The game begins with Doctor Doom and the Masters of Evil launching an attack on the S.H.I.E.L.D. Helicarrier U.N.N. Alpha. Nick Fury sends out a distress call to all available superheroes for assistance. Captain America, Spider-Man, Thor and Wolverine respond to the call. Along with the other heroes, they save the Helicarrier from the forces led by Scorpion, Bullseye, Winter Soldier, Radioactive Man, and Fin Fang Foom. In the wake of the attack, Nick Fury is given permission to start a task force to confront the Masters of Evil and Iron Man allows them to use Stark Tower as their headquarters.