Marvel: Ultimate Alliance

After Doctor Doom and the Masters of Evil attack the S.H.I.E.L.D. Helicarrier, Nick Fury sends a distress call to all available superheroes for assistance. Captain America, Spider-Man, Thor, and Wolverine respond to the call and save the Helicarrier from Ultron sentries led by Fin Fang Foom. 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.

Fury asks the heroes to investigate a message received from Dum Dum Dugan on the Omega Base, a S.H.I.E.L.D. mobile research facility. The team defeats supervillains MODOK, Crimson Dynamo, and Mysterio as well as A.I.M. agents and failed Super Soldier experiments to prevent the Omega Base from crashing into a dam and launching several gamma bombs.

With their mission successful, the heroes travel to Atlantis, where Attuma has usurped Namor and taken control of the Atlanteans' minds. With the help of nano-technology that enables them to breathe and move freely underwater, the heroes fight the mind-controlled Atlanteans, destroy the towers which are guarded by Krang and Byrrah, rescue Namor, and defeat Attuma and Tiger Shark. After defeating Attuma, the heroes encounter Mandarin, who unleashes the Kraken on them. The team defeats the Kraken by toppling pillars on it.

The heroes travel to the Valley of Spirits to confront Mandarin in his palace. After his defeat, Mandarin reveals that he 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 actually Loki, Thor's adoptive brother and the god of mischief.

Upon returning to base, the team learns that Nightcrawler and Jean Grey have been kidnapped as well as Senator Robert Kelly. Due to the involvement of mystical forces, Fury has the team relocated to the Sanctum Sanctorum, offered as a temporary headquarters by Doctor Strange. Professor X tracks Nightcrawler to Castle Doom. Upon trying to transport the heroes there, they are sent to Murderworld by Baron Mordo. After defeating a mind-controlled Jean, Rhino, and Shocker, the heroes battle a mech piloted by Arcade.

Victorious, the heroes learn that Doom has used Nightcrawler to access Mephisto's realm. Upon arriving, minions of Mephisto kidnap Jean Grey and Nightcrawler. Mephisto's son Blackheart puts the two in cages above the Infinity Vortex, stating one must be saved and the other sacrificed. During their battle with Mephisto, the sacrificed hero is resurrected by Mephisto and placed under his control. As a final effort, the resurrected hero sacrifices their life to defeat Mephisto and allow the team to escape.

Meanwhile in Asgard, an army of Super Soldiers attacks and imprisons the Asgardian gods. The heroes travel to Valhalla to free Heimdall, Tyr, and Balder. Looking for Odin in Niffleheim following a fight with Kurse and Ulik, they find his shattered Twilight Sword and learn from Ymir that Doom and Loki have taken Odin to Raven's Spire. After Loki is seemingly defeated at Raven's Spire, the team frees the Destroyer armor to use against Doom. Loki, disguised as Fury, reveals himself and his plot to have the heroes free the armor for nefarious purposes. As heroes defeat Loki and the armor, Doom appears and reveals that he has stolen Odin's power. He uses it to attempt to eliminate the heroes, but Uatu the Watcher saves them and transports them to the Inhumans' base on the moon.

Uatu reveals that Doom's unrestricted use of Odin's power will eventually destroy the universe and that the only way to defeat him is to acquire a piece of the M'Kraan Crystal from a Shi'ar warship and steal the Muonic Inducer from Galactus, who is attacking the Skrull homeworld.

Meanwhile, Doom conquers Earth, defeating and corrupting many of the other heroes who attempted but failed to stop him as well as creating clones of the heroes. In a final effort, the team travels to Latveria to confront Doom. The heroes use the M'Kraan Crystal and Muonic Inducer to weaken Doom. Doom is blasted with lightning by Odin, causing him to disappear. Meanwhile, Galactus vows revenge on the heroes who stole from him and plans to destroy Earth.

Uatu's epilogue

Several optional tasks are available throughout the game. In the game's epilogue, Uatu presents the potential outcomes, regardless of whether the tasks are completed.

If the player saves the S.H.I.E.L.D. Omega Base computer which contains research data on the Legacy Virus, its information is used to create a cure and stop the plague, saving mutants from extinction. If the player does not, the Legacy Virus runs rampant across Earth, dooming mutants to extinction.

If the player finds the rare Walek Seaweed in Atlantis which is needed to produce a medicine that will heal Namor, he will grow to trust surface dwellers and join a worldwide organization of superheroes. Otherwise, Krang will usurp the throne from the weakened Namor, convince the Atlantean soldiers to attack the human warships, and use the stolen nuclear missiles to wage war on the surface world.

If the player locates Senator Kelly in Murderworld and frees him, he will sponsor the Mutant Aid Bill, which supports schools like Professor X's school. If he is not rescued, Kelly will achieve freedom on his own and sponsor a bill that forces all mutants into re-education camps, which brutally forces them to not use their powers.

If the player saves Nightcrawler from being dropped into the Infinity Vortex, Jean Grey does not die in the Infinity Vortex and returns to Earth in the form of the Dark Phoenix to take vengeance on those who did not save her. If the player saves Grey from being dropped into the Infinity Vortex, Nightcrawler's mother Mystique attacks Professor X out of grief. Professor X is left comatose and dies from his injuries several months later, causing the X-Men to disband.

If the player finds Valkyrie's sword Dragonfang, Asgard will easily be freed with her aid, Loki will be imprisoned, and Ragnarök never comes to pass. If the player does not find Dragonfang, Valkyrie will die in the battle to free Asgard, Balder will die trying to save her, and Asgard will refuse contact with Earth for a century.

If the player recovers Volla's ring in Niffleheim, she will warn Odin of an attempt on his life, which will lead to the capture of Surtur in the years to come. If Volla's ring is not recovered, Odin ends up being assassinated, which plunges Asgard into years of conflict. This ends with Thor assuming leadership of Asgard after Sif dies in battle.

If the player frees Lilandra Neramani from her torture device, the Shi'ar will give Earth advanced technology to treat all disease and hunger and colonize other planets. If Lilandra is not freed, the Shi'ar will ignore the plea of the heroes when an asteroid approaches Earth and their attempt to stop it on their own will result in the Western coast of the United States being obliterated.

If the player saves the Skrull homeworld from destruction, the Skrulls will form a tentative partnership with Earth and come to their aid when the Kree threaten to enslave humanity. Otherwise, the Skrull and Kree will enter a deadly decades-long war.

If the player frees Odin from imprisonment at Castle Doom, his intervention will prevent Thanos from enslaving Earth in the near future. If Odin is not freed, he will refuse to aid Thor in battle, causing Thanos to conquer Earth and rule it for centuries before being overthrown.

If the player finds the damaged Ultimate Nullifier at Castle Doom, Mister Fantastic will repair the Ultimate Nullifier and use it to prevent Mephisto from invading Earth. If the Ultimate Nullifier is not found, the fight with Mephisto will result in mass destruction.