As originally scripted, the Golden Gate Bridge sequence was originally in the middle of the film; Magneto was to have moved it to Alcatraz Island to free Mystique, as the facility would have been revived as a special mutant prison. The final battle was to take place in Washington, D.C., which was set to be home to Worthington Labs. Thus, Magneto's plan would have been twofold: destroy the "cure" and take control of the White House. However, when Brett Ratner signed to direct, he decided the bridge sequence would create a more dramatic climax if moved to the end, so the script was rewritten to have Alcatraz transformed into the Worthington Labs facility (which is somewhat nonsensical, since Alcatraz is a National Monument, and thus cannot be owned or altered by a private company).
When Bryan Singer was going to direct, he and his writers Dan Harris-Michael Dougherty wrote a treatment solely based on the "X-Men" storyline 'The Dark Phoenix Saga': the deceased Jean Grey returns, with a new, more destructive personality called the Phoenix. She would be manipulated into joining the Hellfire Club, by their telepathic leader Emma Frost (Sigourney Weaver was intended for the role). A three-way battle occurs between the Club who want to take over the world, the X-Men who want to save their comrade, and Magneto's Brotherhood who want the Phoenix for their own plans. At the end, to save everyone Jean kills herself, but her spirit lives on and transcends into a divine being, which Dougherty compared to the star child in 2001: A Space Odyssey (1968).
In a June 2009 interview, Bryan Singer admitted that he regretted declining to direct this film in favor of Superman Returns (2006), confessing that he realized his mistake "before I was watching [the third X-Men film], during watching it, after watching it."
The popular mutant Gambit was going to appear in the film and would have been a love interest of Rogue and a rival for Iceman, similar to how Kitty Pryde was Rogue's rival for Iceman's affections. However, Fox was developing X-Men Origins: Wolverine (2009) and stipulated that no mutant could appear in both X-Films, and so Gambit was removed from the script. Channing Tatum was in the running for the role before it was removed.
With the appearance of Beast (though he was in the previous film) and Angel, the original X-Men team that were formed in 1963 (Professor X, Cyclops, Phoenix, Beast, Iceman, Angel) now fully appear in this film, though not all together.
Cyclops (James Marsden) appears in the movie for a total of 4 minutes, 40 seconds. In the comic books, Cyclops was a main character of the Phoenix/Dark Phoenix storyline in the X-Men comic books that this film's story was based upon.
Fox originally intended this to be the final "X-Men" film featuring any of the original cast, forming a trilogy somewhat akin to the "Star Wars" films, with possible spin offs based on individual characters from the series beginning with X-Men Origins: Wolverine (2009). Late in post-production, the studio reversed this intent, and director Brett Ratner re-edited and re-shot scenes to make the film more open-ended. After mixed critical and box-office reception for X-Men Origins: Wolverine (2009) and troubled development of a Magneto origin film, Fox made several unsuccessful attempts at developing a fourth film before deciding to reboot the series with X-Men: First Class (2011), and later, X-Men: Days of Future Past (2014) which would eliminate certain plot elements of this film from continuity and allow further "X-Men" sequels with the original cast and characters to be produced.
Halle Berry had initially decided not to reprise her role as Storm for this film, citing lack of character development in the previous two installments and a tense relationship with director Bryan Singer. However, after Singer's departure and suffering a major box-office flop with Catwoman (2004), Berry agreed to return on the condition that her role be expanded. Consequently, in this film Storm replaces Cyclops and Professor Xavier as team leader of the X-Men (which is keeping with the comics, where for a time Storm served as team leader in Xavier's absence).
Cain Marko's line "Don't you know who I am? I'm the Juggernaut, bitch" was inspired by a popular web parody film that made use of scenes from X-Men (1992). Throughout the parody , the Juggernaut character repeatedly says, "I'm the Juggernaut, bitch." According to the Wikipedia, Brett Ratner even has a link to this parody on his own website. (Whether or not the parody itself was inspired by a mis-heard line from an old X-Men video game is irrelevant to film's usage of this line, since it's clearly an homage to the web parody)
The mutant Nightcrawler was going to make a cameo appearance in the film; Alan Cumming, who'd played Nightcrawler in X-Men 2 (2003), was going to reprise the role, despite his discomfort with the prosthetic makeup he had to wear for his role. The cameo was so short, however, that the filmmakers felt the long and costly makeup process was not worthwhile, so he was omitted from the film - the video game X-Men: The Official Game (2006) (VG) mentions that Nightcrawler joined the X-Men, but left because he didn't appreciate their life of action and violence.
