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.

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.

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.

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.

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.

An infuriated Bishop takes Scalphunter's gun and shoots as Cable timeslides to the future, missing him and hitting Professor X.

[4] This series followed the attempts of Cable to protect the Messiah child from the recovered Bishop's time traveling wrath.

[5] The book turned to a focus on Professor Xavier, Rogue and Gambit, and featured plans regarding Magneto, as well as a female character from the New X-Men title.

The team consisted of Dust, Rockslide, Blindfold, Wolf Cub, and Anole (from the cancelled New X-Men series), as well as new members Ink and Graymalkin.

3) which writer Craig Kyle describes as being the follow-up to Messiah Complex and "the middle chapter of what I think will be a major three-part saga, which will continue to define and redefine the X-Universe moving forward".