"X-Men: Messiah Complex" (also known as "Messiah CompleX") is an American comic book crossover storyline published by Marvel Comics from October 2007 to January 2008, which ran through the various X-Men books.

The story is the climax of events that began with "House of M", which led to the decimation of mutants in the Marvel Universe, and the first chapter of a three-part saga, which continued in "Messiah War", released in 2009, and culminated in "Second Coming", a crossover between all X-Men titles in early 2010.

The "Messiah Complex" storyline is the climax of events set into motion in "House of M" and defined the direction of the X-Men franchise for the next several years. The storyline's main plot involves the birth of the first child with the X-gene since Decimation, sparking a race between the X-Men, the Marauders, the Acolytes, the Reavers, the Purifiers, and Predator X to see who will find the child first. The event also marked the return of X-Man Angel, who had been away from the X-Men teams for a while. "Messiah Complex" also involves X-Factor and New X-Men, Sentinel Squad O*N*E*, and Cable.

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 that Scarlet Witch's hex spell flatlined mutants across all possible futures 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.

Cerebro 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.