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StoryEditThe game starts with Dr. Doom having recently formed a new Masters of Evil. The new evil alliance launches an attack on the S.H.I.E.L.D. helicarrier U.N.N. Alpha and Nick Fury sends out a distress call to all available meta-humans, or super heroes. Captain America, Thor, Spider-Man, and Wolverine are seen responding to the call and the heroes proceed to eliminate Dr. Doom's forces led by Scorpion, Bullseye, Winter Soldier, Radioactive Man, and Fin Fang Foom. After saving the helicarrier, Nick Fury is given permission to start a task force to fight this new threat and Iron Man gives them permission to use Stark Tower as their headquarters since the S.H.I.E.L.D. Helicarrier U.N.N. Alpha was badly damaged by the Masters of Evil.
The first mission of the newly formed group of heroes is to investigate an odd message received from Dum Dum Dugan on the Omega Base, a S.H.I.E.L.D. mobile research facility. The player must fight through awakened Super Soldiers, AIM troopers and the super-villains M.O.D.O.K., Crimson Dynamo, and Mysterio so that they can prevent the Omega Base from crashing into Vondrak Dam and the Masters of Evil from launching several gamma bombs.
The next mission for the heroes takes them to Atlantis to investigate a distress call from Namorita telling them that Namor was forcefully removed from the throne by his subjects. With the help of nano-technology that enables them to breath and move freely underwater, the heroes are able to save Namor, whose injuries Namorita proceeds to tend to while explaining to the heroes that Attuma has set up sonic emitters to control the minds of the mermen and take the throne of Atlantis. The heroes proceed to take out all three sonic emitters, one of which was guarded by Byrrah and Warlord Krang, before making their way to the throne room to defeat the evil usurper. After defeating Attuma, aided in battle by Tiger Shark, the heroes learn that the Masters of Evil traded Attuma the sonic emitters in return for free-reign to search the catacombs ant take whatever they want. The heroes search the catacombs and eventually encounter Mandarin, who escapes with the "Tome of Asarius" before unleashing the Kraken, which the player must defeat in order to complete the mission.
The player is then sent to The Valley of Spirits to confront Mandarin, where they fight Dragonman, Grey Gargoyle, and two massive Ultimo robots. While making their way through Mandarin's palace, the heroes encounter Dr. Strange and help him retrieve a magical artifact Mandarin took from him. Once the heroes help Dr. Strange find the artifact he seeks, he returns the favor by agreeing to fight alongside them whenever they need his help. After finding and defeating Mandarin, the heroes discover that he had attempted to take command of the Masters of Evil and, upon failing, left the group. He suggests that the Mandarin they saw in the catacombs was Loki, God of Mischief.
Due to Loki's involvement and the abduction of Nightcrawler and Jean Grey while the heroes were fighting Mandarin the heroes move their headquarters to Dr. Strange's Sanctum Sanctorum. The team learns that Professor Xavier has tracked Nightcrawler to Castle Doom, but upon trying to transport the heroes are sent to Murderworld because of a spell cast by Baron Mordo. While traveling through Murderworld, the heroes rescue Blade from one of Arcade's machines and he joins the Alliance. After defeating a mind-controlled Jean Grey, Rhino, and Shocker, the heroes confront Arcade the master of Murderworld.
Upon defeating the game fanatic, the heroes learn from him that Dr. Doom has used Nightcrawler to gain access to Mephisto's Realm. The team is then sent to Mephisto's Realm. Upon arriving, minions of Mephisto kidnap Jean Grey and Nightcrawler. After the heroes rescue Ghost Rider from Mephisto, Blackheart, one of Mephisto's minions, puts the two X-Men in separate cages above the Infinity Vortex. The player is faced with the choice of whether to save Nightcrawler or Jean Grey. One of them must be saved and another sacrificed, before the team can confront Mephisto, who reveals that Doctor Doom agreed to lure the heroes into his realm in return for the Twilight Sword. The heroes fight their way through a massive horde of demonic creatures to reach Mephisto, who turns the ensuing fight into a puzzle they have to solve in order to use residual astral energy to bring back whoever fell into the Infinity Vortex. Once the heroes solve the puzzle and bring back their friend, Mephisto reveals that what they brought back was actually a copy of their fallen friend. The copy then proceeds to fight the heroes alongside Mephisto until his control over it is broken, at which point the copy sacrifices its remaining energy to save the heroes.
