The Avengers use the Scarlet Witch’s Avengers identicard to track her whereabouts to Westchester County, New York. They deduce that she seems to be held within the property of Charles Xavier’s School for Gifted Youngsters. Iron Man replaces his armor, ruined in the fight with Wolverine, with the experimental Mark 47 suit, and the team sets off in pursuit of their missing teammate.
Meanwhile, the Scarlet Witch awakens in a jungle, and finds herself confronted by Cyclops. He accuses her of attacking the X-Men in their headquarters, a charge she denies.
The Avengers Quinjet sets down on the grounds of the school, where the Avengers are quickly attacked by Colossus, Nightcrawler, Shadowcat, and Storm – who seems strangely familiar to the Black Panther. The two teams clash in a ferocious combat that lasts until Cyclops calls a halt to the hostilities. He and Wolverine have determined to the best of their abilities that the Scarlet Witch is telling the truth and did not attack them.
The two teams gather in the X-Men’s headquarters beneath the school and establish what has happened. Mystique, of the Brotherhood of Mutants, infiltrated the Xavier school. Disguising herself as the Scarlet Witch, she sabotaged the X-Men’s mutant-detecting computer Cerebro, so that when the X-Men’s mentor, Professor Charles Xavier used it, he created a psychic feedback loop that incapacitated all telepaths in the area, including Xavier himself, and Phoenix of the X-Men.
The X-Men and Avengers realize that there is a strange energy signature left behind by Mystique, one that matches the signature left behind by the Brotherhood in their attack on the Avengers. The heroes discover that this is Terrigen radiation, the same energy used by the Inhumans to cause mutation. Magneto and the brotherhood have acquired Terrigen, and have created a bomb. They intend to detonate that bomb in Washington DC, as Senator Robert Kelly convenes a panel to discuss the so-called “mutant menace”.
The two teams agree to combine forces to defeat the Brotherhood. One team heads to Washington to stop the bomb from being detonated. The other travels to Asteroid M to confront Magneto himself.