A new mutant is born who could decide the fate of the entire Mutant Race.
Cerebra detects the birth of a new mutant in Cooperstown, Alaska, the first such birth since M-Day. Professor Xavier sends a team of X-Men consisting of Cyclops, Wolverine, Nightcrawler, Angel and Emma Frost to Alaska to find the child. However, the Marauders and the Purifiers get to Alaska first and both groups fight each other over the child. The X-Men arrive on the scene to find that Prism and Blockbuster of the Marauders and some of the Purifiers have been killed and that the child is missing. Predator X is also shown to be hunting for the child and stops to feast upon Blockbuster's body.
Cyclops has Emma Frost bring in Rictor and Multiple Man (slightly against their wills) with Layla Miller tagging along, saying that she needs to be there for Jamie. Cyclops then asks Rictor to infiltrate the Purifiers, as he is still depowered. Everyone else is going to go see Forge. Professor X and Beast attempt to fix Cerebra, while Wolverine, Nightcrawler, Archangel, and Colossus hunt down former Acolytes Projector, Neophyte, Vindaloo and Gargouille to get information about the current whereabouts of Exodus. Predator X is still on the hunt for the new mutant.
Rictor saves the Purifiers from Wolfsbane, in a ploy to gain their trust and infiltrate them. Cyclops officially tells the New X-Men that they are held back from action when they confront him. Storm and Nightcrawler go to Amelia Voght to ask her for information on the Marauders and the Acolytes. Multiple Man and Layla are sent to Forge by Cyclops. Multiple Man creates 2 dupes to investigate two alternate timelines that spiked when the mutant baby was born. As Forge sent the two dupes, Layla runs to one of them so as to accompany him. Forge reveals that it was supposed to be a one way trip with dupes being implanted with the knowledge that they had to kill themelves once they finish their missions so that their knolwedge is quickly transferred back to Madrox prime. Once Forge tells Madrox prime this, he is furious at Forge for the loss of Layla and passes out. Rictor also makes a startling discovery: the Purifiers' base extends beyond New York, including Washington D.C.
While Madrox Prime still remains in a coma after the events of the previous chapter, Layla and one of the Madrox dupes arrive eighty years in the future to discover that the mutant race has been wiped out following a genocidal conflict with baseline humans, and that no reference remains to their existence in the public consciousness. As a team of X-Men led by Wolverine storm Sinister's Antarctic base in the present (intent on reclaiming Rogue and the mutant newborn), Rictor continues his infiltration of the Purifiers, discovering that the mutant-hating fanatics are massing troops from hundreds of allied churches around the world, and do not have possession of the baby. Meanwhile, Surge, furious that Cyclops has elected to leave her team on the sidelines, organizes the New X-Men (including Armor) against the Purifier's main church in Washington, D.C, in hopes of both finding some information on the baby and avenging the forty-five students murdered during the group's earlier rampage. Elixir, Dust and Prodigy, concerned about Surge's vengeful mindset, opt to remain behind. While the attack is initially successful, the team suffers its first casuality of the conflict when Hellion is mortally wounded by the Purifier's new allies... Lady Deathstrike and her new force of Reavers. All the while, Predator X continues its pursuit of the baby, hunting down and consuming a fire-breathing Canadian mutant for sustenance.
Madrox and Layla are figuring out a way to enter the mutant internment camp. The X-Men attack the Marauders, with added help from Emma Frost. Wolverine threatens Gambit into telling him who has the mutant child. He jams his claws into Gambit's stomach until Gambit gives up a name. Meanwhile, X-23 and Rockslide damage Lady Deathstrike's new Reavers until Pixie can teleport the students and Rictor away. Unfortunately, the team is scattered across the country. Iceman volunteers to go search for them, but the shock of the students' transport distracted Emma enough that she lost contact with the team. Bishop arrives at the mansion at Cyclops' behest. When the X-Men begin to lose the fight, Storm covers Nightcrawler and Wolverine's escape. At the X-Mansion, the Sentinels' programming is corrupted and they begin to attack the X-Men. Meanwhile, Cable is revealed to be alive...and he has the mutant baby girl with him.