The idea of a cure developed by Dr. Kavita Rao, Beast's interest in it, and the prominent roles played by Kitty Pryde and Colossus, were inspired by Joss Whedon's story 'Gifted' which took place in the first six issues of "Astonishing X-Men".
Summer Glau auditioned for the role of Kitty Pryde. She looked to Joss Whedon, who gave her a part in Firefly (2002) and Serenity (2005), for advice because she knew he was a big "X-Men" fan, unaware that he had written issues of "Astonishing X-Men" for Marvel, most prominently the 'Gifted' storyline about the mutant cure. Her audition script turned out to be pages from Whedon's "Astonishing X-Men" #5.
A line that President says "Hell hath no fury like a woman scorned" is originally from a play The Mourning Bride (1697) by William Congreve (English playwright and poet who lived 24 January 1670 - 19 January 1729), and says: "Heaven has no rage like love to hatred turned, Nor hell a fury like a woman scorned".
In the comics, Jean Grey's original costume (Marvel Girl) was green/gold when she first became the Phoenix, keeping the green/gold color scheme. When Jean turns into the Dark Phoenix her outfit's colors changed to red/gold. In this film, the Phoenix is dressed in a red dress from the time she appears in Jean Gray's home. The red dress reflects the Dark Phoenix persona as this story line is heavily influenced by the Dark Phoenix Saga.
For the opening flashback, the VFXperts created a special program that enabled "digital skin-grafting": with the use of old photos of Patrick Stewart and Ian McKellen, complex keyframing (dissolving an image into another image, i.e. old actors into younger-looking versions) was applied to the scene to digitally make them appear 20 years younger.
Brett Ratner cast Ellen Page as Kitty Pryde after seeing Page in Hard Candy (2005). She initially turned down the role, but after Ratner personally called her with the script, she agreed to do the role.
Cast members Patrick Stewart, Famke Janssen and Kelsey Grammer have all appeared on 'Star Trek: The Next Generation (1987)(TV)'. Grammer plays Dr. McCoy in this film. The original crew of the Enterprise also featured a Dr. McCoy.
In Dr McCoy's first scene, he is seen reading an issue of the "Scientific American" magazine, which features as its cover story "Tracking Mutations". The issue is an existing one, which had released on October 2005.
The maneuver where Colossus grabs Wolverine and throws him at something (spinning around a few times to gain momentum) is known as the Fastball Special and is an iconic move in the "X-Men" saga. The Fastball Special in this film is based on John Cassaday's "Amazing X-Men" #6.
The Worthington Labs building in San Francisco Bay (where Angel breaks free and flies off) is actually the Sheraton Hotel Wall Centre in Vancouver, Canada. In a remarkable coincidence, it is just across the street from St. Andrew's Wesley Church, the same church where Jean and Storm find Nightcrawler in X-Men 2 (2003).
Bryan Singer was in the middle of a three-picture deal made with Fox beginning with X-Men 2 (2003), and keen to make X-Men 3, but he and Fox were unable to come to terms. During this time, Warner offered him the chance to direct Superman Returns (2006) immediately. Singer informed Fox that he was going to take this opportunity and would still like to return to direct X-Men 3. As the consequence, his deal was terminated and Matthew Vaughn briefly joined the production before he backed out. Brett Ratner was the finalist for the director's role for the first X-Men movie, having experience of making a successful film out of a rushed production with Rush Hour (1998).
The Danger Room sequence presents the scenario of a war-torn world filled with mutant-hunting robots (known in the film as Sentinels). This scenario is a homage to the "X-Men" storyline 'Days of Future Past', which featured time-travel and a future that was similar to what the Danger Room presented.
