To comic book fans, the Marvel Civil War might seem all too familiar. However, to gamers who have never read any sort of Marvel comic, the plot to Ultimate Alliance 2 might seem a bit confusing and overwhelming at times. To simplify, after a brief mission with Nick Fury, the Government is held up in an uproar about Super Powers and the Superheroes themselves and thus enacts the Superhero Registration Act. This forces all superheroes to reveal their secret identities to the Government and fully revealing themselves to the public. This also causes some tension between the heroes themselves and causes a Civil War.