There were originally more victims in "X-Men: The Last Stand" where Professor X was disintegrated by Phoenix. In a storyboard obtained by Comic Book Movie, Magneto was supposed to meet his demise as well.
In the movie's final version, however, Magneto was saved due to "the cure" Beast injected on him. Magneto originally opposed the serum which was invented by pharmaceutical company Worthington Labs to suppress mutants' X-gene.
Moreover, the film featured the final battle taking place at Alcatraz Island but the storyboard showed Washington DC setting.
Brett Ratner directed the third "X-Men" film after Bryan Singer who helmed the first two films left the franchise to make "Superman Returns". Cyclops also became Dark Phoenix's victims, while Mystique and Rogue were among those taking "the cure" either forcibly or voluntarily.
Patrick Stewart starred as Prof. X, Anna Paquin as Rogue, Kelsey Grammer as Beast, Ian McKellen as Magneto, Rebecca Romijn as Mystique, Famke Janssen as Phoenix, and James Marsden as Cyclops. Released in 2006, the film got mixed reviews but gained success at box office.