In the end of Avengers Disassembled, Wanda was taken by Magneto to the island of Genosha. Unfortunately not even Charles Xavier could help her constantly degenerating mind from losing touch with reality. Eventually the New Avengers and the X-Men decided to go to Genosha and decide the fate of Scarlet Witch (Wanda Maximoff). Once they arrived, they found no-one there. Suddenly a bright light engulfed the world, and they were in a new one.
In this world, Magneto was attacked by Sentinels over Manhattan in 1979 (taking advantage of Marvel's sliding timescale policy, there are no heroes active in the 1970s). At the end of the attack, Magneto revealed an alleged international anti-mutant conspiracy involving Richard M. Nixon. The main result of this was that Magneto was granted sovereignty of the island of Genosha as the leader of the world's mutants. Another result was that the protection of mutant life was judged to be the foremost of all laws (as a result, stem cell research on mutant embryos is illegal, but stem cell research on altered human embryos is permitted). Because of this, the world is a racist society, with mutants controlling governments, businesses and culture, and Humans (or "Sapiens") are looked down on as inferior. (essentially a reversal of the current status quo, where mutants are looked down on and despised instead).
Some exceptions apply to sapiens that live with privileges like Carol Danvers (Ms. Marvel) and Spider-Man. However, while Carol Danvers is widely known to be a sapien, Spider-Man is believed by the House of M world at large to be a mutant.
The House of M has created some serious consequences in the Marvel Universe. The greatest so far is the reduction of the mutant population from millions to hundreds. Fan reaction to these changes has been mixed. Some fans thought the previous reality, in which millions of super-powered mutants existed and lived as outcasts, was far-fetched and not as enjoyable as previously stated scenarios. Others criticized the fact that, despite the fact that 91.4% of the mutant population had been "depowered," few popular, marketable characters lost their abilities. Only two current members of the X-Men (Polaris, Professor X) suffered this fate, although the X-Men's main villain Magneto has lost his abilities as well.
Other consequences include the disappearance of Charles Xavier (only until he returned in Deadly Genesis without his powers), Scarlet Witch, and Quicksilver, and Wolverine's total recall of his past, which will cause a serious change in his status. Quicksilver's disappearance will be dealt with in the Son of M. Though not explicitly expressed in the House of M series, Bendis has stated in an interview with Newsarama that Hawkeye has been revived in the Marvel Universe.
The Collective, a new villain that defeated the Canadian superhero team Alpha Flight, was created as a result of the Decimation event. The Collective was apparently formed from all of the mutant energies displaced by Wanda's actions...
The story begins with a birth. Wanda Maximoff, also known as the Scarlet Witch, is surrounded by friends and family while giving birth. Her attending physician, Doctor Strange, hands Wanda her newborn twins and declares the birth a great success. At Wanda's side is her husband, The Vision, who is very proud of his wife and children. From across the room comes a cold and distant voice -- that of Professor Charles Xavier (Professor X) who demands Wanda return the world to normal. She refuses, clinging to her babies, who shatter and disappear. There are no friends, no family and certainly no babies. Instead, Wanda is resting in a dark room in the devastated mutant paradise of Genosha. Using his fantastic mental powers, Professor X forces Wanda to sleep. Magneto appears, dressed humbly, and asks Professor X about his progress with his daughter. Professor X informs Magneto that his power will no longer be enough to hold back Wanda and that a solution must be found. Magneto, blaming himself for twisting his children through the strength of his own dreams and ambitions, walks on a magnetic field towards the center of the island to be alone.
Meanwhile, Xavier arranges a meeting of superheroes to decide the fate of Wanda Maximoff. Calling the Avengers, the X-Men and several lone heroes, a meeting ensues high atop Avengers Tower, presided over by Professor X himself. Emma Frost, reading the minds of all those in attendance, concludes that killing Wanda is the only way to end her destructive magic. Captain America, however, argues that the group should seek alternate methods of dealing with Wanda including suppression of her powers and her insanity. The X-Men argue that if word about Wanda and her destructive powers gets out, it will set back human-mutant relations by centuries. As the conversation progresses, it is revealed that Professor X asked Doctor Strange to help Wanda, but unfortunately neither was strong enough to combat her magic. Wolverine speaks up, saying that there is no other way -- Wanda must be killed. The rest of the group, however, decides that they must talk to Wanda in person before making their decision.
Back in Genosha, a distraught Quicksilver rushes to Magneto and reveals that he was just in New York where he heard that the X-Men and Avengers are planning on killing Wanda. Magneto angrily replies that he does not know what to do. Quicksilver falls to the floor sobbing and Magneto glances over at his sleeping daughter.
Xavier takes the two groups to Genosha, only to discover that Wanda is missing. Suddenly, the members of the group start to disappear one by one. Spider-Man is soon the only one left and becomes engulfed by a white light...
