This game was made to be a tie-in with the movie X-Men: The Last Stand (2006) and features the movie's logo (an "X" with Wolverine's claws in front to make a roman numeral 3). However, instead of simply repeating the plot of the movie, the story in the game takes place between X2 (2003) and X-Men: The Last Stand (2006).
Zak Penn and Chris Claremont co-wrote the story for this game. Penn is the co-writer of X-Men: The Last Stand (2006), and Clearmont was a longtime writer on the X-Men comic books, establishing the personas for many of the "all-new, all-different" X-Men team, which featured then new members Wolverine, Nightcrawler, Storm, Colossus, Banshee, and Thunderbird. Claremont is also best known for "The Dark Phoenix Saga" which is the main inspiration for the movie, "X-Men: The Last Stand".
Hugh Jackman (Wolverine), Shawn Ashmore (Iceman), Alan Cumming (Nightcrawler), Patrick Stewart (Prof. Charles Xavier), Tyler Mane (Sabertooth) and Eric Dane (Multiple Man) are the only actors from the movies to reprise their roles for the video game. It's a far better turnout than the previous X-Men movie tie-in game, X2 - Wolverine's Revenge (2003), which only had Patrick Stewart reprise his role from the movie.
In this game, Dr. Hank McCoy is seen already transformed into the furry blue haired Beast. Dr. Hank McCoy made a brief cameo in X2 (2003) on a television screen in a bar and still had his more human appearance. In X-Men: The Last Stand (2006), his first full appearance in the films, Beast is seen his furry blue haired form since the movie chronologically takes place after this game.
This game confirms that the movie version of Storm also has claustrophobia, the fear of confined spaces, just like in the comic book. Although Storm's claustrophobia was never brought up before in X-Men (2000) and X2 (2003), it was also not brought up again in X-Men: The Last Stand (2006).