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X-Men Legends II contains expanded versions of the gameplay features from the original X-Men Legends, with several notable additions:

• Online multiplayer modes.
• New characters are playable, including characters from the X-Men and the Brotherhood.
• New powers and abilities are available for all characters, and the player can switch between more than 4 mutant powers at once.
• After beating the game, the player could start a new game with their old stats.

Several characters from the first X-Men Legends were dropped from the roster of playable characters in the sequel: Jubilee, Magma (despite her being the main character of the first game), and Psylocke do not appear in X-Men Legends II, and Beast and Emma Frost appear but are not playable. A boss from the first game, Avalanche, also did not get mentioned in this game.