Marvel: Ultimate Alliance features a deep, rich gameplay experience by offering total team customization, where players create their own team name, icon and vehicle, as well as establish their team reputation as they play throughout the story. Gamers also have the option to level up each character individually to their liking, or all team members at the same time to keep their heroes balanced. With the game's new combat system, players battle against the world's most notorious Marvel Super Villains in the air, underwater, and on the ground, using grappling, blocking and dodging moves, by charging up their Super Hero powers before unleashing them, and using environmental objects as one and two-handed weapons.

Marvel: Ultimate Alliance features a unique storyline where the missions players accept, the objectives they complete, and their interactions with other characters throughout the game directly impact how the story plays out. The game also features a robust multiplayer component where fans can band together with friends as their favorite Marvel Super Heroes, and fight evil in both on and offline cooperative story modes. There's also a Competitive Mode where the game tracks various in-game stats so players can see how well they stack up against one another - affecting the amount of experience points earned and how equipment is distributed.