The following history takes place up until the end of Avengers vs. X-Men.
Due to a sudden leap in evolution, Mutants are born with superhuman abilities, generally manifesting at puberty. They are often hated and feared by humans because they are different and the events of AvX didn’t help matters. However, the end of the Phoenix Force ushered in a new wave of mutants after Scarlet Witch declared “No More Mutants” and later the birth of Hope Summers. The history of the X-Men is long since their beginning in 1963, also being adapted into television, movies and video games, but the core creation comes from the comic book series starting with the original five members and founded by Professor Charles Xavier who spent many of his adult years studying mutation. Following an encounter with the Shadow King, Xavier vowed to protect the world from the threat of evil mutants so with the help of Moira MacTaggart, he eventually decides to start a school for mutants, training them to be what will eventually become the first X-Men. Xavier turns his father’s estate into Professor Xavier’s School for Gifted Youngsters and his earliest student in Jean Grey, who is only twelve years old when her powers manifest. Xavier then constructs a Danger Room to test mutants and develops Cyberno, which is later replaced by Cerebro.
After years of preparation, Xavier decides it’s time to recruit young mutants he’s been keeping track of and starts by traveling to Washington D.C., seeking out FBI agent Fred Duncan who is assigned to investigate reports of mutants, convincing him to allow Xavier to enroll young mutants in his private school and train them to battle evil mutants. In the following days, Xavier recruits Scott Summers after rescuing him from Jack Winters and he becomes the first of his X-Men as Cyclops. Next, he rescues Bobby Drake from an angry lynch mob and he joins as Iceman. The third team member is Warren Worthington III who was already embarking on a solo career as the high-flying Angel, agreeing to join the group after a brief battle. Then Henry McCoy is recruited when he’s rescued from The Conquistador, later rounding the group out with Jean Grey joining the squad as Marvel Girl. After extensive training in the Danger Room, the team is sent on field missions to protect the world from dangerous mutants who use their powers against humanity, bringing them to Florida and in direct confrontation with Magneto who becomes their most frequent enemy in the beginning.
Their next adventure has the team defending Washington D.C. from the Vanisher and they also have their first interaction with the super-hero community when they clash with Iron Man and also find out not all mutants are interested in joining when they invite Blob into their ranks. When Magneto returns to plague the X-Men, he brings the Brotherhood of Evil Mutants (BOEM)and they first clash with the X-Men when the Brotherhood take over the nation of Santo Marco and later attempt a full-on capture of the team. The X-Men later aid the Sentry against the General and clash with the Fantastic Four when Xavier becomes trapped by the Puppet Master as well as have three more clashes with the Brotherhood when the BOEM attempt to recruit Namor and Thor into their ranks. Following the X-Men’s graduation, they face Unus and aid Spider-Man against Menace and Sundown while Xavier briefly leaves Scott in charge of the school while attempting to stop Lucifer from conquering the world. This attempt is foiled thanks to the assistance of the X-Men and Avengers, which begins the groups’ long-standing association and the team also gains an ally in Ka-Zar when they discover the Savage Land by aiding him and Zabu in defeating Swamp Men.
Eventually, the X-Men see the supposed end of the Brotherhood following an encounter with the Strange which ended when he took Magneto and Toad to his planet for study while turning Mastermind into dense matter. But as the Brotherhood go away, new threats arise such as Juggernaut, but he’s defeated with the help of Human Torch and when Bolivar Trask invents Sentinels, they eventually revolt against him by capturing him and Xavier for Master Mold, but the X-Men save Charles and defeats the Sentinels at the cost of Trask’s life. While recovering from the Sentinel battle, the X-Men are targeted again by Magneto who is defeated and recaptured by the Stranger and also aid in the defense of Reed Richards and Susan Storm’s wedding from a legion of villains gathered by Dr. Doom. The X-Men then face Mimic after he has gained the ability to mimic other people’s super powers and learns the X-Men’s secret identity, but the battle ends when he is stripped of his powers and no memory of their civilian identities. When Lucifer resurfaces, he uses Blob and Unus to pose as X-Men to besmirch the team with the public, but is ultimately defeated.
The X-Men then face two non-mutant threats and Jean is also forced by her parents to leave Xavier’s school for Metro College but she still remains part of the group and the rest of the team battles El Tigre. When Xavier starts to fear an imminent threat he presses the group to find new recruits by unsuccessfully pursuing Scarlet Witch, Quicksilver and Spider-Man, but they do recruit Mimic after regaining his powers despite being used as a pawn of Puppet Master in order to destroy the X-Men. The team soon learns of Factor Three and after rescuing Banshee from Factor Three’s control, they lose Mimic as a member when he loses his powers again while stopping Super-Adaptoid and then the team stops Warlock’s plot for world domination as well as Cobalt Man’s rampage at Stark Industries. When Factor Three strikes again, the Juggernaut is revived, but is stopped with the aid of Dr. Strange when he forces Marko into the Crimson Cosmos, but Xavier is kidnapped. When Banshee attempts to contact the X-Men after learning of Factor Three’s European headquarters, his message is interrupted, leading to a brief battle with Spider-Man when he’s believed to be a member of Factor Three, but eventually arrive in Europe and captured.
