Conceived as a prequel to Scott's 1979 "Alien", rewrites of Spaihts' script by Lindelof developed a separate story that precedes the events of Alien, but which is not directly connected to the films in the Alien franchise. According to Scott, though the film shares "strands of Alien's DNA, so to speak", and takes place in the same universe, Prometheus will explore its own mythology and ideas. Principal photography began in March 2011, with filming taking place in England, Iceland, and Spain. Prometheus is scheduled for release on June 8, 2012 in various territories through 20th Century Fox.
Since the early-2000s, a fifth installment in the Alien franchise had been under consideration. James Cameron had initially worked on a story for such an installment; it was to explore the origins of the Alien creatures. However, Cameron dropped the project after learning that Fox was pursuing Alien vs. Predator - a plot which he felt would "kill the validity of the franchise". By this time, Scott and Weaver had also expressed interest in returning to the series and both supported the idea of exploring beginnings. Scott furthered that the most logical course would be to explore the origins of the "space jockey" - the unknown extraterrestrial being, who only had a brief appearance in Scott's 1979 science fiction horror film Alien, as the derelict spaceship's deceased pilot - as well as the Aliens, should the series continue. "I think it would be great to go back, because I'm asked that question so many times: 'Where did the Alien come from?' People really want to know in a very visceral way," Weaver said. By 2008, Scott was fully attached to the project with Weaver commenting that "[he's] enthusiastic about it."
In May 2009, Fox first reported the project as a "reboot" to the Alien franchise, which was soon afterwards expressed as a then untitled prequel to Alien. Being so, Scott set the story in 2085, 30 years prior to Alien - Weaver's character, Ellen Ripley, would not play a role; neither would the "original" Alien creature. The film would explore the nature, origin, and "staggering civilization" of the alien race of the space jockey, as well as the beings' fictional anthropogenic role in the origins of humanity on Earth. Such ideas were "partially" inspired by Erich von Däniken's writings about ancient astronauts. Scott told the Hollywood Reporter, "NASA and the Vatican agree that [it is] almost mathematically impossible that we can be where we are today without there being a little help along the way... That’s what we’re looking at (in the film), at some of Erich von Däniken’s ideas of how did we humans come about." Scott's prequel, which originally went through several drafts, featured a female lead character and would also focus on terraforming and the fictitious Weyland Industries before its merger with the Yutani Corporation. Scott furthered that the original Zeta II Reticuli planetary system would be part of the prequel story and that the plot would also entail "technologically feasible" approaches and applications towards "near faster-than-light travel" which would play a key role. "Time dilation and the effects of essentially de-materializing and re-materializing" also factored in the drafts. Elaborating more, the director commented in an interview that "the film will be really tough, really nasty. It's the dark side of the moon. We are talking about gods and engineers. Engineers of space. And were the aliens designed as a form of biological warfare? Or biology that would go in and clean up a planet?" He later added, "The cast find an establishment which is not what they expected it to be, it’s a civilization but what we find in it is very uncivilized behaviour."
Scott initially sought to produce the prequel in two parts and in 3D. He also anticipated having former commercial director Carl Erik Rinsch direct it, but 20th Century Fox, which owns the Alien franchise rights, wanted Scott to be the director. By July 2009, Scott was attached to direct the film. Screenwriter Jon Spaihts had pitched to Fox his approach to the prequel. The studio and Scott liked the pitch and hired Spaihts to write the screenplay. Lindelof was later hired to revise Spaihts's screenplay. In October 2010, Lindelof submitted the revised screenplay to 20th Century Fox. The studio was pleased because it had contested Scott's proposed budget of $150–160 million and found Lindelof's screenplay to be more budget-conscious; Scott had initially requested a $250 million budget along with an R rating, but 20th Century Fox was reluctant to invest so much money in a film that was not PG-13.