Using the Super Soldier Serum, stolen from the Omega Base, a massive army of Super Soldiers attacks Asgard and imprisons the Asgardian Gods. The Alliance is called in to help free Asgard. The team heads to the Bifrost Bridge to defeat the Wrecking Crew so that Bifrost Bridge can be opened to allow the reinforcements on Midgard to arrive.
The player must travel to Valhalla to liberate it from its invading force, and to free Tyr (who is guarded by Scorpion and Lizard), Heimdall (who is guarded by Rhino and Shocker), and Balder followed by a battle with Enchantress and Executioner. The team is victorious although the Enchantress escapes.
Later, the heroes head to Niffleheim and defeat Kurse and Ulik. The Twilight Sword is found to be shattered, having been used to take Odin's powers as stated by Sif. The heroes learn before their battle with Ymir that Dr. Doom and Loki took Odin to Raven's Spire. After a battle with the betrayed Baron Mordo and Ultron, the heroes face off against Loki. After Loki is apparently defeated at Raven's Spire, the player is sent to free the Destroyer Armor, to use against Dr. Doom. After the armor is released, Loki reveals that he tricked the heroes into it so he could claim the armor and use it against them. The heroes defeat Loki and the armor, but Dr. Doom appears, and reveals that he has stolen Odin's power. He uses it to try and kill the heroes; or so it seems. Uatu saves them and transports them to Attilans, the base of the Inhumans on the Moon. Uatu reveals the only way to beat Doom is to find the M'Kraan Crystal and steal the Muonic Inducer from Galactus, who is currently attacking the Skrull homeworld.
The player is sent to the Shi'ar Empire to convince Lilandra Neramani to let them take a piece of the M'Kraan Crystal. Upon arriving, the heroes discover that Deathbird, aided by several members of the Shi'ar elite guard, siezed the throne and imprisoned Lilandra. The heroes fight Gladiator, shut down the ship's engines, beat Starbolt and Warstar, send a distress signal to the ships still loyal to Lilandra, disable the ship's weapons, and fight Neutron and Hussar before confronting Deathbird. When she can't beat them in combat, Deathbird sets the ship to self-destruct before making her escape. The heroes stop the self-destruction sequence and retrieve the M'Kraan Crystal piece they need.
After retrieving the crystal, the heroes travel to the Skrull homeworld to steal Galactus' Muonic Inducer. The heroes eventually make their way through a war-torn hangar and encounter the Skrull queen, who offers them information about Galactus in return for opening the hangar doors so she can escape. After the heroes make their way to the control-room and open the hangar doors, they return to the queen, who reveals that she lied to them and orders Paibok and Super-Skrull to fight them before fleeing in her escape-hatch. The heroes defeat Paibok and Super-Skrull and continue to make their way to Galactus. Along they way, they encounter Titannius trashing the Skrull labs in an attempt to get revenge for the horrible experiments he was put through. The heroes stop his rampage, finally reach Galactus, and, with the help of the Silver Surfer, disable him to obtain the Muonic Inducer.
While the heroes are away, Dr. Doom conquers Earth and corrupts many heroes after defeating them as well as using Odin's powers to create evil clones of the playable heroes. Upon arriving back at Stark Tower, the team finds that Doom has converted it into "Doomstark" tower. The player must fend off an army of Iron Man-based robots so that they can reactivate the tower for their use.
The final level is set in Latveria, home of Doctor Doom, and whilst there they defeat the corrupted evil heroes, evil clones of the heroes, many clones of the Fantastic Four, and confront Dr. Doom. The heroes use the two devices obtained earlier to weaken Doom and upon being struck down by the heroes, Doom is blasted by a bolt of lightning sent by a rejuvenated Odin, leaving nothing but his mask behind.
Nick Fury tells the heroes that the team must disband and asks the heroes if S.H.I.E.L.D. can count on them when another threat happens. Captain America replies by saying that the world can count on them. Meanwhile, Galactus vows revenge on the heroes who stole from him and plans to destroy Earth.
