First-time director David Fincher disowned the film, citing constant studio interference and actually walked out of production before final editing began. He did preside over a rough cut that became the basis for the 'Assembly Cut', a longer version of the movie later released on DVD and BluRay.
One possible idea for the film included a chest-burster coming out of Michael Biehn's character, Hicks. A replica of the actor with his chest torn open was created, but after Biehn discovered this, he threatened to sue the producers for using his likeness without his consent, and the idea was dropped. Later, the producers paid him to use his picture at the beginning of the film for the computer sequence. Apparently he received more money for use of this one image than for his role in Aliens (1986).
At one point, David Fincher was denied permission by the film's producers to shoot a crucial scene in the prison understructure between Ripley and the alien. Against orders, Fincher grabbed Sigourney Weaver, a camera and shot the scene anyway. This scene appears in the final cut.
Original Alien (1979) Director Ridley Scott turned down the chance to direct. Scott, and later Renny Harlin both thought the third film should explore the origin of the Xenomorph species. This concept was deemed too expensive by David Giler and Walter Hill, so Scott declined to return and Harlin later quit the film. Scott ultimately got his wish with the movie Prometheus (2012).
William Gibson wrote a very early script treatment for the film, which was initially intended as a two-parter to be shot back-to-back. As Sigourney Weaver's involvement was in question, the main focus of this script was between Hicks and Bishop, two characters from Aliens (1986). Many consider this to be a much superior script. The only carry-over from this original script, however, is the bar-codes on the back of the convicts' necks.
With the release of the definitive Alien Quadrilogy on DVD in 2004, 20th Century Fox proffered David Fincher the proverbial olive branch and asked him to assemble and comment on his own Director's Cut. Fincher declined. He was the only one of the four Alien directors to refuse to have anything to do with the project.
Cinematographer Alex Thomson replaced Jordan Cronenweth after only two weeks of filming, after he began to suffer the onset of Parkinson's Disease. Though Cronenweth insisted that he was well enough to make it until the end of production, and David Fincher supported him, line producer Ezra Swerdlow forced Cronenweth off the film, largely because he had lost his own father to the same illness several years previously and knew that if anything, the demanding schedule would likely take a fatal toll on Cronenweth's health.
Because of continuing troubles with the film, Fox halted production in Pinewood Studios in England in late 1991. The crew returned to LA, and an initial screening identified the missing parts of the film. A major part yet to be shot included killing of the alien in the lead pool. By the time of the new shots in LA, Sigourney Weaver's hair grew back, and she had an agreement with the producers that if she would have to cut her hair she would be paid a $40,000 bonus. The producers therefore hired Greg Cannom to create a bald cap with very short hair on it. The make-up process cost $16,000 and was very difficult and time-consuming because the hairline required the cap to be placed very precisely on Weaver's head.
One early draft of the script focused almost entirely on Hicks, Bishop and Newt, played in Aliens (1986) by Michael Biehn, Lance Henriksen and Carrie Henn respectively. The story would tie up loose ends from the preceding film with Newt returning to Earth to live with her grandparents, as well as Hicks and Bishop and a new team of Colonial Marines battling a rival faction of planets who use the Alien as a bio-weapon. The latter was used somewhat in Aliens: Colonial Marines (2013)
Dr. Clemens' line about Fury-161 being one of 'Weyland-Yutani's backwater prison planets.' was the first time the name Weyland-Yutani was spoken out loud. It had appeared on computer screens and props in the previous two films, Alien (1979) and Aliens (1986), but characters always referred to it as 'The Company' in dialogue.
An advanced type of facehugger, one that impregnates Ripley with a queen embryo, was designed and built, but was cut from the Theatrical Version. It does however make a brief appearance in the extended Assembly Cut.
The original budget was $45 million which included Sigourney Weaver's fee of $5.5 million. The budget soon spiraled however, with first Renny Harlin and then Vincent Ward both leaving the project before novice feature film director David Fincher came on board. Extensive last minute re-shoots - especially after the finale was deemed to be too similar to Terminator 2: Judgment Day (1991) - ultimately pushed the budget into the region of $65 million.
Much more of the autopsy scene was filmed than ended up in the final film. A rough cut of the scene originally contained so much gore, that it even made crew members who had worked on it sick to their stomach.
David Twohy contributed to the pile of abandoned scripts the movie's pre-production generated. In his version, the only returning character is Ripley, who only briefly appears on a file card. As in previous scripts the story involves experiments in genetically-engineering aliens as bioweapons. This script introduced a high-security prison facility in space and its morally ambiguous inmates (one of which is an escape artist), themes which made it into both the finished product, and Twohy's own Pitch Black (2000).
