There are three modes of play in the game: the first is Story Mode, which allows a single player to complete the game story with a limited selection of heroes available; the second mode is Challenge Mode, which allows up to four players to play together with an increased choice of thirty different Marvel superheroes and supervillains; the final mode of play is Freeplay Mode, which allows the player to go back to any level and replay it as any playable character.
The game features levels based on locations from the animated series, and also has a number of collectable objects from the Marvel Universe that unlock additional in-game content such as costumes, as well as some items being unlocked by completing mission objectives.
The Story Mode is loosely based on the Marvel: Ultimate Alliance franchise. After completing the first three missions, the player gets sent to the Hellicarrier to continue with their mission, try out Freeplay or even find some hidden objects in the Hellicarrier each time a mission is completed.