Professor Xavier's step-brother, and sworn enemy, the Juggernaut loses his powers to a bumbling archeologist. He must overcome the pain of their childhood together, and have the powers restored to him to save his life.

Gambit, Rogue, and Wolverine take a ski trip in Germany. While Gambit and Rogue seem to be enjoying themselves, Wolverine is restless, and longs for some action. When he hears reports of a demon hiding in a local monastery, his investigation reveals not a demon, but a mutant, Nightcrawler, whose devilish appearance is in stark contrast to his peaceful and deeply philosophical nature. Later the townsfolk attack and burn the monastery. The X-Men convince the townsfolk not to fear what they do not understand, Wolverine, too, learns something about the nature of faith.

A cryptic postcard unleashes a flood of maddening and painful memories in Wolverine that threaten to drive him insane. To keep his mind from being torn apart, Wolverine and Beast travel to the one location that may hold the answers to his hidden past: the ruins of the top-secret Weapon X lab where Wolverine's bones were laced with adamantium. There he encounters other former 'test subjects'—Sabretooth, Maverick and Silver Fox—who are suffering similar mental breakdowns. Later they find out that many of their memories were implanted, and their true memories are destroyed with the lab.

Bishop & Shard recruit Wolverine & Storm for a time travel mission to save Professor Xavier's life. Except they're from the parallel timeline where he died before founding the X-Men, a world where humans and mutants are in a constant war with one another. Not only do they pair lack a connection to him, but correcting history may put an end to their marriage.

Bishop, Shard, and the alternate-present versions of Wolverine & Storm, will have one more chance to save Xavier from being killed before he founded the X-Men... if they can survive the alternate-future ruled entirely unopposed by Mastermold.

The long hidden secret patient of Muir Island, a reality-warping mutant teen known as Proteus, escapes from his 15 year long captivity, and wreaks havoc across Scotland searching out his father.

Tracking down his father, who is now a candidate for Secretary of State, Proteus continues threatening lives with his uncontrolable powers. It's up to Professor X alone to try to stop the boy who brought even Wolverine to his knees.

Apocalypse steals Cable's computer in the year 3999, allowing him to time travel to the past, where he schemes to bring an end to his struggle against inferior mutants once and for all. This leads to Bishop becoming trapped amid the timestream, and brings

When Oracle, the psychic member of the Imperial Guard is kidnapped by Apocalypse, Professor Xavier deduces his scheme involves capturing mutants with telepathic abilities. The X-Men are split up to track them down before the villains can, which puts Wolverine & Shard in the middle of a scuffle between Archangel and a ninja named Psylocke.

After swiping the government's own time machine, Cable ends up recruiting the X-Men on his mission to destroy Apocalypse's source of immortality at its creation.

Two of Apocalypse's former evil allies, the captive Wolverine, the loose cannon Cable, and the exiled Bishop, come together to free the kidnapped psychics and save reality from being rewritten.

Jubilee's first Christmas with the X-Men doesn't go exactly as she expected, when she, Storm, and Wolverine become involved with a mission to save the Morlock child known as Leech.

Finding himself continually losing control, Wolverine takes a sabbatical to Japan, in an effort to find inner peace in temple-building. Instead, he faces a village under siege by a group of bandits, and struggles to help them without compromising his search for his true nature.

X-Factor's Quicksilver, and his sister, the Avenger called Scarlet Witch, seek revenge against Magneto when they learn that he was responsible for their birth mother's death. But the trio is unaware of the common bond between them, nor the true purposes of the mysterious man who brought them all together.

Nightcrawler gets a mysterious message. He is informed that his birth mother (whom he never knew) is in trouble. He turns to the X-Men for assistance. Jubilee is baffled that Nightcrawler wants to help the mother who abandoned him -- she has never known her birth parents and feels pretty hostile toward them, whoever they are. Nightcrawler admits there has been pain, but his faith in God has helped him overcome her rejection. The plot thickens when one of the team members recognizes Nightcrawler's mother's voice. There are more 'bloodlines' here than anyone imagined, including the Friends of Humanity who arranged this 'reunion' in the first place.