? [he continues the shot] This is basically a stabilizer. I really ought to shave your head. We have a big problem with lice here.
Ripley: Where are the others?
Clemens: They didn't survive.
Ripley: I have to get to the ship.
Ripley gets out of bed naked.
Clemens: You're in no condition for that.
Ripley: You want to get me some clothes, or should I just go like this?
Clemens: Given the nature of our indigenous population, I would suggest clothes. None of them have seen a woman in years. . . . [under his breath] Neither have I, for that matter.
While Clemens escorts her to the ship, he explains that the refinery has been kept in operation as a methane foundry.
Clemens: We have a foundry, Lieutenant Ripley.
Ripley: How do you know my name?
Clemens: It's stenciled on the back of your shorts.
They arrive at the escape pod and Ripley becomes alarmed when she sees peculiar burns on the cryotube.
Later, they arrive at the morgue and inspect the bodies.
Ripley: And the girl?
Clemens: She drowned in her cryotube.
Ripley: Yes, I have to be sure how she died.
Ripley: Could I have a moment alone, please?
Ripley whispers to the dead Newt.
Ripley: Forgive me.
Suspicious of what caused the escape pod to jettison and what killed her companions, she fears that Newt may be carrying an Alien embryo in her body, though she does not share this information.
Ripley: No. We have to do an autopsy. . . I have a very good reason.
Clemens: Perhaps you would like to share that reason.
Clemens begins the autopsy, but he finds nothing unusual.
Clemens: Everything's in place.
Ripley: Chest. Open her chest.
The autopsy continues and no embryo is found in Newt's body.
Clemens: Lungs. Filled with fluid. Ergo she drowned.
Andrews and his security assistant, Aaron arrive and protest the autopsy and Ripley not being confined. Ripley is warned by Andrews that her presence among them may have extremely disruptive effects.
Ripley: We have to cremate the bodies.
Andrews: Nonsense, we will keep the bodies on ice until the rescue team arrives.
Andrews continues his protest, but relents when Clemen falsifies it's required due to suspicion of Cholera.
Andrews: We're 25 prisoners in this facility. All double-Y chromos. All thieves, rapists, murderers, child-molesters. All scum. Just because they have taken on religion doesn't make them any less dangerous. I try not to offend their convictions. I don't want to upset the order. I don't want ripples in the water. And I don't want a woman walking around giving them ideas.
Ripley: I see. For my own personal safety.
A funeral is performed for Newt and Hicks, during which their bodies are cremated in the facility's enormous furnace.
Dillon: Why? Why are the innocent punished? Why the sacrifice? Why the pain? There aren't any promises. Nothing certain. Only that some get called, some get saved. She won't ever know the hardship and grief for those of us left behind. We commit these bodies to the void with a glad heart. For within each seed, there is a promise of a flower, and within each death, no matter how small, there's always a new life. A new beginning. Amen.
In another section of the facility, the prison dog begins having convulsions, and a larger than normal Alien bursts from its body.
Later, with her head now shaved and after she has showered, Ripley enters the mess hall where the men have gathered.
Ripley: I just wanted to say thanks for what you said at the funeral. My friends would have appreciated it.
Dillon: Yeah, well, you don't want to know me, lady. I'm a murderer and rapist of women.
Ripley: Really? . . . Well, I guess I must make you nervous.
Dillon: Do you have any faith, sister?
Ripley: Not much.
Dillon: Well, we've got a lot of faith here. Enough even for you.
Ripley: I thought women weren't allowed.
Dillon: Well, we've never had any before. But we tolerate anybody. Even the intolerable.
Clemens explains the back story on the inmates and their beliefs.
Clemens: Dillon and the rest of the alternative people, embraced religion, as it were, about five years ago. Tincture?
Ripley: I'm on medication.
Ripley: What kind of religion?
Clemens: Some sort of apocalyptic, millenarian, Christian fundamentalist, uh .. .
Clemens: Exactly. Point is, when the company wanted to close the facility down, Dillon and the rest of the converts wanted to stay. And they were allowed to remain as custodians with two minders and a medical officer. And here we are.
Ripley: How did you get this wonderful assignment?
Clemens: How do you like your new haircut?
Ripley: It's okay.
Clemens: Now that I've gone out on a limb for you with Andrews, damaged my already less-than-perfect relationship with that good man and briefed you on the humdrum history of Fury 161; can you not tell me what you were looking for in the girl?
Ripley: Are you attracted to me?
Clemens: In what way?
Ripley: In that way.
Clemens: Very direct.
Ripley: I've been out here a long time.