When the light departs, we see that the world has changed: Spider-Man is married to Gwen Stacy in New York; Cyclops and Emma Frost are married; Dr. Strange is a psychologist; Carol Danvers -- known usually as Ms. Marvel -- is now Captain Marvel, America's most beloved superhero; Gambit is a criminal; and Steve Rogers is an aged veteran. As we follow vignettes of their lives, it becomes readily apparent that none of them remember the change. Meanwhile, Wolverine, who is now in charge of the S.H.I.E.L.D. House of Magnus Red Guard, wakes up onboard a helicarrier sleeping next to Mystique. Unlike his comrades, Wolverine remembers.
Wolverine immediately rushes outside for a breath of fresh air. Leaping from the helicarrier, he finds himself in a world where Homo superior, instead of Homo sapien, rules the planet.
Attempting to make sense of the strange world he finds himself in, Wolverine first seeks Professor X at the Xavier Institute for Higher Learning. He finds, however, a family who has lived in the mansion for fifteen years and who have no recollection of any Charles Xavier. Wolverine then sets out to find either Peter Parker or Tony Stark, the Iron Man. However, when he reaches the lobby of Stark Tower, he is stopped by his teammates in the elite Red Guards. He escapes, but is promptly contacted by his former New Avengers teammate, Luke Cage, when he is transported to the hideout of the "Human Resistance Movement" by Cloak. To make matters even stranger, he is then threatened by Hawkeye.
After enduring a less than pleasant security check from Hawkeye, Wolverine realizes that the Red Guard has followed the tracking chip that Hawkeye just removed from his neck. The room explodes and Wolverine's teammates storm the underground headquarters. In the middle of the battle, Cloak teleports everyone he can to the Kingpin's office, which he knew would be empty. There, Wolverine relates to the Sapien Underground Resistance the series of events that led to the establishment of this alternate world, including the Scarlet Witch's nervous breakdown and the subsequent murders of Hawkeye, Vision, Jack of Hearts, and Ant-Man, resulting in the destruction of the Avengers. Wolverine theorizes that his personal history under the Weapon X program had so drastically wiped clean his memory that he alone could remember how things were. Furthermore, Wolverine asserts that as of yesterday he could remember every day of his life, and that he had what he most desired. Eventually Wolverine hypothesizes that Magneto used his daughter to give everyone what they wanted, so that the Master of Magnetism could have what he wanted -- global domination and a world where mutants dominate over the common man.
An incredulous Luke Cage asks how did Magnus know what they wanted; Wolverine simply states that Charles Xavier, whom Magneto had kidnapped prior to the final transition into the House of M, would have the power to ascertain these desires. When Wolverine questions if the group believes his story, they say that yes, they do. Questioning why they believe him so easily when his story is so fantastic, Wolverine is presented with young Layla Miller, a mutant girl in the alternate world who awoke that morning to realize she had the power to show people the real world. Wolverine decides that the best way to proceed is to get all his former teammates together to kill Magneto and the rest of the House of M. Wolverine and the resistance then arrive, via Cloak's transporting power, at Emma Frost's home; Wolverine asks the young girl known as Layla Miller to "enlighten" Ms. Frost, just as she had previously done with Luke Cage. It is still unknown why Layla remembers the world before the change, but it is believed she is a mutant with the ability to see alterations in reality.
Having illuminated Emma Frost, the resistance movement then contacts various heroes, including Cyclops, Shadowcat, Spider-Man, Rogue, Mystique, Nightcrawler, Toad, She-Hulk and Daredevil. As Layla awakened the heroes, Rogue, being distraught and confused, touched Layla; the power appeared overwhelming for Rogue as it emanated from her and awakened others in the vicinity. Hawkeye, unable to handle reliving his own death, flees the group, and is seen again in The Pulse #10 acknowledging his own death. The group considers reawakening Captain America, but appears to decide against it, seeing that, in this reality, Steve Rogers was never frozen during World War II, is now roughly in his early eighties, and thus unable to aid them in the fight against Magneto. Meanwhile, in Genosha, Lord Magnus ignores his daughter, Lorna, in order to look at a memorial gravestone in the Genosha gardens that commemorates the death of Professor Charles Xavier.
Meanwhile, the 'awakened' heroes travel to the S.H.I.E.L.D. helicarrier where Emma Frost uses her mental powers to commandeer a vehicle to take them to Genosha. While travelling, the heroes sit down in the ship's cafeteria to enjoy a meal. While there, Cyclops informs the team that since the upcoming battle with Magneto may be the most important battle of their lifetimes, no one should restrict themselves or hold back in the least. This causes Jessica Drew to object -- if Magneto has given each of them everything they've ever wanted in this illusion, shouldn't they be content to just live in his world? Wolverine quickly dismisses the idea.
