It's interesting to note though there's a shot in the theatrical cut where Newt looks like she's screaming with her mouth wide open (shown above). This contradicts Clemens saying, "I don't think she was conscious." Obviously, since you see a Facehugger break the glass on her cryotube in the opening, this is the idea the filmmakers intended, and that Newt mannequin with her mouth ajar could've been constructed that way to shoot the Queen crawling out of her throat.

Clemens walks alone on the cold surface of Fiorina 161. He looks out at the ocean and sees a strange object sticking up out of the water. It's the crashed EEV. Then a body washes ashore. He runs over and finds Ripley, now covered with mud and lice. Clemens picks her up and carries her back to the prison. He orders some inmates to look for more survivors. They use oxen to pull the EEV onto land. There's also different shots of Andrews typing a message to the company and Frank looking at the inside of the EEV (this part was obviously completely reshot later with only the new footage appearing in the theatrical cut). This scene wasn't in the workprint, and there's a shot for it in one of the trailers that doesn't appear in the assembly cut either (the camera is low, looking up at Clemens as he walks under a structure, it's shown above). Strangely, Newt's age changes from 10 to 12 between the assembly cut and the theatrical version.

Before Andrews does his "rumor control," 85 tells everyone, "Alright, alright. Let's get it going. Keep it together. Come on. Right? Right, here we go, Mr. Dillon." Prisoners bow to pray. Dillon says, "Give us strength, O Lord, to endure. We recognize that we are poor sinners in the hands of an angry God. Let the circle be unbroken until the day." Dillon puts his fist in the air and concludes, "Amen." The inmates raise their hands and repeat, "Amen." It's a brief scene, but it gives a little more insight into their religion.

As Ripley and Clemens enter the morgue and walk down the spiral staircase, Clemens asks, "Is there any particular reason that you're so insistent?" Ripley replies, "Yes, I have to be sure how she died." He continues, "I hate to be repetitious about such a sensitive subject, but it's perfectly clear that she drowned." As the two walk across the long room, he asks, "Was she your daughter?" She responds, "No, she wasn't." The assembly cut differs from the workprint in that Clemens deliberately stops at the bottom of the stairs to ask Ripley if Newt was her daughter, and this exchange happens in closeups versus an impersonal wide shot. The assembly version also opens with a closeup of Hicks's freezer.

The Facehugger in this cut scene is commonly referred to as a Super Facehugger, because of its large size, webbed fingers, and ability to impregnate two hosts.

Boggs, Rains, and Golic sit at a table in the mess hall. Rains says quietly to Boggs, "I'm telling you, somebody's got to do something about this. You or me?" Boggs whispers something in response. Dillon walks up to the prisoners and sits down with them saying, "Okay. There's a lot of talk going around that we've got some disharmony here. You guys want to tell me what the problem is? Hey, come on, speak to me." Rains replies, "All right, I'll tell you. I don't mind the dark. I don't mind the bugs. I don't mind wandering around in some cold, wet damp tunnel for a week at a time. I don't mind anything, but I mind Golic." Dillon asks Boggs, "Is that the way you feel about it?" He replies, "Yeah, the guy's crazy and he smells bad. I ain't going out with him anymore." Dillon asks Golic, "You got anything to say for yourself?" Golic just sits there and finally smiles like an idiot. Dillon continues, "Well, he's going with you. Golic is just another poor, miserable, suffering son of a bitch, just like you and me." Rains adds, "Except he smells worse," and Boggs chips in, "He's crazy." Dillon responds, "Knock off the shit. You got a job to do. I don't want to hear another word about Golic. Okay?" The prisoners are silent. He repeats slowly, "Okay?" Boggs slams down one of his eating utencils and Golic smiles. Dillon stands up to leave.

Before Golic, Rains, and Boggs go out to light candles and forage among the abandoned mine shafts, Dillon tells Golic, "Light a candle for Murphy, will you?" Golic replies, "I'll light a thousand." As the three walk away, Golic says, "Into the dark. And a machines open a store. What are you looking for? And away their cigarettes. Deodorant." Rains says, "Deodorant, that's a good idea." It's not clear what Golic is talking about in the Alien³ Workprint, but in the script, he talks about Murphy and says, "He was a special friend. He never complained about me. Not once. I loved him. Did his head really get split into a million pieces? That's what they say."

