A mutant activation is detected in Alaska and Cyclops and several X-Men investigate, discovering bodies of Purifiers and Marauders. After discovering the source of the battle was for possession of a newborn baby, the group returns home and Cyclops seizes control of the X-Men from Professor X as Predator X detects the newborn mutant, and devours the bodies of the dead Marauders present.
Cyclops creates an "assault team" (consisting of Wolverine, Storm, Colossus, Angel, and Nightcrawler) with the intent of locating the Marauders, who have a comatose Rogue captive. Cyclops sends X-Factor leader Multiple Man and member Layla Miller to visit Forge, and has member Rictor (who lost his powers on M-Day) pretend to join the Purifiers to see if they have the baby. Forge tells Madrox thatScarlet Witch's hex spell flatlined mutants across all realities until the baby's birth, which spawned two futures with mutants present. Madrox sends a duplicate to each timeline, and Layla Miller runs in the portal with the second dupe as Madrox falls comatose and Forge takes care of his body.
Rictor joins the Purifiers and discovers they are working with Lady Deathstrike and the Reavers, and that they do not have the baby, as a group of New X-Men attack the Purifiers base. In the fight, Hellion is wounded and in an escape, Pixie accidentally scatter-teleports Rictor and her friends. The assault team track the Marauders to Alaska and attack them with Emma Frost's assistance, until Hellion's wounding leads to the assault team's defeat and Nightcrawler's injury. In New York, the O*N*E* Sentinels are infected by nano-Sentinels and turn on the X-Men, but they are defeated when Iceman returns with the scattered New X-Men. When the assault team returns and Wolverine tells Cyclops he learned Cable has the baby, Cyclops assumes his son used the nano-Sentinels to attack them for some reason, so he dispatches a new X-Force (consisting of Wolverine, Hepzibah, Warpath, Caliban, X-23, and Wolfsbane) to locate him. Cable wanders Alaska with the baby while Predator X continues killing mutants, making his way to the X-Mansion when it loses the baby's scent.
In the future, Layla and Madrox discover there are mutant concentration camps, a result of mutant activity, and they get themselves locked in one and permanently marked with "M" DNA face tattoos. In present day, X-Force finds Cable, who is battling Deathstrike and the Reavers. X-23 defeats Deathstrike at the cost of Caliban's life, and Cable steals X-Force's Blackbird, making a path for Texas, where he goes to Forge's headquarters to use a time traveling device. Cable is hit from behind by X-Man Bishop, who in the future, Madrox and Layla discover would kill the mutant "messiah" since she killed a million people and lead to the camps' creation. Bishop is ambushed by the Marauders, who take the baby to Muir Island under Gambit's leadership. Once on Muir Island, it is revealed that Mister Sinister, who has the baby, is actually Mystique and that Mister Sinister is dead by her forcing him to touch Rogue.
Cerebra is repaired and used to track Gambit as Cyclops rescues X-Force, Bishop and Madrox. Bishop says Cable knocked Forge out and ran away after both him and Cable lost the baby. Cyclops sends Bishop and X-Force ahead to Muir Island in a faster O*N*E* ship. After they leave, Madrox reawakens after Layla uses a stolen grenade to kill his duplicate and send future Madrox's memories to Madrox Prime, now with the duplicate's M scar. He tells the group about Bishop. Predator X arrives at the X-Mansion and fights the New X-Men until Pixie teleports them to Muir Island, and Cable uses his stolen Blackbird to get Xavier to help him, explaining that in his future, the baby was a Messiah who united all of man and mutantkind.
Mystique explains to Gambit that Destiny, her former teacher, had told her about the baby and that it would heal Rogue. She holds the baby to Rogue's lips, and Gambit removes her hand, saying Rogue wouldn't want an innocent to die for her, as the Marauders and Acolytes battle X-Force and the newly arrived X-Men. Professor X interrupts Gambit, coming in with Cable, and when Cable gets the baby again, Bishop walks in along with Predator X, and the mutant killer bites Bishop's arm off, and is killed by Wolverine. Rogue awakens and disowns Mystique as punishment for risking a baby's life, then touches her before realizing that the baby wiped her memories away. She leaves Gambit, along with her and Mystique's memories. Cyclops demands that Cable hand over the child, and Professor X, in a sudden change, tells Cable to do it, so that Scott can see what everyone's been fighting for. Cyclops remembers what it was like to lose Nathan, and tells Cable to take the baby and give it the chance Cyclops never gave his own son. An infuriated Bishop takes Scalphunter's gun and shoots as Cable timeslides to the future, missing him and hitting Professor X. After Professor X is shot, his body is teleported away as Cyclops declares there are no X-Men.
X-Men: Messiah CompleX 1
Uncanny X-Men 492
New X-Men 44
Uncanny X-Men 493
New X-Men 45
Uncanny X-Men 494
New X-Men 46
Angel, Beast, Bishop, Cable, Caliban, Colossus, Cyclops, Emma Frost, Hepzibah, Nightcrawler, Professor X, Rogue, Storm, Warpath, Wolverine
Jamie Madrox, Layla Miller, M, Rictor, Siryn, Strong Guy, Wolfsbane
Anole, Armor, Dust, Elixir, Gentle, Hellion, Indra, Mercury, Pixie, Prodigy, Rockslide, Stepford Cuckoos, Surge, Trance, Wolf Cub, X-23
Forge (Inactive X-Men)
Marauders: Mr. Sinister, Arclight, Blockbuster, Gambit, Harpoon, Lady Mastermind, Mystique, Omega Sentinel, Prism, Riptide, Scalphunter, Sunfire, Scrambler, Vertigo
Acolytes in Marauders: Exodus, Frenzy, Random, Tempo, Unuscione
Ex-Acolytes: Gargouille, Neophyte, Projector, Vindaloo, Amelia Voght
Purifiers: Matthew Risman, Predator X, Lady Deathstrike and the Reavers
Following Messiah CompleX, X-Men vol. 2 was renamed X-Men Legacy. New X-Men was replaced by Young X-Men, which was then replaced by New Mutants after one year. X-Force (vol. 3) was launched.
Previous: X-Men in the 2000s (Pre-Messiah CompleX)
Chapter 1: X-Men: Messiah CompleX 1
Chapter 2: Uncanny X-Men 492
Chapter 3: X-Factor 25
Chapter 4: New X-Men 44
Chapter 5: X-Men 205
Chapter 6: Uncanny X-Men 493
Chapter 7: X-Factor 26
Chapter 8: New X-Men 45
Chapter 9: X-Men 206
Chapter 10: Uncanny X-Men 494
Chapter 11: X-Factor 27
Chapter 12: New X-Men 46
Chapter 13: X-Men 207