Back in Genosha, Magneto receives the incoming representative from Latveria -- Victor Von Doom. There is to be a great event held that night to commemorate the mutant triumph over humanity, an event for which the House of M will act as host. Magneto and Doom smile and pose for the cameras, but it's clear that there is no love lost between the two. The party begins in the royal Magnus palace as the guests are introduced: King T'Challa (also known as the Black Panther) of the African Commonwealth of Wakanda, King of Latveria Victor Von Doom, Genis-Vell (a visiting delegate from the Kree Empire), Princess Ororo (also known as Storm) of Kenya and King Namor of the Kingdom of Atlantis. Finally, the hosts of the evening are introduced: the House of Magnus, comprised of Magneto, the Scarlet Witch, Quicksilver, Polaris and Magneto's two psychic grandchildren. Suddenly, from high above, a S.H.I.E.L.D. Sentinel plunges towards the castle. Magneto uses his magnetic powers to hold the Sentinel back from crashing into the castle when our awakened heroes attack. Leading the attack are Wolverine, Daredevil, Nightcrawler and Spider-Man. From the back, Cyclops calls out Magneto's name. When he turns, Cyclops unleashes a furious optic blast, apparently vaporizing Magneto on the spot. Rogue, finally able to unleash her powers to their full extent, tackles both Namor and Princess Ororo and absorbs their abilities, causing her to overflow with power.
Elsewhere, Cloak transports Emma Frost and Layla Miller to Magneto's Genosha garden. Searching for Xavier, they instead find the memorial commemorating his death. Emma Frost collapses to the ground weeping, crying out that "It's all over!" Suddenly, Cloak fades into the ground and reemerges, revealing that Xavier's remains aren't in his grave.
The battle between the House of M and the heroes continues with great ferocity. While the chaos ensues, the Scarlet Witch disappears from the battlefield only to be discovered by Dr. Strange in a tower with her children. The two begin to talk as Dr. Strange attempts to discover the origin of the madness that is happening. Wanda reveals the answer to him in a flashback to the beginning when Quicksilver is confronting Magneto about the fate of Wanda. It turns out that Quicksilver himself was the one responsible for the creation of the alternate world, conspiring with Wanda to make everyone happy in an almost perfect world. After this revelation, Emma Frost tells Strange to ask about the fate of Charles Xavier, but before he can Wanda is struck in the back by an arrow.
The attacker is Hawkeye, who begins to break down emotionally to Wanda about his death in the real timeline. After a heated exchange, Hawkeye is killed for the second time as one of the Scarlet Witch's antagonized sons - who, as in Avengers Disassembled, are both conduits for Wanda's own almost Schizophrenic mind - uses his mutant powers to make the poor avenger non-existent again. Meanwhile in the memorial garden, Magneto confronts Emma Frost and Layla Miller, who reveals the truth to Magneto about all that has happened. He then unleashes his wrath on everyone, especially his son Quicksilver. He nearly kills Quicksilver by pummeling him to a bloody pulp with large pieces of steel. Suddenly the Scarlet Witch appears, stopping Magneto and returning her brother to healthy form. She begins to lash out saying, "We're freaks, Mutants... you chose this over us and you ruined us..." Then, with four words, "Daddy... No More Mutants", things begin to break down and everything burns out to white once again.
With a blinding flash, the world seemingly came back to the way it was. New York was back to normal when Layla Miller woke up from what she thinks must have been a lucid dream where she played an important part.
Peter Parker woke up confused with Mary Jane Watson at his side. Together with the Avengers, they tried making sense of what happened that night -- some of them remember, some don't -- only to be confronted by a distraught Doctor Strange bringing in the fact that the House of M really took place and its effects are slowly being felt on a wider scale.
Outside of the X-Mansion, Emma Frost woke up with her nose bleeding. Screams came pelting from the mansion as the students of the Xavier's School for Higher Learning one by one faint and lose their powers. Two confirmed students to lose their powers are Wind Dancer and Tag from New X-Men: Academy X. Helplessly, the X-Men watched most of their students lose their gifts, hoping in vain that Emma would soon give them an answer to all their questions. As Nightcrawler raced to find Wolverine, Emma Cerebra-scanned the whole world for Mutant activity only to find out the great decimation the mutant population has endured and among them depowered is a sweating Iceman, Bobby Drake. Meanwhile, Wolverine awoke remembering everything about his past.
Back at the Stark Tower, the Avengers sought possible explanations from whatever useful sort of media report they could get when they are interrupted by an abrupt appearance of someone in the Mansion's ruins. What they saw when they came there was Hawkeye's uniform and an article written by Kat Farell publicizing his death, leaving tears and a great sense of pride among his former teammates.
Still in desperate pursuit of answers, the X-Men fly to Genosha to confront Magneto who also lost all his powers. He was not able to satisfy them with the answers they've been seeking, and for all his past evil deeds, Wolverine decides to keep him alive to live the life of a powerless, and aging normal human: the kind of person Magneto never wished to be.
Whatever caused the majority of the mutant population to lose their powers, the heroes can only guess. With Xavier still missing, and with the Scarlet Witch probably depowered (as she could not be detected by the Cerebra scanner or by Doctor Strange and she later appears to be living a normal life), the mutant population can only hold on to Hank Pym's word that all these powers could not simply vanish... they are contained somewhere; and that for every action, there's an equal and opposite reaction. The question remains, as Hank Pym said, "What will be the reaction?"
As if to Punctuate this Statement, a Colossal red ribbon of Energy begins to orbit Earth...
Characters who have gone through changes include: