The primary villain of the crossover was the Magus, who was created when Adam Warlock expelled good and evil from his soul after attaining omnipotence in the conclusion of the Infinity Gauntlet limited series. The evil portion of his soul became the Magus, while the good portion of his soul became the Goddess, who is eventually seen at the end of Infinity War and is the main villain of Infinity Crusade. To battle the Magus and his army of evil doppelgängers, Adam Warlock and Earth's heroes teamed up with Thanos, the villain of the Infinity Gauntlet.
The Magus sends doppelgangers after some of Earth's heroes. Reed Richards and Iron Man were defeated and replaced. Reed's double assembles many of Earth's heroes, intending to destroy them with a large bomb. His plan fails, thanks to the heightened senses of Wolverine and Daredevil, as well as Invisible Woman's force fields. Another confrontation with Thanos led to further confusion and general chaos.
The heroes decides to split their forces, with a team remaining on Earth while another team travels to the far reaches of space and time. The Earth team is again attacked by doppelgangers, many heroes are subsumed and taken over. The traveling heroes fight with Thanos and the Infinity Watch, believing them to be the enemy.
Galactus arrives to join in the efforts against the Magus. It was decided the Infinity Gauntlet would help, but the Gauntlet had been rendered powerless by Eternity. Galactus and the warrior-woman Gamora leave in an effort to revive Eternity and reactivate the Gauntlet. Just after they leave, Warlock and the glove itself are kidnapped by Magus and the Thanos duplicate.
Doctor Doom and his ally Kang, both of whom plan to betray the other, invade Magus' stronghold. The controls for the Cosmic Cubes are damaged and several fights break out. Just then, Galactus succeeds in his attempt to reactivate the Gauntlet. Unfortunately, the Magus has it and swiftly becomes omnipotent.
The remaining heroes stormed Magus' fortress as a distraction, fighting an army of doppelgangers. Many fell and are absorbed. Thanos, in a reversal, absorbs his own double and then attacks Magus. The battle ends with Magus as the victor. Adam Warlock confronts Magus, revealing that the Reality Gem in the Gauntlet was a fake. Warlock uses this distraction to re-establish his unique bond with the Infinity Gems and usurp control from Magus. Warlock banishes the Magus to the world within the Soul Gem, living as a spirit unseen and untouched by the other spirits.
Eternity decrees the Gauntlet can never be used again. The cosmic containment units were not to be found at all, seemingly stolen by Warlock's good half; a female entity later revealed to be The Goddess. She would cause the Infinity Crusade.