The helicarrier is attacked by the Masters of Evil, a group a supervillians lead by Dr. Doom. Nick Fury, the Commander on board then sends a S.O.S. to team of superheroes which include Captain America, Spider Man, Thor, and Wolverine who aid in defending it and not to mention defeating villians such as Winter Soldier and Fin Fang Foom plus stopping a nuke from going off.
They then find out the Hellicarrier is to badly damaged so Tony Stark (Iron Man) offers S.H.I.E.L.D. to use Stark Tower as a base.
They then go to Omega Base after receiving a distress signal from a S.H.I.E.L.D. agent known as Dum Dum Dugan, with him telling them it's going to crash because of the Masters of Evil controlling it. So they protect Dugan until they reach the control room where he takes omega back but they figure out its locked. The heroes then unlock it in time by defeating M.O.D.O.K. and save the base.
They return to Stark Tower where they figure out that there is a riot in Atlantis and they have thrown Namor (the King) out of the throne. After a series of enemies they figure out the atlanteans sre being brainwashed by sonic emitors owned by the Masters of Evil. After defeating a kracken and saving Atlantis they find Mandarin where they track him to the valley of spirits.
Arriving at the valley of spirits they beat everyone in their path and manage to help Doctor Strange locate the orb of Agamotto who in return joins your team and offers his home as a base when you get back. They finally make it to Mandarin and defeat him. They find out the whole thing was a decoy by Mandarin explaining he left the Masters of Evil and the Mandarin they saw at Atlantis was a shape shifter known as Loki. They find out that while they were gone 2 heroes were captured.
S.H.I.E.L.D. moves to the sanctum sanctorum (Dr. Strange's home) because of the fact that his home is filled with magic to teleport them to the heroes.
They use an orb to transport to their next destination, Dr Doom's castle itself to rescue 2 kidnapped x-men, Jean Grey and Nightcrawler. Unfortunately they find themselves in murderworld after one of doctor strange's nemesis and Dr. Doom's officers, Baron Mordo uses his dark magic to sabotage the orb they used to teleport. So they have to fight their way out of the twisted place and defeat Arcade, the creator of Murderworld which they do along with getting extra info from arcade by threatening him. They also find Jean Grey but have no luck with nightcrawler. Arcade tells them the X-Man is in hell being captives there by Mephisto.
After arriving they find that Xavier, leader of the X-Men is defending nightcrawler with a shield but Blackheart (Mephisto's son) is quickly breaking through them. So Jean Grey arrives in hell to help Xavier with protecting nightcrawler. The second the heroes leave Jean the masters of Evil alone they abduct her and gain both X-Men again. They go through Mephisto's realm, even defeating blackheart. Then they find the x men but must choose whoever they want to save because once they open one's cell the other will drop. After choosing they battle Mephisto plus the x-man you didn't save who now belongs to Mephisto. After weakening the devil he lets his grip go on the x-man. Then sadly after a short reunion nightcrawler or Jean Grey sacrifices him or her self to deafeat the devil. They then return to the sanctum sanctorum