The storyline for Marvel Ultimate Alliance 2 is based on two recent comic book arcs, Secret War and Civil War. The first act features A-listers Cap, Iron Man, Spidey, and Wolverine, led by Nick Fury on a... well... secret war. The fallout from this event, plus a nice cut scene taken directly from the Civil War miniseries, leads to the heroes dividing. One side, led by Iron Man, supports the registration and deputizing of all superhumans. Cap leads the anti-registration forces. This story is quite compelling, and thought provoking.