Wolverine goes to recover part of his past as a Weapon X agent and finds Maverick's daughter. As Weapon X doesn't want Logan to remember anything about his time in their organization, they send Sabretooth to deal with him. Meanwhile, Rogue finds it hard to adjust to her new settings as she overhears Quicksilver getting a mission from Magneto. When she finally visits the X-Mansion, she is upset to learn that Wolverine is not there.

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.