Writer/Producer David Giler has stated he regrets writing this movie, as it eroded his authority as producer. Giler only committed to writing the film upon demands from Sigourney Weaver who, after Vincent Ward's departure, would only sign on to the film if Giler and Walter Hill would pen the screenplay. Giler claims this later generated conflicts between himself, director David Fincher and Fox Studios executives, with Fox taking Fincher's side over Giler's. After one particularly heated disagreement, Giler walked off the set, leaving his duties to producer John Landau.
The creature that the alien impregnates was originally an ox, but was eventually changed because an ox was cumbersome and was seen as somewhat incongruous when placed in the film's environment. This sequence was later restored for the extended "Assembly Cut."
The concept by Vincent Ward based on which the movie was green-lighted involved an artificially constructed wooden planetoid and a group of monks who thought they were living in post-apocalyptic dark ages, and had a middle-ages lifestyle. The group refused all kinds of modern technology, and when Ripley and the Alien crash-land on it, they would blame Ripley for the Alien attacks. Ripley was to be impregnated by the Alien "the old-fashioned way" rather than through a face-hugger, and therefore being impregnated with a human-alien hybrid. According to the storyboards, she would dream of half human-half Alien hybrids. Other storyboards included horse-Alien and sheep-Alien hybrids. The film was to end with one of the monks performing an 'exorcism' on the Ripley, transferring the Alien embryo to his own body, and then killing it by walking into a fire. Ward left the project after the producers insisted that he change the monks to prisoners and drop the wooden planet idea. However, since many of Ward's ideas were carried over to the final screenplay, it still earned him a story credit.
Sigourney Weaver had a clause in her contract specifying that Walter Hill and David Giler would write the final shooting script. Weaver has said that she considers Ripley a very difficult character to write, and, with the exception of James Cameron, only Giler and Hill have really ever written the character correctly.
Novelist Alan Dean Foster who wrote the novelization of the film objected to the storyline, most specifically, the deaths of Newt and Hicks. His initial draft of the novel had Newt survive but the studio rejected this, forcing Foster to keep his adaptation consistent with the film. For this reason, the author declined to write any other adaptation of the franchise.
A cross is briefly seen on the planet surface to suggest the religion that some of the inmates have turned to. The model department held a competition to see who could design the best one. Four different models were created, and then David Fincher chose the version he liked best.
On the set at Pinewood Studios, a giant lead foundry took 12 weeks to construct and put the production way behind. Even with 6 day weeks and 14 hour days, the crew were unable to keep up with the schedule.
The damages inflicted on Bishop were too severe to have Lance Henriksen work a prosthetic head while hiding under a table/chair/platform, so the filmmakers ended up having the android being played by... an android. A mechanical copy of Henriksen's likeness was used in this movie for the portrayal of the Sulaco-Bishop.
This is the only film in the Alien Quadrilogy that does not feature an android character unique to that film. The only android that appears is Bishop (in a severely damaged state), and he had previously appeared in the film prior to this.
A series of Aliens comic books were published that were set after the events in Aliens (1986), featuring an adult Newt returning to space with a shell-shocked Hicks to stop the retrieval of an alien specimen by Weyland-Yutani corporation. The books were re-published to accommodate Alien³ (1992), with Newt re-named Billy.
Some of H.R. Giger's design for the film involved a puma-like alien with claws. The producers also instructed him to do more sexy designs, so he created a drawing of an alien, which, in close view, had the lips of a woman. One of his ideas involved the alien kissing the victims and killing them that way (an idea that was later used in the movie Species (1995) where the main creature was also designed by Giger).
When Ripley retrieves Bishop from the trash heap and re-activates him to find out what happened on the Sulaco, she asks him, "Was there an alien on board?" This is the only time in the entire "Alien" franchise (including the "AvP" films) where the term "alien" is used to describe the creature. Everyone else uses other names (baddies, dragon, serpent, creature, xenomorph, animals, bug) to identify it.
Initially Renny Harlin was attached as director, but left to direct Die Hard 2 (1990). Then Vincent Ward came on board, but only lasted a few months before being fired after several disagreements with the producers. The scriptwriter, Walter Hill, was considered to direct the film as well, but he stepped back after David Fincher became available.
After the first draft was complete (in which the Alien attacks a monastery), construction work began on the sets. The construction shut down, leaving the crew in limbo, as the script was reworked. Although the location changed to a prison, it was decided that they would use the already half-built monastery sets.
