Part 1: "The House that Xavier Built" Several ambassadors arrive at the Jerusalem Habitat, responding to a telepathic message sent by Charles Xavier to recognize a new sovereign nation of
mutants, called
Krakoa. The ambassadors are met by the newly appointed Krakoan ambassador
Magneto. Near the sun, spacecraft approach the station known as "The Forge," home base of a human group called
Orchis. Orchis is the self-proclaimed "last hope" for humanity, made up of various members of human organizations such as
A.I.M.,
S.H.I.E.L.D.,
Hydra,
Alpha Flight, and others, allied to prevent the extinction of
homo sapiens to mutants. Meanwhile, a team made up of
Mystique,
Sabretooth, and
Toad infiltrate the base of
Damage Control searching for information in the databases. While they get what they searched for, Sabretooth maims several guards in the chaos and is eventually captured by the
Fantastic Four.
Part 2: "The Last Dream of Professor X" In the past,
Moira MacTaggert meets with Charles Xavier. In the present,
Mystique gives the intel she stole to Professor X and Magneto. A hundred years into the future, the remnants of mutantkind on Earth war with the Man Machine Supremacy; the mutants Rasputin and Cardinal flee with intel stolen from the machines while their comrade Cylobel is captured and later killed by
Nimrod and
Omega Sentinel as the machines attempt to learn what intel the mutants stole. A thousand years into the future, a post-human referred to as the Librarian and Nimrod (now reduced to a small flying unit) reminisce about mutantkind and the surprising end of their war with humanity and the machines.
Part 3: "The Uncanny Life of Moira X" Moira MacTaggert is retroactively revealed to be a mutant with the ability to be reborn after dying while retaining all of the memories of her past lives. In this way, the different histories of the X-Men are seen to be timelines that she has lived through. She is told during one of her timelines by
Destiny that she has 10, perhaps 11 timelines in total.
Part 4: "We Are Together Now, You and I" In the past, Professor X and Moira MacTaggert meet with Magneto and recruit him to their cause. In the present, Professor X and Magneto meet with
Cyclops and order him to form a team to assault the Orchis Forge and destroy Mother Mold. A hundred years into the future, it is revealed that the intel the mutants stole was an index machine to help them find the actual information they need, but retrieving said information will be a suicide mission;
Apocalypse, the leader of the mutant remnants, vows to lead them in this mission. A thousand years into the future, the Librarian alongside his post-human brethren await the arrival of the
Phalanx, who have responded to post-humanity's summons.
Part 5: "This Is What You Do" A hundred years into the future, the mutants carry out their mission, splitting into two teams. Rasputin's team attacks a human church to draw out Omega Sentinel and the rest of the machines, and everyone dies in the mutants' ensuing suicide attack. Meanwhile Apocalypse's team retrieves the information they are after (the date of Nimrod's creation) but are confronted by Nimrod himself; Apocalypse dies fighting Nimrod to ensure Wolverine's escape. Wolverine awakens Moira from stasis, imprints the intel into her, then kills her to reset the timeline, revealing this future to be Moira's ninth life.
Part 6: "Once More unto the Breach" Cyclops informs X and Magneto that he has assembled a team in order to attack the Mother Mold facility orbiting the Sun. After meeting, they embark on the mission.
Part 7: "It Will Be Done" On Krakoa, X and Magneto contact
Marvel Girl to monitor the mission. Wolverine and
Nightcrawler are successful in destroying the collars, but the ship is boarded by Orchis forces. The humans activate Mother Mold, not knowing whether it will be sane or not. X tells them to do whatever it takes to stop it. Nightcrawler teleports Wolverine onto the collar before being instantly evaporated by the sun. Wolverine's healing factor allows him time to carve through it before he too is evaporated as Mother Mold hurtles into the sun. With the mission complete, Cyclops tries to locate Jean's pod, but Doctor Gregor executes him. The Sentinel drones arrive, intercept Jean's pod, and work to kill her. As his proteges have seemingly all died at the hands of humans once again, X cries and vows "no more".
Part 8: "Something Sinister" In the past, Professor X and Magneto meet with
Mister Sinister to elicit his help in building a database of mutant DNA. Several months before the Krakoan nation is established, Professor X arranges a meeting between
Cypher and Krakoa, and gets the former to work on developing a unique language for mutantkind. A thousand years into the future, post-humanity offers to be willingly assimilated by the Phalanx, and await to see if the Phalanx finds them acceptable.
Part 9: "Society" On Krakoa, X,
Magneto,
Storm, and
Polaris assemble and are joined by five other mutants:
Tempus,
Proteus,
Hope Summers,
Elixir, and
Egg.
Magneto explains that the five mutants, collectively known as The Five, are able to combine their powers to revive deceased mutants. Storm brings The Five and the revived mutants out, proudly announcing that The Five has allowed the nation of Krakoa to defeat death. The revived mutants enter the crowd as Storm calls them the "Heroes of Krakoa".
Part 10: "For the Children" In the past, Professor X meets with
Forge to discuss modifying
Cerebro in order to create a backup for every mutant mind on the planet. Several months before the Krakoan nation is established, Professor X and Magneto recruit
Emma Frost to their cause. Professor X later uses Cerebro to invite every mutant - hero or villain - to Krakoa.
Namor refuses Professor X's invitation. A thousand years into the future, the Phalanx agree to assimilate post-humanity, with the Phalanx eventually merging with their masters, the godlike Dominion. However the assimilation of post-humanity will destroy the Earth and kill every living thing on it.
Part 11: "I Am Not Ashamed" One month prior to the events of the series, Xavier uses Cerebro to offer Krakoa's miracle drugs to all of humanity.
Part 12: "House of X" A thousand years into the future, a conflicted Librarian confronts Wolverine and Moira in post-humanity's mutant reservation. The Librarian reveals post-humanity's plans for ascension and its consequences, as well as the truth of post-humanity's role in the resolution of the human-mutant-machine war. Having learned what they needed to know, Wolverine kills the Librarian and Moira to reset the timeline, revealing this future to be Moira's sixth life. In the past, the young Charles Xavier reels at the knowledge from Moira's mind; Moira swears to break the goodness out of Xavier for the cause and tells him to give up his dream. In the present, despite Moira's cynicism that mutantkind is destined for defeat, Professor X and Magneto vow that things will be different this time. ==Characters involved==