In the scene where Clemens meets with Andrews, there was footage taken out in which Andrews presses Clemens for more information on Ripley. Andrews asks, "Is there anything I should know?" Clemens responds, "About what?" Andrews says, "About the woman. Don't play with me, Mr. Clemens. You spend every second you can with her, and I have my suspicions that not all your concerns with her are medical. Has she said anything to you? Anything about where she's from? What her mission is? What the hell she was doing in an E.E.V.?" Clemens replies, "She told me she was part of a combat unit that came to grief. Beyond that, I assume it's all classified. I haven't pressed her for more." Andrews walks around him like a vulture, asking, "That's all?" He responds, "That's all." Andrews says, "You're sure?" Clemens replies, "Yes." "Nothing more?" Andrews asks. "No," Clemens answers. Finally, Andrews says, "Get out of here."

A prisoner, who is identified as Eric the Cook in the script, carries plates out into the cafeteria and sees Golic eating at a table. He walks up to him and Golic turns around smiling. His face is still smeared with blood from his previous encounter with the Alien, and Eric drops his dishes in shock. Golic continues eating while Eric gets others, who sneak up on Golic and carry him away to the infirmary. According to the script, the prisoners who captured Golic were Dillon, Andrews, Aaron, Morse, and Arthur. In the Alien3 Workprint, there are cuts to this outtake during the scene where Ripley talks to Bishop about an Alien on the Sulaco.

During the scene where Clemens explains his past to Ripley, Golic says, "In an insane world, a sane man must appear insane." Clemens replies, "That's very profound, Golic. Thank you." Golic smiles as he lays in bed. After the Alien kills Clemens and takes his body up into the vents, Golic stares up in shock at where the Alien left, muttering, "Magnificent," twice. In the script, Golic speaks to the Alien as it stands next to Ripley. He says, "Hey, you. Get over here. Let me loose. I can help you. I want to be your friend." The Alien just looks at him. Then it leaves.

When Andrews is informing the prisoners of the facts in the cafeteria just after Clemens is killed, there's a line and some accompanying footage left out of the theatrical cut. Andrews says, "At 14:00 hours, prisoners Boggs, Rains, and Golic left on a routine foraging mission in the underground network." Also, when Ripley interrupts them later, she says, "It's here," twice. The video clip with this footage is the same as one of the files above so be careful not to download it twice.

In the scene where the prisoners are trying to figure out what to do after Andrews is killed, there was a line taken out. Morse says, "Why don't we just get her head and shove it through the fuckin' wall?" Ripley replies, "Sounds good to me." In the theatrical cut, she didn't respond.

A large amount of footage was cut from the fire scene and most of it involved Junior, a prisoner who tried to rape Ripley earlier. In this outtake, Ripley and Junior work together to put the flames out on a prisoner. Ripley tries to calm the burnt prisoner by saying, "It's all right. It's all right. You're going to be all right. We've got you. The fire's out. It's okay." According to the script, the prisoner is either Gregor or Frank. Dillon comes up to them and says, "Junior! Junior! Get to the sprinklers and turn them on." Ripley tells Dillon, "Get him out of here. Come on, we've got to get him out of here." Ripley and Dillon move the wounded prisoner while Junior runs to turn on the sprinklers. Junior turns a corner and another prisoner shouts, "Junior! Behind you!" The Alien crawls down a wall dividing Junior from the others, who quickly gather to help him. Ripley tries to get Junior to come to her and the others by yelling, "Come on! Come on!" Junior shouts at the Alien, "Come and get me fucker!" He takes off running toward the waste tank and the Alien follows him. Ripley and the others run to the waste tank's door and close it. Junior's screams can be heard through the door and the prisoners gather outside the waste tank. Dillon is furious and shouts, "Shit!" Then he punches out the glass which guards the sprinklers' switch and activates the sprinklers. The Alien was originally trapped because Junior heroically sacrificed himself.

