Development on a fifth film in the Alien franchise was in progress by 2002. Scott considered returning to the series he created with his 1979 science fiction horror film Alien, to pursue a sequel that would explore the engineered origins of the series's Alien creatures, and the "space jockey"—the extraterrestrial being, who briefly appears in Alien, as the deceased pilot of a derelict spaceship. Alien star Sigourney Weaver also expressed interest in returning to the series. Aliens director James Cameron discussed the potential for a sequel with Scott, and began working with another writer on a story for the film. It was then that 20th Century Fox approached Cameron with a script for a crossover film that would pit the series's monsters against the titular characters of the Predator films; this project became the 2004 science fiction film Alien vs. Predator. After Fox confirmed that it would pursue the crossover, Cameron stopped working on his own project, believing the crossover would "kill the validity of the franchise." In 2006, Cameron confirmed that he would not return to the Alien sequel project, believing that the series was Fox's asset, and he was unwilling to deal with the studio's attempts to influence the potential sequel.
In May 2009, Fox said that the project was a "reboot" of the Alien franchise, and soon afterwards was reported as an untitled prequel to Alien. Development stopped in June 2009 when Fox clashed with Scott over his selection of former television advertisement director Carl Erik Rinsch as director. Fox was only interested in pursuing the project if Scott directed. By July 2009, Scott was contracted to direct the film, and screenwriter Jon Spaihts was hired to write the script based on his pitched idea for a direct Alien prequel. With the director and writer in place, and pleased with Spaihts's pitch, Fox scheduled a release date for December 2011, but this was eventually canceled. In June 2010, Scott announced that the script was complete and that pre-production would begin, and a filming date was set for January 2011. Fox eventually pushed to develop the project into an original work, and by July 2010, Lindelof had been hired to redevelop Spaihts's screenplay. In October 2010, Lindelof submitted his rewritten screenplay to Fox. Scott had initially requested a $250 million budget and an adult oriented project, but Fox was reluctant to invest this amount of money, and wanted to ensure the film would receive a lower age-rating to broaden the potential audience.
In December 2010, it was reported that the film would be called Paradise, named after John Milton's poem Paradise Lost, but Scott considered that this would convey too much information about the film. Fox CEO Thomas Rothman suggested Prometheus, which was confirmed as the title in January 2011. A release date was scheduled for March 9, 2012, but weeks later the release was postponed until June 8, 2012. With the name confirmed, the production team began to publicly distance the film from its Alien origins, and were deliberately vague about the connection between the films, believing it would build audience anticipation for Prometheus. Scott stated that "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 June 2011, Scott and Lindelof confirmed that Prometheus takes place in the same universe as the events of the Alien series. In July 2011, Scott 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]."
"...We're exploring the future... away from Earth and [asking] what are people like now? ... Space exploration in the future is going to evolve into this idea that it's not just about going out there and finding planets to build colonies. It also has this inherent idea that the further we go out, the more we learn about ourselves. The characters in this movie are preoccupied by the idea: what are our origins?"—Damon Lindelof, concerning the scope of Prometheus.
Spaihts met Scott in late 2009 and they discussed Scott's desire to pursue an Alien prequel. Spaihts offered his concept, including a "bridge" that would connect the story of the film's human characters to the Alien saga. Spaihts was quickly hired, which he credited to the reception of his "bridge" idea. Spaihts claimed he created the concept spontaneously, without preconception. Spaihts wrote a 20-page "extremely detailed outline"; within three and a half weeks he had completed his first draft, and he submitted it to the producers on Christmas Day, 2009. Within 12 hours, Scott returned the script with notes for changes, and Spaihts spent the Christmas holiday redrafting.
Spaihts was tasked with exploring unresolved mysteries from Alien, such as the Space Jockey. He considered the mysteries of Alien to be alien in nature, and said, "all the mysteries have alien players: the exoskeleton nightmare and ... the elephantine titan that was called the 'space jockey' ... How do you make anyone care about events between creatures like this?" His solution was to link the alien mysteries to the past and future of humanity. He said: "if that story is somehow ours, and deeply enmeshed with the human story. That story changes meaning within our own life, things of such significance that we think of our own lives differently." Spaihts found translating Scott's stylistic visual concepts to text difficult, and he periodically constrained some of Scott's ideas. He reminded Scott that in the scene they were discussing, the characters were subject to gravity and so could not simply float. By April 2010, the script was on the fourth draft. Scott said about the script, "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?" In June 2010, Scott announced that the script was complete and ready for filming.
