After being defeated by the brainwashed Jean Grey, the X-Men have been split up. Believing the others to be dead, Wolverine and Cyclops lead Colossus, Dazzler, Polaris, Beast, Angel, and Nightcrawler to hopefully save Jean and defeat Magneto's Brotherhood. Meanwhile, Iceman, Magik, Gambit, and Shadowcat, believing themselves to be the only ones left, try to defeat the Brotherhood on their own and convince Rogue that the Brotherhood is evil. They end up discovering that Professor X, Storm, Havok, and Psylocke are being held hostage has bait for Cyclops and Wolverine's group. And Scarlet Witch and Quicksilver begin to question Magneto's ethics.
Releases after Ultimate X-Men: The Dark Phoenix Saga Part One and before Spider-Man 3: The Symbiote Saga