The X-Men work together to take down the Sentinels. Several X-Men are injured and the mansion is thoroughly destroyed. The New X-Men member Gentle was "nuetralized", but his death is not confirmed nor denied. All the telepaths are hit hard. It is revealed that Cassandra Nova's Nano-Sentinels mutated the pilots into human-sentinel hybrids, and that Cable is the accused assailant. As a result, Cyclops tells Wolverine to gather the X-Force and to hunt down Cable and return the baby by any means necessary. Meanwhile, Mister Sinister explains to Mystique that, while they were unsuccessful in battle, gaining the knowledge the Cable is alone, injured, and on the run with the baby is a worthy reward.
Professor X voices his concerns to Cyclops over his willingness to have his own son Cable killed by the newly reformed X-Force. Cyclops tells Charles that they will continue to argue, and that Charles needs to leave the mansion permanently. Meanwhile, Cable is on the run with the mutant baby when he is confronted by Lady Deathstrike and the Reavers who eventually corner him. Peepers is killed by Predator X, but not before calling X-Factor for help, but Siryn only finds a few uneaten parts of his body. X-Force is searching a Cooperstown Hospital to pick up the trail of the fugitive Cable. Wolverine doesn't trust that Warpath will be willing to kill Cable should the need arise, and he asks Wolfsbane to keep an eye on him, but she learns that he while he won't like it, he'll do what needs to be done. Multiple Man continues his investigation in the future by capturing a guard from the mutant prison camps, and interrogates him to learn that a mutant is somehow responsible for this future, but he and Layla are soon captured by more guards.
In the future, Jamie and Layla are processed in the mutant internment camp, their heads shaved and faces branded by the brutal camp officers. Their brand is the same "M" as Bishop's. Back in the present day, The X-Men arrive to help X-Force, but are too late. As the bloody remains of the Reavers lie around them, Warpath is consumed with grief over Caliban's death. Hepzibah tries to comfort him, but Warpath is inconsolable, saying that he'll never have a chance to repay him for saving his life. Wolverine tells Cyclops what happened before the team's arrival and blames himself for letting Cable escape. Cyclops tells him it was no one's fault and says he had to stop the baby from being killed. X-23 remarks that Cable was doing the same thing. Cyclops tells Strong Guy and Warpath to load Caliban's body onto the aft storage locker and to do so with respect as Caliban died an X-Man. As the Blackbird takes off in pursuit of Cable, M tells Warpath that Cyclops meant what he said about honoring Caliban once everything is over. Warpath says that there will be a lot more people who need burying by then. Back at the Xavier Institute, Prodigy, the Stepford Cuckoos, Rockslide, Mercury, and Surge are able to fully restore Cerebra. Cable ditches the Blackbird in Texas and steals a truck for him and the baby to ride in. The Cuckoos discover that Cable is headed down to Forge's Aerie in Texas looking for a chronal slippage regulator, which Cyclops surmises as an attempt by Cable to escape through time with the baby. Cable arrives at Eagle Plaza only to find Forge injured by gunfire and unconscious. Cable is soon shot from behind afterwards by Bishop, who has betrayed the X-Men and is poised to shoot the baby.
As Forge and Cable lie unconscious inside the Eagle Plaza building, Bishop stands over the mutant newborn with his gun drawn. Before he can kill her however, he is ambushed by the Marauders. He manages to wound Vertigo, but is quickly overpowered by Gambit and Sunfire, who ignore his protests that the child has to die. While Malice/Omega Sentinel seizes the baby, noting the child has no fear of her, Gambit brings a section of the ceiling down on Bishop, immobilizing him. Knowing the X-Men will arrive in moments, the Marauders depart with the baby, but not before Gambit ponders what could make Bishop turn on the X-Men. Meanwhile in the future, Jamie is trying to find Layla, but finds the hostility of both the prisoners and the guards is impeding his progress. Eventually he does locate her, who tells him there is someone he should meet. That someone turns out to be a child named Lucas Bishop and it appears that they are in the future timeline he originated from. Back in the present, after an unsuccessful attempt to locate the baby, Bishop lies about the battle with the Marauders, painting Cable as the one responsible for shooting Forge, who is in the Eagle Plaza's infirmary along with Madrox-Prime. Emma notes that she isn't receiving any messages from the future from him, saying he's virtually brain dead. Cyclops orders X-Force to go with Bishop, but Warpath wants Hepzibah to stay behind, fearing for her safety. Hepzibah objects to this and Wolverine agrees, telling Warpath he has no say about who is on his squad. At the Institute, Prodigy and the Stepford Cuckoos are having trouble tracking the baby, so Emma instructs them to concentrate on finding the Marauders instead. Cyclops wants them to find Cable as well, who is on the outskirts of Dallas, berating himself for losing the baby. As he boards the Blackbird, realizing he can't save the baby alone, he contacts Professor X and tells him he is the only one left who can help him save the future.
Madrox and Layla meet a young Bishop in the future and find out that the mutant baby is responsible for killing over one million baseline humans, fulfilling Stryker's prophecy of a "mutant antichrist." This causes the United States government to round up the remaining mutants and put them into camps. Young Bishop says that if he has a chance he would go back in time and kill the child. Layla then kills the Madrox dupe. In the present, Madrox Prime awakens and warns the X-Men of Bishop's treachery but also demanding to go back for Layla. Emma psionically sedates him.
Xavier has met up with Cable, and repairs all his injuries the best he can, but soon confronts him on the accusations of his possible treachery. Cable explains he was not the one who set the Sentinels on the mansion and that the baby is a savior of the future, responsible for saving both humanity and mutantkind from an unspecified threat. Xavier seems to believe him, saying he's found the baby on Muir Island, but is afraid about what they'll find.
Outside of the Xavier Institute, Dust, Rockslide and Mercury discover Predator X has arrived at the mansion, and is eating the remains of victims from the bus attack.
The Cuckoos use Cerebra to track Gambit (and the rest of the Marauders) back to their current hideout on Muir Isle. What they don't know is that Gambit let them track him. Before they arrive, Gambit presents the baby to Sinister, who changes into Mystique away from the eyes of the other Marauders. The real Sinister is on the floor in a pool of his own blood, dead with shock etched into his face, as Mystique says it's time for the next step. When X-Force and Bishop arrives, Lady Mastermind attempts to use her powers to hide the Marauders, but Wolverine's sense of smell gives away her position, and he stabs her in the chest, apparently killing her and causing her to drop the illusion showing the Marauders and Acolytes ready for battle.
Story starts 3 hours before X-Force gets to Muir Island. Mystique is talking to Sinister about her history with Muir Island and how she's going to lose Rogue there as well. Sinister confirms that Rogue is going to die. Angry, Mystique quickly grabs Sinister and presses his face against Rogue's, effectively killing him due to Rogue's currently enhanced powers.
Later, Gambit arrives with the baby and gives it to Mystique. When he sees Sinister dead, he says that he can't believe he's finally free from him. Then X-Force arrives. Lady Mastermind is on the ground and she appears pretty dead.
The joint forces of the Marauders and the Acolytes attack X-Force. Mystique tells Scalphunter than she and Sinister need more time with the baby and to keep the X-Men at bay at all costs. Suddenly the rest of the X-Men and X-Factor arrive, optic blasts blazing.
Mystique goes back to the lab where Gambit is with the baby. Gambit asks her if she's sure about her plan and she says its meant to be. She says that Destiny foretold that she and he would be in the lab with the baby and Rogue and that she was meant to save Rogue's life. She then takes the baby and places it up to Rogue's face.
Back at the X-Mansion, Predator X attacks Rockslide, Mercury, and Dust. Rockslide tells them to go get help then suddenly, Predator X busts into the mansion where Wolf Cub, Trance, and Indra are standing. Predator X is about to eat Indra when Surge jumps in and blasts Predator X.
Riptide is holding Wolfsbane by the throat when suddenly he falls asleep. Cable and Xavier have arrived, Xavier having put Riptide to sleep telepathically. They examine Wolfsbane and determine that her wounds are superficial and that she'll heal. They then continue into Muir Island.