However, Scott instead contacted Lindelof and asked him to review Spaihts's script. Within the hour, a messenger delivered the script to Lindelof and informed him that he would wait outside to return it as soon as Lindelof had finished reading it. Lindelof was unaware of what Scott and the producers liked about the existing script, and informed them that he found the general concept appealing, but that the story relied too heavily on elements of the Alien films, such as the Alien creatures' life-cycle. As a direct prequel to Alien, it was focused on leading into that film's story, and recreating the familiar cues of that series, and Scott wanted to avoid repeating his previous accomplishments. Lindelof said, "If the ending to [Prometheus] is just going to be the room that John Hurt walks into that's full of [alien] eggs [in Alien], there's nothing interesting in that, because we know where it's going to end. Good stories, you don't know where they're going to end." "A true prequel should essentially precede 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."
Lindelof said that the other parts of the script were strong enough to survive without the Alien hallmarks, such as the Alien creature, which he believed had been diluted by the exposure it had received. He said, "[The producers] were just looking for someone to say to them, Hey, we don't need the Alien stuff in here. It shouldn't be about that. It can be a part of this movie, but it shouldn't be what it's about." Lindelof said that the film could instead run parallel to the Alien series, and that a sequel would be Prometheus 2 and not Alien, and submitted an idea for how such a sequel could work. Lindelof met with the producers the following morning, and was hired shortly afterwards in late 2010. Under Lindelof, the script diverged from Spaihts's Alien prequel into an original creation. Scott and Lindelof worked together five days a week between July and August 2010 to construct the vision Scott wanted to convey and decide what script changes were needed, including scaling back the Alien symbolism and tropes. In August and September 2010, Lindelof spent almost five weeks writing his first draft, which he submitted in mid-September 2010. Inspired by Blade Runner and Spaihts's script, Lindelof thought that it would be possible to combine an Alien story of action and horror with "the Blade Runner thematic," to ask bigger questions than he felt were normally posed in science fiction films. Lindelof said,
Blade Runner might not have done well [financially] when it first came out, but people are still talking about it because it was infused with all these big ideas. [Scott] was also talking about very big themes in Prometheus. It was being driven by people who wanted the answers to huge questions. But I thought that we could do that without ever getting too pretentious. Nobody wants to see a movie where people are floating in space talking about the meaning of life ... That was already present in [Spaihts's] original script and [Scott] just wanted to bring it up more.
Scott's story concept was partially inspired by Chariots of the Gods?, Erich von Däniken's work about the theory of ancient astronauts which hypothesizes that life on Earth was created by aliens. Scott said, "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." Spaihts originated the idea that David, the android, is like humans but does not want to be anything like them, eschewing a common theme in "robotic storytelling" such as Blade Runner. He also developed the theme that while the human crew are searching for their creators, David is already among its creators. Scott liked these ideas and further explored them in Lindelof's rewrite. For Shaw, Lindelof felt it was important that she was distinct from Alien 's Ripley, to avoid inevitable comparisons between the two characters. In Spaihts's draft, Shaw was directly responsible for the events of the plot because she wants to seek out potentially dangerous knowledge. As with David, Lindelof expanded this facet of the character during his rewrites. He spent approximately eight months developing the script, finishing in March 2011 as filming began.
Pre-production began in April 2010. A team developed graphic designs for the film. Scott convinced Fox to invest millions of dollars to hire scientists and conceptual artists to develop a vision of the late 21st century. The production of Prometheus was marked by a high degree of secrecy and story details were kept "extremely under-wraps." Ridley Scott was determined to maintain the secrecy of the plot, and he 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 actor outside the US, and then stood guard while the actor read the script. Scott said, "I was insistent that the script not leak onto the internet, where it gets dissected out of context, which spoils it for everyone."
In July 2011, Lindelof said that the film would rely upon practical effects, and would use CGI generally for on-set pre-visualization of external space visuals. Scott said that "you can pretty much do anything you want" with digital technology, and, "Doug Trumbull once said to me 'If you can do it live, do it live.' That was 29 years ago. Even though we have remarkable digital capabilities I still say do it live. It's cheaper." Cinematographer Dariusz Wolski convinced Scott that it would be possible to film in 3D with the same ease and efficiency of 2D filming. 3D company 3ality Technica provided some of the rigs and equipment to facilitate 3D filming, and trained the film's crew in their proper operation. According to Scott, the decision to film in 3D added $10 million to the film's budget. Since 3D films need high lighting levels on set, the hallmark dark and shadowy atmosphere of the Alien films was added in post-production using color grading processes, and the 3D equipment was based on post-Avatar technology.
