Like the X-Men Legends series, Ultimate Alliance is an action role-playing game and retains much of the same gamplay and combat. However, some of the role-playing elements have been simplified. Character powers can still be upgraded as the characters gain experience points, but there are fewer powers compared to X-Men Legends II, and the game now defaults to automatically upgrading them. Character stats are only upgraded automatically.
All of the main versions of the game allow the players to select a team of four characters from a roster of at least 23 playable characters. Some characters from the base roster are not initially available and need to be unlocked, and certain consoles feature additional exclusive characters. Players can create their own superhero teams or recreate famous teams from the comics. Bonuses are also available if forming certain groups (e.g. the Avengers, Defenders, Fantastic Four, Marvel Knights, or X-Men).
All versions of the game (except for PSP) feature local multiplayer with up to four players playing at once, and many contain online multiplayer as well. The game has multiple possible endings depending on which optional missions the player completes. Throughout the story, the player can play trivia and collect concept artwork and "simulator discs", which unlock additional comic book missions that take place outside of the story.