Dillon gives a victory speech to the prisoners as Ripley and Aaron watch. Dillon says, "Even for those who have fallen, this is a time of rejoice. We salute their courage. They will live forever. Those that are dead are not dead. They have moved up. They have moved to a higher place." 85 comments, "Crazy bastards. Andrews used to call them, Dillon's god squad. It keeps them out of mischief." Ripley asks, "You're not the religious type?" Aaron replies, "Me? Shit no, I got a job." After a moment of pause, he continues, "Look I, I figure the rescue team gets here in 4, 5 days, 6 tops. They open the door, go in there with smart guns, and kill it right?" Ripley asks, "What have you heard from them?" Aaron responds, "Nothing much. We had a message received. Later we had something that said you were top priority. They don't count us in on much. We're the ass-end of a totem pole out here." Ripley says, "What if they don't want to kill it? What if they want to take it back?" 85 asks, "Take it back?" She responds, "Yeah," and he says, "You're kidding. They're not lunatics, you know. They got to kill it. Right?" Ripley pauses and then replies, "Right." The video clip with this footage is the same as the clip above so be careful not to download it twice.

Morse sits and shaves his head while he guards Golic in the infirmary. Golic tries to get Morse to set him free, saying, "Please, what did I do? Just tell me what did I do?" Morse replies, "I'll tell you what I'm going to do. I'm going to sit here and guard your ass like I'm supposed to. I don't need any fuckin' trouble with Dillon." Golic continues, "All I did was tell them about the dragon. What it did to Boggs and Rains. I wasn't lying. You saw it." Morse replies, "Fuckin' A, I saw it." Golic says, "If that thing comes in here, I can't even run. I'm dead meat." Morse responds, "It's not gonna get in here. We got it trapped." Golic pleads, "So what's the big deal? Come on Morse, please. Let me loose, please. Don't I always give you cigarettes first?" Morse replies, "Yeah," and Golic asks, "Aren't I your friend? Morse, I love you." Morse gives in and says, "Fuck it. Why not?" Morse stops shaving, walks over behind Golic, and unstraps him. Morse lightly hits Golic on the head and pulls him close saying, "But behave yourself. No fuckin' around or I'll get nothing but shit." Morse returns to his shaving and Golic asks, "So where they got it?" Morse responds, "In the waste tank. We got that sucker nailed. I mean tight." Golic grabs a fire extinguisher and sneaks up behind Morse saying, "I've got to see it again." Morse asks, "What the fuck you talking about?" Golic hits Morse unconscious with the fire extinguisher and says, "No more cigarettes for you." Then he rushes off to see the Alien. In the script, Golic says that the Alien is his friend.

Ripley and Aaron decide to transmit messages to the company. 85 types, "Report death of Supt. Andrews, Medical Officer Clemens, eleven inmates," and then asks Ripley, "Right we got the first part. Now what do we say?" Ripley replies, "Tell them we trapped it." Aaron asks, "What do we call it?" She responds, "A Xenomorph." 85 says, "Right," and then pauses at the keyboard. He asks, "How do you spell it?" Ripley says, "Here," and starts typing on the keyboard. She types, "Have trapped Xenomorph. Permission to terminate?" Aaron says, "Hey, wait a minute, we can't kill it. We don't have any weapons right?" Ripley responds, "Right." Then a new message appears which says Weyland-Yutani received their message. 85 says, "See, that's all they ever tell us. Treat us like shit." Another message appears which reads, "Permission to terminate Xenomorph denied. Rescue unit arriving in eighteen hours with medivac biological management team," and then a new message is received which says, "Recommend lockdown procedures for inmates' protection." After this message, the company sends two more and both read, "Repeat -- Permission to terminate Xenomorph denied." Ripley puts her head down. The messages were transmitted in all caps. In the script, Ripley and Aaron reported that eight prisoners died not eleven inmates as in the Alien³ Workprint. Also, the response that the company sends is different in that it says that the rescue unit will arrive at 12:00 hours and to avoid contact until they arrive.

Golic walks up to the waste tank's door and says, "Off and on me now?" A prisoner, who is identified as Arthur in the script, stands guard and asks Golic, "What the hell you talkin' about?" Golic replies, "Talk to me, the beast." Arthur says, "You can't go in there dickhead. The big motherfucker will eat you alive." Golic walks up to Arthur, who gets nervous, and he says, "Sorry." Then Golic, who has turned around, faces the guard and slashes his throat with what the script says is a straight razor. Golic repeats, "Sorry," several times as Arthur falls to the ground and then he turns his back to the dying prisoner. Golic waits until silence has returned and then he opens the waste tank's door. He leaps back and says, "Tell me what to do next." He slowly walks into the darkness of the waste tank and then the Alien kills him from behind. His scream echoes. In the script, Golic calls the Alien his brother, saying he's with it all the way.