Matthew Vaughn was hired in March 2005. Vaughn cast Kelsey Grammer as Beast (Dr. Hank McCoy) and Vinnie Jones as Juggernaut (Cain Marko), and also conceptualized several scenes for the film. He got no farther, however, because family issues forced him to drop out of filming. Vaughn was also cautious of Fox wanting to rush production: "I didn't have the time to make the movie I wanted to make. I had a vision for how it should be, and I wanted to make sure I was making a film as good as X-Men 2 (2003), and I knew there was no way that could be." Vaughn's ideas and casting of Grammer and Jones stayed in the final film though.
The Juggernaut in this film is based on his appearance in the "Ultimate X-Men" comics (in that series he is a natural mutant, while in the original Marvel comics he got his ability from a mystical jewel).
The mutant Kitty Pryde was named after an actual person, a former classmate of "X-Men" writer John Byrne. Upon the release of X-Men (2000), reporters tracked down Pryde in Calgary to interview her about the film (she has now changed her name to K.D. Pryde, and states that she appreciates the comics, but wishes to be known as more than just a heroine's namesake). The comic-book Pryde appears in all three X-Films, but is played by different actresses (Sumela Kay, Katie Stuart, Ellen Page) and only has a major role in X-Men: The Last Stand (2006), until X-Men: Days of Future Past (2014).
When director Bryan Singer dropped out of production, Hugh Jackman recommended Darren Aronofsky to replace him, having worked with Aronofsky in The Fountain (2006). Joss Whedon turned it down to work on a "Wonder Woman" movie (ironically his "X-Men" comic 'Gifted' would inspire the final film's plot). 'Rob Bowman' and Alex Proyas were considered for the job. Zack Snyder was approached, but he was committed to 300 (2006); Peter Berg was approached, but turned down the job. Matthew Vaughn was hired in March 2005, but with a release date set of May 2006, he realized he could not put together a good film in such a short time and left. Finally Brett Ratner was hired, who had experience of making successful films out of rushed productions, as seen with Rush Hour (1998).
According to VFX supervisor John Bruno, about $35 million (a sixth of the film's budget) was spent on the Golden Gate sequence. This included constructing a full-scale section of the bridge that was about the size of a basketball court (94 feet), and then using computer-generated imagery on the rest of the Bridge and its background.
After Brian Singer saw the movie, he said he would have done it differently. He would have had a distraught Cyclops build the danger room to become he felt the X-Men needed to be stronger and faster to have saved Jean. Also, he said he would have had Phoenix on a quest around the world freeing trapped mutants and rescuing them.
Kelsey Grammer's casting as The Beast is somewhat ironic. In Frasier: The Show Must Go Off (2001), the titular character played by Grammer, goes to a comic book convention to look for X-Men comics for his son. Being a snob, and obviously dismissing comics as lowbrow and unintelligent, he felt that the comic books would contribute to the decline of his son's intellect.
According to writer Simon Kinberg, the film's plot is inspired from the "X-Men" storylines 'The Dark Phoenix Saga' (the appearance of the Phoenix) and 'Gifted' (the development of a cure for the mutant gene, sparking controversy and conflict among mutants and humans). The 'Phoenix' story represented the main/emotional theme of the film and the 'Gifted' story would be the political subplot.
Cyclops' sunglasses are modified Oakley's "Penny" model, a limited edition sunglass, with a custom tint created specifically for the film. Also, Hank McCoy wears Oakley "Why 3" glasses specially made to fit his character.
Philippe Rousselot was hired as cinematographer by Matthew Vaughn, and initially stayed on when Brett Ratner took over as director. Not long into shooting, however, Rousselot quit the project (later saying that signing on to shoot the film was the biggest blunder he'd ever made). Dante Spinotti, the cinematographer on Ratner's previous two films, was available, and he took over for most of the remaining filming. He had to leave about a week before the end of shooting as he was committed to working on The Contract (2006), and so James M. Muro was hired for the remainder of shooting.
Stan Lee, Chris Claremont:
The "X-Men" creator and longtime "X-Men" writer appear in the opening scene, as neighbors of Jean Grey. They are credited as "Waterhose Man" and "Lawnmower Man," respectively. (Claremont created the "Dark Phoenix Saga" in the "X-Men" comics, which was the basis of the Jean Grey/Phoenix storyline in this film.)
The trivia items below may give away important plot points.
