Ultimate War is the first crossover event in the Ultimate Marvel universe. Magneto is back, and he exacts revenge on the human race. The Ultimates begin a hunt for Magneto, the Brotherhood of Mutants, and the X-Men, who they hold responsible for keeping Magneto alive. The X-Men must simultaneously run from the law while trying to stop Magneto. This entire story is collected in the miniseries Ultimate War #1-4 and concludes in Ultimate X-Men #26-33.
Years ago, Charles Xavier abandoned his family to join Erik Lensherr. The two led a sanctuary in the Savage Land, where mutants could live in peace. As the years passed, their ideologies drifted until Xavier decided he had to leave. To stop him, Magneto crippled Xavier. With Xavier gone, Magneto began to launch terrorist attacks around the world, in the name of mutant supremacy.
In the present, Magneto and the Brotherhood of Mutants execute an attack that leaves many civilians dead. Nick Fury activates the Ultimates, sending them to hunt Magneto. The Ultimates intercept and take down a cell of the Brotherhood, capturing many mutants, including Rogue.
The X-Men go into hiding, fearing that the world will blame them for Magneto’s attacks. Wolverine and Kitty return from the Savage Land, and tell the others that Scott didn’t make it out.
Magneto attacks the Triskelion, and easily subdues the Ultimates. He shoots Quicksilver in the kneecaps as punishment for betraying him.
Tensions arise in the X-Men’s hiding place, as Jean Grey suspects that Wolverine has killed Cyclops in the Savage Land. Magneto meets with Xavier to offer him one last chance at joining the Brotherhood.
Meanwhile, the Ultimates discover the X-Men’s hiding place and launch an attack. The X-Men fight back, aided by Iceman, who has run away from home to help his friends. After a long battle, the X-Men manage to escape, but the Ultimates capture Xavier.
Nick Fury deploys a group of Sentinel soldiers to hunt down the X-Men. Mutants all over the world go into hiding. Magneto continues his attacks on civilians, but also extends an invitation to the X-Men to join him. The X-Men refuse the invitation and realize that they must stop Magneto, even it it means coming out of hiding.
A flashback reveals that Wolverine tried to kill Cyclops in the Savage Land by dropping him into an abyss. Cyclops survives his fall and is captured by the Brotherhood, who don’t recognize him at first. He is taken back to Magneto’s secret base and receives medical attention.
At the same time, a group of Brotherhood mutants break Xavier, Nightcrawler, and other mutants out of prison.
Once Cyclops awakens, he alerts the X-Men of his location and fights his way to Magneto. The X-Men arrive and battle the Brotherhood. Rogue defects and helps the X-Men. Together, they defeat Magneto and he is arrested.
The remaining members of the Brotherhood are arrested. The X-Men are cleared of wrongdoing. And Magneto begins to plan his escape.
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