X-Men: The Official Game acts as a story bridge between the second and third X-Men movies. In the game, the player takes control of Wolverine, Iceman and Nightcrawler, as they deal with the aftermath of the incident at Alkali Lake. The heroes return to Alkali Lake to recover two stolen Cerebro parts, and find out that an unknown organization is doing a salvage operation on the base. What they uncover reveals to be a threat to all mutants...

The three playable characters have distinct fighting abilities. Wolverine fights from a fixed third-person view; the player essentially has to "button mash" his way through hordes of soldiers and classic X-Men villains as Sabretooth and Lady Deathstrike. Iceman can fly; his abilities are widely used when he traverses the ice bridge to fly out and save places such as a nuclear power plant and the Statue of Liberty. As Nightcrawler, the player views the world from a free third-person perspective; he possesses a teleportation ability, which allows him to drop on his enemies while getting the missing Cerebro parts and saving the Brooklyn Bridge from Mirror Man.