While James Marsden was unavailable due to filming "Superman Returns" at the same time as this film, 20th Century Fox had always planned to have Jean Grey kill off Cyclops in the film. Screenwriter Zak Penn talked about the lack of Cyclops in "X-Men: The Last Stand" on the message boards of the now-closed website The X-Verse, in which he participated in Q&As with fans and could only say to the fans while the film was being made that if they expected to see more of Cyclops, then fans were going to be disappointed. Penn would later say after the film's release that he and co-writer Simon Kinberg fought with Fox not to kill Cyclops but the studio insisted the character die to have a more emotional impact. The decision to kill off Cyclops received heavy backlash from fans and moviegoers, and fans still debate whether the character actually even died since his death wasn't shown on-screen and neither Storm nor Wolverine bothered to search for him when they find Jean alone at Alkali Lake.
The last scene in the film was to have Magneto regaining his abilities as he plays chess with a stranger (who he discovers is Professor Xavier, in another man's body). Neither were available for filming their scenes together, so instead two separate scenes for the two were filmed, bookending the credits.
The last scenes of Magneto and Professor X (Magneto discovers the return of his powers, Professor X reveals his survival) were not in the script, and were secretly filmed. Sirs Ian McKellen and Patrick Stewart admitted even they didn't know whether their scenes would be in the final film or not.
Magneto ending up a normal human and Wolverine's snide comment ("I'm..." "One of them?") is a tribute to the "X-Men" storyline 'House of M', which ended with Magneto rendered human with Wolverine stating he deserves "every second of his crap sapien life."
Fox Studio heads Tom Rothman and James Gianopulos debated on Rogue's final scenes: since she took the cure, Rothman wanted her to passionately kiss Bobby Drake and Gianopulos wanted her to simply hold his hand. The two executives screened the film for their daughters and the studio's female marketing executives, and the hand-holding prevailed: Gianopulos stated that the kissing "was all about sex, and they didn't want that."
The design of Cyclops and Jean Grey's tombstones is taken from the "X-Men" storyline 'Days of Future Past', where the X-Men's gravestones were in a similar deco (The X symbol with the member name below).
An early draft of the script leaked onto the Internet in June 2005 during Matthew Vaughn's brief tenure as director. The script contained notable deleted scenes and characters, including a sequence in which Rogue and Beast break into Worthington Labs to further research the "cure" serum, lifted directly from Joss Whedon's "Gifted" storyline, and a sexual relationship between Storm and Wolverine. This draft also included the character of Cecilia Reyes, a mutant scientist and rival of Dr. Kavita Rao. Somewhat ironically, Shohreh Aghdashloo was originally cast as Reyes before the character was eliminated and the actress recast as Rao instead. This version of the script also sparked the controversy surrounding the reduced screen time of Cyclops, Mystique and Professor X. In order to combat negative buzz surrounding the film, director Brett Ratner ordered several major changes in editing, and shot several new scenes to leave the film more open-ended, allowing potential for future sequels: originally Cyclops was to die on screen, murdered by Jean Grey, Professor X's death was meant to be definitive, as was the loss of Mystique's powers. Ratner re-edited Cyclops' scene to only imply his death, leaving the potential for the character to return in future sequels and added the after-credits coda of Moira MacTaggart discovering Xavier's mind transferred to a new body. Also scripted, but not shot, were scenes of Jean Grey's grave-site exploding in a fireball, implying her resurrection, and a scene of Mystique playing chess with Magneto, where she offers him a drug that will restore his powers.
The filmmakers intended the death of Professor Xavier to be a dramatic turning point. Simon Kinberg and Zak Penn were initially cautious of killing Xavier, but grew to like the idea, saying it paralleled Spock's sacrifice in Star Trek II: The Wrath of Khan (1982). To keep Xavier still in the X-Films, though, they wrote the post-credits scene where Dr. MacTaggert discovers Xavier in another man's body.
The death of Cyclops (James Marsden) was based on Marsden's availability (he had decided to film Bryan Singer's Superman Returns (2006)). The studio considered killing him off-screen with a dialogue reference, but Simon Kinberg and Zak Penn insisted that Jean be seen killing him, to emphasize their relationship.