During the game a subplot takes place where Weasel attempts to find proof that the Black Widow is a double agent, and the player needs to obtain various pieces of information to aid his efforts. Ultimately the players call Nick Fury with information of Black Widow's apparent betrayal, but he reveals that Black Widow is innocent and her suspicious activities were part of an operation to try and retrieve plans that Dr. Doom had stolen from S.H.I.E.L.D. However, a phone call made during the credits reveal that the Black Widow had been using Weasel to steal information from S.H.I.E.L.D. then setting up Weasel for the fall.
After the game, Uatu tells the player of how his/her actions in the game (such as not completing missions the right way, or not completing side missions) have changed the future. Here are the futures that Uatu explains:
- If the player prevents the Super Soldiers from destroying the S.H.I.E.L.D. Omega Base computer that contains research data on the Legacy Virus, it's information will lead to a cure several years later that will save the mutant race from possible extinction. If not, the Legacy Virus will become a plague that runs rampant across the Earth several years later and the mutant race may go extinct.
- If the player succeeds in finding the rare Walek Seaweed as one of the ingredients to a medicine that will heal Namor, he will begin to trust surface-dwellers and join a world-wide organization of superheroes that will save the Earth from many dangers that would've destroyed it. Otherwise, Warlord Krang will usurp the throne from the weakened Namor, convince the Atlanteans to attack human warships, and use the stolen nuclear weapons to wage a devastating war upon the surface world.
- If the player succeeds in saving Senator Kelly from within Murderworld, he would successfully sponsor the Mutant Aid bill which will allow government funds for schools (similar to Professor X's) which will prove to be very effective in training young mutants how to control their powers. If Senator Kelly isn't rescued, he achieves freedom on his own and successfully sponsors a bill where all mutants are sent to re-education camps where they will be brutally educated to NOT use their powers.
- If the player chooses to save Jean Grey from being dropped into the Infinity Vortex, Mystique will avenge Nightcrawler by infiltrating the X-Mansion at night to vent her frustration upon Professor X where he will die in a coma months later and the X-Men will disband forever. If the player saves Nightcrawler from being dropped into the Infinity Vortex, Jean Grey doesn't die in the Infinity Vortex and will return to Earth in the form of the Dark Phoenix to exact vengeance upon those that didn't save her.
- If the player finds Valkyrie's sword Dragon Fang, Asgard will be easily freed with her aid, Loki will be imprisoned in chains, and Ragnarok, the end of the Asgardian Realm, never comes to pass. If the player doesn't find her sword, Valkyrie will die in the battle to prevent Ragnarok, Balder will die trying to save her, and the people of Asgard will be forbidden to contact Earth for a century.
- If the player recovers Volla's ring, she will warn Odin about an attempt on his life which will lead to the capture of Surtur in the years to come. If not, she won't warn Odin about an attempt on his life and the death of Odin will plunge Asgard into years of chaos during which Thor will rule Asgard after Sif dies in battle.
- If the player frees Lilandra Neramani, the Shi'ar will give Earth their advanced technology that will wipe out Earth's diseases and hunger and the Shi'ar technology will eventually enable humanity to colonize other planets. If the player doesn't, the Shi'ar will refuse to help the heroes when they fail to stop an asteroid that comes to obliterate the Western coast of the United States.
- If the player saves the Skrull homeworld from destruction, the Skrulls will soon form a tentative partnership with Earth and later come to the aid of Earth when the Kree threaten to enslave humanity. Otherwise, the loss of the Skrull's homeworld will destabilize the entire sector of space when the Kree and the Skrull go to war with one another for decades costing millions of lives.
- If the player frees Odin from his dark magic machine confinement at Castle Doom, his intervention will prevent Thanos from taking over Earth in the near future. If the player doesn't, he won't help Thor fight Thanos who will end up enslaving Earth which will take centuries before it is liberated.
- If the player successfully finds the damaged Ultimate Nullifier in a laboratory at Castle Doom, Mr. Fantastic will repair it and use it one day to prevent Mephisto from invading Earth before all is lost. If the damaged Ultimate Nullifier isn't found, the team of heroes will band together once again to fight Mephisto with the battle causing a tremendous amount of destruction.