Ripley and Dillon talk about the company. Ripley says, "They don't want to kill it. We've got to figure out a way to do it before they come here." Dillon asks, "Why do we have to kill it? You just said the company's coming for it." Ripley replies, "That's right. They want to take it back. Some sort of weapon." Dillon asks, "Yeah, what's wrong with that?" Ripley responds, "They can't control it. They don't understand. It'll kill them all." Dillon says, "Like I said, what's wrong with that?" Ripley says, "Well, nothing's wrong with that, except a lot of innocent people will die. I thought you were a religious man." Dillon replies, "You don't understand, do you sister? That place out there doesn't exist for us anymore. We've got our own little world here. It ain't much, but it's ours." Ripley asks, "So fuck everybody else?" Dillon responds, "Yeah, fuck them." Morse runs in and says, "Hey, Dillon!" Dillon responds, "Yeah," and Morse continues, "Uh, Dillon, we, uh, got a teeny-weeny problem." Ripley slowly turns her head to face Morse.

In the scene where Dillon, 85, Ripley, and Morse try to figure out what to do next after the fire disaster, they originally dealt with the fact that Golic let free the captured Alien. They gather outside the waste tank and Dillon kneels beside the guard's corpse. Aaron says, "Fucking great! Miserable, crazy, son of a bitch let it loose! Got what he fucking deserved. Well, now what are we going to do? Andrews was right. We should've kept the shithead chained up." It then shows footage from the theatrical release up until 85 says, "I said that. You're the dumb prick that let Golic out. You miserable, little shit." Dillon responds, "Come on, cut that shit out!" Aaron says, "Tell your fuckin' bozo to shape up! All this shit is his fault." More theatrical footage is shown, and then when 85 and Morse fight over causing panic, Morse shouts, "Fuckin' screwed!" Aaron replies, "Yeah, and who's fault is it then eh?" The rest of the scene just continues the same as the theatrical cut.

In the scene where Ripley finds the Alien in the basement, there was some footage taken out. The Alien hits Ripley's pipe away and she falls back onto the ground. The Alien looks at Ripley and then bolts away. On card 27 of the Star Pics cardset, it says, "I startled it from its nest inside the infirmary air ducts. My only weapon, a heavy lead pipe, was useless. The Alien batted it out of my hand like a matchstick, then crept toward me. But it didn't attack. I didn't think it would. Not when I had its queen gestating inside me." In the script, Ripley shows no fear when she finds the Alien at the rusty Hydro-Converter. She says, "You fucker," and rams her pipe into the Alien, which reacts with a huge roar and cry. Ripley yells, "Come on fucker - kill me!" She hits the Alien again with her pipe and then the creature knocks it away. They stare at each other for a long frozen moment and then the Alien leaves. Ripley says, "Bastard." There is no footage of this outtake in the Alien³ Workprint.

In the scene where Ripley tries to get Dillon to kill her, a line was taken out after Dillon lets Ripley fall to the floor in which he says, "Go kill yourself."

The speech that Dillon gives to the prisoners to get them to lure the Alien into the leadworks and the rest of that scene was originally different than the theatrical release. Dillon says, "This is the choice. You die sitting here on your ass or you die out there. At least we take a shot. We owe it one! It's fucked us up. Maybe we can get even for the others. Now how do you want it?" Morse asks, "What the fuck are you talking about?" Dillon replies, "I'm talkin' about killin' that big motherfucker." Aaron says, "Hold it. The rescue team's on its way. We could just sit this out." Ripley asks, "The rescue team for whom?" 85 responds, "For us." Ripley says, "They just want the beast. You know that." Aaron replies, "I don't give a damn what they want. They're not going to pick us off one by one, are they?" Ripley says, "I wouldn't be so sure." 85 says, "Come on. They're going to take us home." Dillon responds, "They're not going to take us home." The rest of the footage is the same as the theatrical release up until Ripley says, "When they first head about this thing, it was crew expendable. Next time they sent some marines. They were expendable too. What makes you think they're going to care about a bunch of lifers who found god on the ass-end of space. You think they're going to allow you to interfere with their weapons research? They think we're crud and they don't give a damn about one mate of yours that died. Not one." More theatrical footage is shown up until Dillon's last speech in which he says, "You're all going to die. This is as good a place as any to take your first steps to heaven. Only question is how you check out. Do you want it on your feet or on your fuckin' knees beggin'? I ain't much for beggin'. Nobody ever gave me nothin'. So I say, fuck that thing, let's fight it!" The scene concludes with the theatrical footage. The video clip with this footage is the same as the clip above so be careful not to download it twice.