Much like first Alien movie, Alien 3 also had problems with negative reactions of audience who saw rough cut of the movie in early test screenings and were horrified from all the scenes of gore and violence. Because of this and also to avoid NC-17 rating by MPAA, Alien 3 was heavily cut. Some of the graphic scenes that were deleted from rough cut which is said to be 3 hours long include; Longer and more disturbing version of Newt's autopsy scene, close ups of melted face of prisoner who gets hit with Alien's acid and some gore was cut from scene where he falls into giant fan, bloodier version of Clemens' death scene and some parts from final chase and fight between prisoners and Alien.
In the scene where the warden is addressing the prisoners regarding the deaths of the other prisoners, right after Ripley bursts in to warn them of the Alien and the Warden orders her removal, when the Alien yanks the Warden into the ceiling, you can see that one of the prisoners is wearing a Weyland-Yutani Corporation jacket, the logo is emblazoned on the back.
The trivia items below may give away important plot points.
The final shooting script, the novelization and the comics adaptation confirm that Newt was the first one to be facehugged. This is merely hinted during the opening credits since the facehugger attacks and cracks Newt's cryotube. When the scanner shows the facehugger attached to a person, Ripley is shown in a seizure state but she is clearly in her intact tube. After the EEV crashlanded Newt drowned. She was sadly conscious and cried for help. After she died the alien embryo crawled out of her mouth and proceeded to Ripley's chamber since it requires a living host to grow properly. It opened Ripley's mouth and forced itself into her throat. Although the scenes were storyboarded they were never filmed because the effect of the creature switching hosts could not be portrayed realistically. The Theatrical Cut adds more confusion to the backstory since the inmates discover Ripley perfectly clean in her tube meaning that her capsule was never violated. The Extended Cut however shows Clemens discovering a half-drowned Ripley in the shore covered in dirt and lice, meaning that she was already out of her cryotube. This also accounts for the continuity error in the theatrical cut since Ripley is spotless in the EEV but she is dirty when Clemens carries her in the infirmary.
The script went through so many rewrites and the film was slated to be helmed by so many different directors that when David Fincher came on board he stated that the egg on Sulako was just a plot device to propel the story of the film and there was never any intention of explaining its presence. There is a lot of controversy about how the egg was found on the Sulako. Some very early drafts of the script however reveal that Bishop's milky fluid was combined with the Queen's acid after the sting and produced a new egg. This mirrors the Director's Cut of Alien where Ripley finds the nest with a cocooned Brett. The alien had covered him with its fluid in order to transform him into a new egg and Dallas was kept as a potential host for the facehugger. This backstory was finally deleted because of the various drafts the screenplay went through but it provides a viable explanation as to why the egg did not hatch immediately. It took a few days until the egg was fully formed and then it opened when the facehugger sensed living hosts in the cryogenic compartment.
Although this is one of the last big science-fiction movies to use mostly traditional special effect techniques (miniatures, animatronics and optical visual effects), there is one notable effects shot that was computer-generated: the head of the Alien cracking after it has been cooled with water. Other uses of computer-generated graphics include minor details, such as added shadows and debris particles.
Special Effects company Amalgamated Dynamics built a special puppet of the queen alien for a sequence cut from the film. Originally, the queen alien was supposed to gestate in Newt until the EEV crash, when it would swim out through the mouth of Newt's dead body and embed itself in Ripley. This accounts for the confusing sequence at the film's opening when the facehugger is seen attacking Newt's cryotube, not Ripley's, which only cracks during the actual ejection sequence. Though not in the final film, this scene does appear in the comic book adaptation.
The company name written in Japanese can be briefly seen on the black box as Ripley retrieves it and on a poster in the office where 85 and Ripley contact the company for the second time. In a scene towards the end of the movie where Ripley and the inmates discuss the killing of the alien, several Kanji characters can be seen on the wall: "Chô-kô'on kiken" (danger: extremely high heat). The scrap yard where Bishop is discarded also displays a large red "tetsu" (iron).
Rex Pickett wrote the draft before David Giler and Walter Hill turned in their final shooting script. Pickett's screenplay keeps the former prisoners more faithful to their convictions since they never curse or use bad language. In the scene where Ripley conducts a cat scan the screenplay by Rex Pickett clarifies that the larva is a distinctively visible queen because there are tiny white spots which are the future eggs. This explains how Ripley knew that she was carrying a queen embryo. The Company also knew this vital information since the catscanner data are transferred to their mainframe.
Michael Behin had stated in an interview that he was deeply hurt that his character from "Aliens" Corporal Duane Hicks was killed off, after escaping with Ripley, Newt and Bishop at the end of the previous film and did not understand why Hicks had to be killed off.
One of the reasons for Newt being killed off, the Fiorina 161 prison planet has convicted child molesters, which would had resulted in a attempted child molestation scene, which the child molester convicts attempted to rape Newt. Instead, the rapist convicts try to rape Ripley.