Director Bryan Singer left the project in July 2004 to make Superman Returns for Warner Bros., admitting he 'didn't fully have X-Men 3 in my mind' at the time.

Singer's original treatment with X2 writers Dan Harris and Michael Dougherty focused on Jean Grey's resurrection and would have introduced villainess Emma Frost, a role intended for Sigourney Weaver.

Several major directors turned down the film before Brett Ratner was hired, including Darren Aronofsky, Joss Whedon (who instead integrated his comic storyline 'Gifted' into the script), Zack Snyder, Peter Berg, and Guillermo del Toro.

Matthew Vaughn was originally hired to direct and cast Kelsey Grammer, Dania Ramirez, and Vinnie Jones, but withdrew due to family issues and concerns about Fox's tight deadlines; in 2023 he also said he left after executives tried to sign Halle Berry using a fake script.

James Marsden's Cyclops was killed off early in the film specifically because of a scheduling conflict with Superman Returns, which also caused Marsden, editor John Ottman, and writers Harris and Dougherty to leave the X-Men franchise.

Channing Tatum was considered for the role of Gambit before the character was ultimately written out of the film entirely.

Alan Cumming's Nightcrawler was cut from the script because the studio felt his minimal part didn't justify the long, costly prosthetic makeup process he had found uncomfortable during X2.

Elliot Page initially declined the role of Kitty Pryde, not wanting to jump into Hollywood filmmaking, but changed his mind after reading the script and wanting the experience of playing a superhero.

Ian McKellen's tight schedule, juggling The Da Vinci Code and London theater work, required filming him separately in England before digitally superimposing him into the Vancouver sets.

Both ending scenes were kept secret and not included in the shooting script; Ratner filmed the post-credits Xavier scene with a small crew during a lunch break and later traveled to London to film Magneto in the park.

In a 2017 interview during the MeToo movement, Elliot Page accused director Brett Ratner of outing him as a lesbian at a cast and crew meet-and-greet during production, which co-star Anna Paquin corroborated.

Visual effects supervisor John Bruno distributed 900 effects shots across eleven companies in four countries, emphasizing practical effects and only using CGI when necessary, including a Cirque du Soleil flying rig for Angel and Storm's aerial stunts.

The Golden Gate Bridge sequence consumed about one-sixth of the effects budget and combined a physical miniature filmed over two months in Santa Clarita with CGI, since the real bridge and San Francisco could not be used or filmed from the air.

A technique called 'digital skin-grafting' by Lola Visual Effects was used to digitally rejuvenate the faces of Patrick Stewart and Ian McKellen.

Composer John Powell finished scoring Ice Age: The Meltdown early so he could accept the job of scoring The Last Stand, and incorporated musical references to the previous two films' scores as well as lyrics from Benjamin Britten's Requiem Mass for the Phoenix theme's choir parts.

Studio executives Thomas Rothman and Jim Gianopulos debated whether Rogue should kiss or simply hold hands with Iceman at the film's end, ultimately screening both options for their daughters and female marketing executives before choosing the hand-holding version.

With a $210 million budget, X-Men: The Last Stand became the most expensive film ever made at the time of its release, a record broken later that year by Pirates of the Caribbean: Dead Man's Chest.