Following a tragic Super Hero operation that resulted in many casualties, the Superhuman Registration Act was ratified, forcing heroes to reveal their secret identities and subject themselves to government oversight. Iron Man agreed with the policy and gathered a team of Pro-Registration heroes around him to enforce it. Captain America, on the other hand, felt heroes needed to be above direct government control. Other Anti-Registration heroes joined him, becoming outlaws and forming the Secret Avengers. Inevitably a violent conflict broke out between the two sides and now the villains sit by the sidelines as once-allied heroes clash against each other in an all-out Civil War!

This expansion brings an entirely new way of playing Marvel United! The Civil War play modes make it a true Player vs Player game, in which two teams of Heroes clash against each other, with no Villain in sight.