In the scenes where the prisoners are running through the tunnels trying to lure the Alien into the leadworks there were several scenes taken out. In one, a prisoner, who is identified as Kevin in the script, says, "Section 29 closed," before he shouts, "This thing is really pissed off!" In another scene, a prisoner, who is identified as Jude in the script, yells, "Get a fuckin' move on!" Dillon shouts, "Troy! Troy! Help them! Help them!" Troy just looks around and then runs off. Dillon continues, "What the hell is going on? Get back to the doors everybody!" Prisoners are shown running all over the place. Troy is in the piston area and asks, "How did I get here?" He runs down another corridor. Ripley asks, "Dillon, where the hell are they going? What about the plan?" Dillon responds, "Look you're immune. They're not." Ripley asks, "So what are we doing?" He replies, "Improvising." In another scene, Dillon stumbles upon Troy's carcass as he walks down one of the corridors, and he says, "Troy." He stands over the body for a while and then moves on. Following that scene is one of Jude, who is the prisoner that carries scissors, and Morse running down a corridor. Jude slips on something and falls on the ground. Morse stops and shouts, "Get up!" He walks back to Jude with his torch to see what happened. Jude says, "For fuck's sake," and looks at his hands which are covered with blood. He looks up and screams. His screams echo to the piston chamber where Ripley can hear them. Later in another scene Ripley comes upon the remains of Eric.

When the company arrives and 85 welcomes them, there was some footage left out from the theatrical release. Aaron says, "I tried to tell them," and one of the company men asks, "Have you seen the beast?" Aaron replies, "Yes sir. Horrible. Unbelievable. She's got one inside her." Bishop II says, "We know that," and behind him a large cage is set down. Aaron looks back and then turns around. He says, "You're going to need a bigger cage than that." In the script, no cage is brought in and Bishop II nods to the Commandos, the company men who wear armor and carry Pulse Rifles, after telling Aaron that they know about Ripley's impregnation. The Commandos blast 85 with their Pulse Rifles and he falls to the floor with a look of disbelief on his face.

Ripley used to be a lot more suicidal when she grabs the Alien's tail and Dillon pulls her back. She yells, "Kill me! Kill me! Come on!" Dillon yells, "Come on! This is our last stand!"

When the Alien leaps out of the lead, there was a line cut in which Morse yells, "Oh fuck!" The scene where Morse tells Ripley to turn on the sprinklers was originally very different. Ripley thinks of activating the sprinklers herself, and before doing so, she says, "For the last time." There was also some footage of the Alien removed.

After Bishop II says, "We want to kill it and take you home," there was a line cut from the theatrical release. Bishop II continues, "We know what you've been through. You've shown great courage." Then more theatrical footage is shown up until Ripley asks, "You don't want to take it back?" Bishop II responds, "Ripley, time is important. Let us deal with the malignancy. We've got a surgical bay set up on the rescue ship. Come with me." One of the company men says, "It's very quick, painless. A couple of incisions. You'll be out for two hours." Bishop II adds, "And then it's over." Then it goes to back to the theatrical release up to where Bishop II says, "Please, trust me. Let me help you. Hmm?" Following this line, is a very long shot of Ripley as she struggles to decide. During the pause, there are clips of Bishop II, Aaron and the company man, and Morse. Finally, Ripley answers, "No," and the footage goes to back to the theatrical release. When Morse gets shot, the exchange between him and Ripley is slightly different. Morse shouts, "Shit! Christ!" Ripley says, "Morse, you help me," and he replies, "What do you want me to do? Tell me." She responds, "You'll know." After Bishop II is attacked by Aaron, he touches the side of his head in pain and looks at what appears to be blood on his hand. He turns back toward Ripley and shouts, "I'm not a droid!" The rest of the footage is the same except there is an added clip of Bishop II asking, "What are you doing?" It's shown just after Morse stops the crane which is long before Bishop II asks the question again in the theatrical footage. There was also some short clips of the company men removed. The video clip with this footage is the same as the one above so be careful not to download it twice.