Cyclops, still lamenting the loss of his dear beloved Jean Grey, believes Mister Sinister has taken her. He fights the Marauders with the help of the X-Men until he realizes Jean is not with them. An amnesiac Jean is revealed to be alive and well in a hospital, supposedly having been in a coma.

Magneto sends his Acolytes to break several mutants out of prison. Meanwhile, the X-Men fight the Brotherhood and find Tildie Soames (a young mutant whose nightmares can manifest into monsters) is attacking the city while still in a coma-like state. Rogue's true purpose in joining the Brotherhood is revealed and she has to make a choice between her old friends and her new ones. Meanwhile, Bobby sums up the courage to ask Kitty out on a date.

Mystique calls Wolverine to warn him that Maverick's daughter, Kristie, is in danger. The two of them infiltrate Weapon X and have to fight Maverick and Sabretooth - and some old ghosts from the past as well.