In late 2010, it was reported that the film would be called "Paradise", but in January 2011, the title was confirmed as Prometheus with a release date scheduled for 2012. Scott downplayed the film's ties to the Alien franchise, saying "while Alien was indeed the jumping-off point for this project, out of the creative process evolved a new, grand mythology and universe in which this original story takes place. The keen fan will recognize strands of Alien's DNA, so to speak, but the ideas tackled in this film are unique, large and provocative." In February 2011, Scott maintained that the film was not an Alien prequel, but confirmed in December 2011, that the Space Jockey was still an aspect of the plot. Fassbender stated the film would feature elements of Alien, saying "Prometheus is absolutely connected to Alien... There's a definite connecting vein." In June 2011, Lindelof stated that he concurred with Scott's belief that the Alien creature had been "diluted" by the exposure it had received since Alien and did not want the film to be "burdened by all the tropes of that franchise with Facehuggers and Chestbursters". Lindelof stated that the film takes place in the same universe as Alien, but is not a story about the events leading into that film, saying "a true prequel should essentially proceed [sic] the events of the original film, but be about something entirely different, feature different characters, have an entirely different theme, although it takes place in that same world." In June 2011 Scott said that Prometheus does occupy the same general universe as Alien, and in July 2011 he stated that "by the end of the third act you start to realize there’s a DNA of the very first Alien, but none of the subsequent [films]" and called it "pretty organic to the process and to "Alien", but maintained a distinction between the two films, saying "we go back, we don't go forward." In a February 2012, interview, Lindelof described the film as a hybrid in tone between Alien and Blade Runner, pushing a philosophical idea alongside action.
Production of Prometheus has been marked by a high degree of secrecy with story details "extremely under-wraps." Determined to maintain the secrecy of the plot, Scott required the cast to sign clauses to prevent them disclosing story details, and the cast were only allowed to read the script under supervision in Scott's production office. One exception was made when a courier flew to one of the actors in a foreign location and then stood guard while the actor read the script.
On November 10, 2010, a tweet by Henry South, a visual FX designer working on the Alien prequel, indicated the film had gone into production. Production designer Arthur Max is heading the film's Pinewood Studios art department, whose task is to deconstruct the first Alien and reverse-design the prequel from the original art and visuals. Scott stated that the alien itself would not appear in the film, saying "they [the Alien sequels] squeezed it dry. He [the alien] did very well. He survived...and no way am I going back there." Scott brought Alien creature designer H. R. Giger onto the project to design murals that would appear as some of the first artefacts of the alien world in the film. At Comic-Con, Lindelof stated that the film would be keeping as many practical effects as possible. The only mention of CGI used was for on-set pre-visualization of external space visuals. Scott recalling advice special effects artist Douglas Trumbull gave him on the set of Blade Runner stated, "if you can do it live, do it live", with Scott claiming that although "you can pretty much do anything you want" with digital technology, practical effects are more cost effective. In designing the space suits worn by the ship's crew, Scott was inspired to have the suits include spherical glass helmets, inspired by a story in the autobiography of Apple co-founder Steve Jobs about building an office out of Gorilla Glass, with Scott remarking "If I’m in 2083 and I’m going into space, why would I design a helmet that has blind spots. What I want is something where I have 360 [vision]. Glass, by then, will be light and you won’t be able to break it with a bullet."
Roger Christian, art director on the first Alien, speculated that the film would be shot in 3-D, which was eventually confirmed by Ridley Scott. Since 3-D films need high lighting levels on set, the hallmark atmosphere of the Alien films with darkness and shadows will be added in post-production through grading processes, while the 3-D equipment will be based on post-Avatar technology.
Filming began in March 2011 using Red Epic cameras fitted with Element Technica Atom 3D rigs. After three weeks' filming at Pinewood Toronto Studios, production moved in May to Pinewood Studios in London. The 007 Stage was used for one of the set pieces. On using the 007 Stage and other filming facilities, Scott stated, "It's the story of creation, the gods and the man who stood against them. It's not a small film. I'm using the giant James Bond 007 stage at Pinewood and six other sound stages to film it." Filming went underway in Iceland for a two-week shoot. Ridley Scott stated that this location would occupy the first 15 minutes of the film as a "beginning of time" sequence. It was also reported that filming would move over to Spain in November where scenes involving a water tank and a ship would be shot. Construction reportedly went underway in Alicante to recreate the ship of the protagonists in the film.
Actress Charlize Theron stated that, while on set, "Ridley started doing this interesting thing, where he would have me stand in corners and lurk all the time, and it wound up being really mysterious." Generally speaking, Rapace shared, "I was out there filming for about six months and it was super-intense, my body was in so much pain sometimes but it was absolutely amazing." She also confessed that it felt like returning to Earth after the conclusion, in Iceland, of principal photography.
After spending two weeks working on additional dialogue recordings for the film during December 2011, Noomi Rapace described Prometheus in post-production as "brutally beautiful." Scott stated that he will edit both PG-13 and R-rated cuts of the film to be submitted to Fox for review when the film is finalized.
Marc Streitenfeld, who worked on several of Ridley Scott's previous films, will be composing the musical score for Prometheus. Scott processed Streitenfeld's score at Abbey Road Studios in London, England, the studio formerly used by The Beatles.
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