When the baby touches Rogue's skin, there's a huge flash and surge of energy. Gambit, fearing for the baby's life, grabs it away from Mystique and pushes Mystique down. He asks her how she could have killed the baby but when he looks down, the baby is unscathed. He asks how the baby survived when Sinister couldn't and Mystique says it's destiny. Mystique goes over to Rogue, hoping that she'll wake up but she doesn't. Mystique is confused and says that she did all of this because she wanted to help Rogue so Rogue would love her again. Gambit says that Rogue would never forgive her if her life was saved at the baby's expense, that she would rather die. and that she would die trying to stop Mystique from killing the baby and so would he. Then Xavier appears in the lab and tells Gambit that he is pleased to hear him say that.
The X-Men, X-Factor and X-Force battle the combined forces of the Acolytes and Marauders. Emma senses another telepath blocking her from the baby, even through Exodus' interference, and that its not Sinister. Tempo tries to stop time and make an escape but Cable knocks her out. Xavier then mental messages Cable that he has the child. Xavier then asks Gambit what he's going to do and he says he'll stay with Rogue.
At the X-Mansion, the rest of the New X-Men appear, Prodigy in full command mode and they fight Predator X. Pixie then gets it in her head that they need to go where X-23 is because she was the only one who can hurt Predator X. She then casts her teleportation spell and transports the entire New X-Men team, Beast, Nightcrawler, and Predator X all to Muir Island into the middle of the battle!
Predator X attacks the first mutant it sees, which happens to be Vertigo. She's subsequently gnawed in half. Suddenly, everyone is looking at Predator X, ready to defend themselves, when it gets a whiff....the mutant signature its been chasing for weeks is within its grasp!
In the lab -- Xavier delivers the baby to Cable. Xavier tells Cable to take the baby to the future and keep it safe. Suddenly, Bishop arrives and tells Cable that he isn't going anywhere and that the baby must die. Cable is about to engage Bishop when suddenly Predator X arrives in the lab ready to finally eat the baby.
Cyclops decides to send the New X-Men into battle (even though Emma doesn't agree). Then switch over to Cable pointing a gun at Cyclops when he asks Cable to turn over the baby. Professor X tells Cable to do as Scott says. Rogue wakes up to a crying Mystique and Gambit, and they begin to argue. Back at the fight, Pixie has just taken down Malice who is still possessing Omega Sentinel. Emma faces off against Exodus, and in the process Exodus starts coughing and Dust emerges from inside of him having killed him by using her sand form to destroy his lungs. Logan gets fed up with nothing working against Predator X so he lets it swallow him. Logan busts out of Predator X's stomach killing it.
Back to Rogue and Mystique, Rogue says she's tired of people getting hurt whenever Mystique is around. She takes her glove off and grabs Mystique's face fully absorbing Mystique into herself and killing her. Rogue tells Gambit that when the baby touched her it healed Rogue of everybody she has ever touched. That right now it is only Rogue and Mystique in her mind. She says she needs to be alone and tells Gambit not to follow.Cable, Cyclops and the Professor have a discussion where Cable hands the baby over to Cyclops. Cyclops starts to think about all of the sacrifices he has had to make about his children and Jean. He gives the baby back to Cable and tells him to teleport away with the baby. As Cable teleports away with the baby, Bishop appears and tries to shoot Cable, he misses and shoots Professor X in the head, killing him. Cyclops lets off a major optic blast taking out Bishop. All of the X-Men are standing around his body and Cyclops says " There are no X-Men". Immediately after saying this, Professor X's body vanishes.
- No special notes.
- In comic number 12, Wolverine is shot through the eye by Scalphunter, obliterating the right side of his mask near his eye. However, in the next comic, his mask is completely whole, showing no evidence of the bullet. Yet, when Xavier is shot, Wolverine is once again shown missing the right part of his mask.
- Pages referring to the "Messiah Complex" event
- Images showing "X-Men: Messiah Complex"
- Event Gallery: X-Men: Messiah Complex