Doctor Doom obtains the
Cosmic Cube, and he uses it to incinerate
the Watcher. After responding to a theft at Queens, the player travels to the
Raft, where
Madame Hydra and
Hydra have facilitated a breakout, freeing several superpowered inmates. The player manages to reactivate the security system, lock down the cell blocks, and recapture
Green Goblin and
Living Laser; however, many villains escape. After the breakout, Madame Hydra meets with Doom, declaring it a success. Doom gives Madame Hydra a chip with the ability to exploit a flaw in
Tony Stark's security system, after which their transaction ends. After the breakout,
Daredevil manages to recapture
Rhino in
Hell's Kitchen, while the player recaptures
Shocker in an abandoned subway.
Doctor Octopus tries to steal the Tablet of Life and Time from the Blood Rose nightclub, but he is stopped and recaptured by the player. The heroes temporarily gain possession of the tablet; however,
Hood appears through a portal and steals it. The player then travels to Industry City, combating forces from both
Advanced Idea Mechanics and Kingpin's
Maggia while hunting the Hood. Eventually, Hood is defeated and taken into custody, only to reveal that he has already sold the Tablet to the Hand. The heroes travel to
Madripoor, the Hand's base of operations, and soon discover that Hydra is also attacking the Hand in an attempt to take the Tablet for themselves. The heroes subdue Madame Viper, culling the Hydra invasion, and then defeat the Hand's leader,
Gorgon and his top assassin,
Elektra, reclaiming the tablet. However, upon returning to New York, Kingpin uses his legal connections to force the heroes to return the Tablet to him. Knowing that the Tablet is too powerful to be left in the Kingpin's hands, the heroes work to expose his involvement in illegally smuggling Mutant Growth Hormone into the city. With the help of detective
Jean DeWolff, the heroes expose the Kingpin and defeat him, finally securing the Tablet. However, shortly afterwards, the Tablet is again stolen by professional thief
Ghost, who delivers it to Doctor Doom. The heroes are then summoned to the X Mansion by Professor
Charles Xavier, who explains that anti-
mutant terrorists called the
Purifiers have launched a genocidal attack on
Mutant Town. The heroes rush to Mutant Town to stop the killings, fighting not only the Purifiers, but also the Reavers, a group of psychotic cyborg mercenaries led by
Lady Deathstrike, who has allied herself with the Purifiers due to her grudge against the mutant
Wolverine. The heroes fight the Purifiers back to their base in an abandoned train yard, where they discover that the Purifiers have taken advantage of the
Juggernaut's hatred of Xavier in order to trick him into defending their base. The heroes subdue Juggernaut and force the Purifiers to retreat from Mutant Town. Upon returning to the X-Mansion, they are contacted by
Nick Fury, who reveals that the Purifiers' leader, Reverend
William Stryker, is colluding with AIM to create an anti-mutant superweapon. The heroes rush to the Purifier main base, Fort Stryker, in order to destroy the superweapon and apprehend Stryker. However, when they arrive, they find that Stryker is already under attack by Magneto and his
Brotherhood of Mutants in retaliation for their attack on Mutant Town. Magneto threatens to kill Stryker, but the heroes refuse to let this happen and defeat him. As Stryker is arrested, the heroes discover that he has sold genomes from the mutants his forces captured to
Mister Sinister for an unknown purpose. The heroes track Sinister to the
Savage Land, which is under attack by not only Sinister's Mutate army, but also hostile tribesmen under the control of the mutant
Sauron and a
Brood invasion force. The heroes defeat Sinister, but he manages to escape and deliver a clone of
Lucas Bishop to Doctor Doom. The heroes are then called to the
Helicarrier, where Nick Fury takes them with ending the threats of AIM and Hydra. After defeating both
MODOK and the
Mandarin, Doctor Doom steals one of the
Mandarin's rings and reveals his master plan. It was he who originally orchestrated Hydra's attack on the Raft which led to the mass breakout of super-villains, as well as commissioned Mr. Sinister to gather mutant DNA through the Purifiers to create a clone of Bishop. The purpose of the clone is to create a conduit with which Doom can control the Cosmic Cube, while the super-villain breakout was intended to keep the heroes occupied while he finalizes his plan. Several supervillains try to prevent the heroes from interfering with Doctor Doom's use of the Cosmic Cube. The villains fail, and the heroes are able to thwart Doom's attempt to gain omnipotence. After stopping Doctor Doom, players may travel across the
Bifrost Bridge to
Asgard, where
Loki has summoned hordes of
Dark Elves,
Frost Giants, and other monsters in an attempt to seize Asgard's throne while Odin slumbers. The heroes defeat Loki's minions before confronting Loki himself in
Odin's throne room where he reveals that he has stolen the power of Doom's Cosmic Cube. Eventually, the heroes defeat him. Before judgement can be passed on Loki, the heroes learn that the dark god
Surtur has reforged the Twilight Sword. Surtur plans to use the chaos caused by Loki in order to launch his own invasion of Asgard. The heroes defeat Surtur and his minions in his home dimension of
Muspelheim. Odin soon reawakens, enraged at Loki's crimes. Loki claims that he simply wanted to be acknowledged as a hero. As a punishment, Odin decides to trap Loki in an endless time loop covering the events of the game, giving him the opportunity to become a hero. Shortly after Surtur's defeat,
Professor X suddenly goes missing. While investigating his disappearance, the heroes discover that
Red Skull has merged with
Onslaught, becoming Red Onslaught. Onslaught has launched a genocidal campaign against the sovereign mutant nation of
Genosha. In order to combat Red Onslaught, the heroes are forced to enlist the aid of supervillains through the
Thunderbolts program, including
Magneto and Green Goblin. The heroes and super-villains are able to defeat Red Onslaught and save Genosha, after which the Red Skull is imprisoned and Onslaught is destroyed. Sometime later, after defeating
Ultron's invasion of Manhattan, the heroes are confronted by Doctor Doom. Doom explains that he had been captured by
Thanos following his initial defeat. He then reveals that the
Skrulls are planning a massive invasion of Earth. The heroes are summoned by
Nick Fury to the
S.H.I.E.L.D. Helicarrier, only to discover that the entire base has been infiltrated by Skrulls. After defeating the Skrulls, the heroes meet with
S.W.O.R.D., who escort them to the real Nick Fury's base in an abandoned toolshed in
Madripoor. From there, the heroes combat Skrull activity throughout the world until discovering that the leader of the invasion,
Kl'rt the Super-Skrull, has established his primary base in Madripoor's Hightown. The heroes confront Super-Skrull and defeat him. As he is taken into custody, his ship manages to escape. Thereupon, Super-Skrull exclaims that the heroes should be thankful because of its cargo. Sure enough, the ship is revealed to be carrying an
Infinity Gem, catching the attention of Thanos. ==Characters==