Principal photography began on March 21, 2011, lasted 82 days, and had an estimated $120–130 million budget. Filming began at Shepperton Studios and Pinewood Studios in England. Scott used eight sound stages for filming, including the 007 Stage. Studio space was limited and the crew had to make five stages work for approximately 16 sets, and increased the size of the 007 stage by over 30%.
Exterior shots of the alien world were shot in Iceland, where filming occurred for two weeks. It commenced on July 11, 2011, at the base of Hekla, an active volcano in southern Iceland. Speaking about working at the volcano, Scott said, "If one is afraid of nature in this profession then it would be best to find a different job". Filming also took place at Dettifoss, one of the most powerful waterfalls in Europe. The Iceland shoot involved 160 Icelandic crew members and over 200 imported crew. Scott said that the filming in Iceland comprised approximately fifteen minutes of footage for the film, and that the area represented the beginning of time. Morocco had been chosen as a location for these scenes, but the 2010 Arab Spring protests forced the change of venue. Alternatives including the Mojave Desert had been considered, but Scott explained that Iceland was ultimately chosen because "here it is so rough and 'Jurassic-like' and that proved decisive".
In September 2011, filming moved to the Ciudad de la Luz audiovisual complex in Alicante, Spain. Shooting areas included the complex's large water tank, and a nearby beach. The complex was booked from August 22, 2011, through to December 10, 2011, and set construction occurred from August until late September. Approximately 250 people worked on the three-month-long Spain shoot, generating over €1 million in the local economy. Filming also took place in the Wadi Rum valley in Jordan.
Scott avoided using green screens unless necessary. Instead, he used various items so the actors would know where they should be looking in any particular scene on the practical sets where CGI elements would be inserted in post-production. Rapace said that green screens were used fewer than six times during filming. The production used five 3ality Technical Atom 3D rigs, four of which were configured with Red Epic 3D cameras set on camera dollies and tripods, which were continuously in use during filming. The fifth rig used an Epic camera as a steadicam, which was used only occasionally.
Scott focused on using the 3D footage to increase the illusion of depth. Despite this being his first 3D film he found the process easy. He said, "You can literally twiddle a knob and the depth will increase", and, "the trick is not to overdo it". In December 2011, Rapace undertook additional dialogue recordings for the film. Additional pick-up scenes were filmed during January 2012, including a one-day shoot on the Isle of Skye, Scotland, and a new scene shot at a cave in the Scottish mountains. For dark scenes, the film was color graded to specifically compensate for the light loss of 3D glasses, to ensure the image was comparable to the 2D version.
In July 2011, Scott said that he was filming Prometheus with both adult-oriented R and more accessible PG-13 film ratings in mind, allowing the more adult content to be cut if necessary without harming the overall presentation. Scott said he had a responsibility to 20th Century Fox to be able to present a PG-13 cut of the film if the studio demanded, allowing it to be viewed by a wider potential audience. When asked about the rating, Scott said, "the question is, do you go for the PG-13, or do you go for what it should be, which is R? Financially it makes quite a difference ... essentially it's kinda R ... it's not just about blood, it's about ideas that are very stressful." Scott also said that, regardless of rating, he would present the most aggressive cut of the film he could, while Rothman said that Scott would not be forced to compromise the film's quality to avoid an R-rating. On May 7, 2012, Fox confirmed that the film had received an R-rating and would be released without any cuts being made. According to Scott, the scene of Shaw surgically removing her alien offspring was the significant cause of the restrictive rating, and it was suggested that removing the scene entirely would be the only way to gain a lower one. A fight scene between Shaw and the Engineer was shortened because Scott decided that Shaw directly wounding the Engineer diminished his role. Scott concluded work on the film in March 2012.
Marc Streitenfeld, who had worked with Scott on earlier projects, composed the musical score for Prometheus. It took just over a week to record with a 90-piece orchestra at Abbey Road Studios in London, England. Streitenfeld began writing ideas for the score after reading the script before filming commenced. He used some unusual techniques to compose the score, and said, "I actually wrote out the sheet music backwards so the orchestra played it backwards and then I digitally flipped it. So you're hearing the score as it's written, the same melody, but with a backwards sounding orchestra which gives it a kind of unusual, unsettling sound." The Prometheus (Original Motion Picture Soundtrack) album was released on iTunes on May 15, 2012, and on CD on June 4, 2012. It features 23 tracks by Streitenfeld and two supplemental tracks by Harry Gregson-Williams. Frédéric Chopin 's "Raindrop prelude" (1838) is also featured in the film.