Factor Three finds the X-Men to be guilty of betraying mankind and sentence them to death, but before executing them, reveal their plans to initiate World War III by attacking the United States and Russia so the X-Men split into two teams and confront Mutant Master at his headquarters in the US. They free Xavier with Changeling’s help and Banshee reveals the Mutant Master is the alien race, Siris, so the X-Men and Factor Three work together to stop Mutant Master and part on peaceful terms, later being awarded new costumes designed by Jean. When Xavier learns of an impending invasion from the Z’Nox race, he approaches the terminally ill Changeling and imparts part of his mental powers on the dying mutant in order to aid him in his role as Xavier while he prepares for an invasion, leaving only Jean with the knowledge of his plan and Xavier goes into seclusion while Changeling takes his place. While in a battle with Grotesk, Changeling sacrifices his life to stop him and after his funeral the X-Men are captured by Magneto after reforming the Brotherhood, allowing Angel to escape in the hopes he would lure the Avengers to his hideout.
When they arrived, the Avengers and X-Men eventually defeated Magneto and he seemingly perished in an explosion. After returning to the Mansion, the X-Men are visited by Agent Duncan and the team is left all of Xavier’s fortunes while also battling Juggernaut before he is returned to the Crimson Cosmos once again. After the battle, Duncan informs the group they are to disband by order of the government so they split for a time until they are drawn back together when a large number of mutants are detected by Cerebro in the San Francisco area. While investigating, the team meets Lorna Dane and learns Mesmero was amassing an army of mutants in the name of Magneto to enslave humanity, capturing Iceman and Lorna and taking them to the Mutant City outside San Francisco. Lorna’s mutant powers are activated while both her and Iceman are rescued by the X-Men, but Lorna stays behind while remaining loyal to her supposed father, Magneto who turns out to be a robot version of the Master of Magnetism. When the X-Men returned to destroy the Mutant City, Cyclops posed as an evil mutant named Erik the Red in order to infiltrate the militia. During the battle, Iceman revealed evidence to Lorna, proving she was not Magneto’s daughter so she helped the team defeat Magneto and Mesmero.
This act prompted Magneto to leave and detonate Mutant City while Lorna returned to New York with the X-Men where they attended the wedding of Yellowjacket and Wasp. Later, an accident during a test of one of Xavier’s inventions led to the X-Men accidentally teleporting Blastaar to Earth, but he was seemingly killed when the machine short-circuited. Scott then reentered Alex’s life after just graduating from college, but Alex was captured by the Living Pharoah so Scott tracked them to Egypt and the X-Men battled him while learning Alex was a mutant. During the battle, Alex was sealed in a special sarcophagus which allowed the Pharoah full access to Alex’s powers and transforming him into the Living Monolith, but Alex managed to break free which cut off the Pharaoh’s powers. Before the X-Men could help Alex control his powers, he was captured by Sentinels and given a suit by Larry Trask which controlled his powers, naming him Havok and the confused mutant aided Trask in capturing the world’s known mutants. Alex later aided the X-Men in defeating the Sentinels when he learned Trask was himself a mutant and had no intent on keeping his word to Alex, with Cyclops gaining the upper hand when he convinced the Sentinels to destroy the source of mutations by flying into the sun.
The X-Men then put Havok into the care of Dr. Karl Lykos who secretly required energy from other people to survive, but the energy from mutants turned him into Sauron and he battled the X-Men, later fleeing to Tierra del Fuego and reverting back to Lykos. When the X-Men tracked Lykos they were unable to stop him from committing suicide in order to prevent himself from draining the energy of his lover Tanya. The X-Men then traveled to the Savage land in order to find Lykos’ body and they were reunited with Ka-Zar who they agreed to help against the Savage Land Mutates. Angel was tricked into joining the Mutates by the Creator (secretly Magneto); however, Warren soon learned the truth and assisted the X-Men in defeating Magneto and destroying his citadel, resulting in the Mutates reverting back to their normal forms. When the team returned to the States, they went to Washington D.C. so stop Sunfire from interrupting a delegation between US and Japanese officials. The X-Men were shocked to find Xavier alive and he explained the reason for his ruse so with the help of Cyclops and Havok’s powers, Xavier linked every mind on Earth in order to drive the Z’Nox invasion away, leaving him on the brink of death.
This required the X-Men to seek out the Dr. Bruce Banner who had the knowledge to cure Xavier, learning of a device that could cure him which they used. After aiding the Fantastic Four in an altercation with Dr. Doom, the X-Men returned to training with Xavier, but Iceman briefly leaves the team due to the new romance of Havok and Lorna, as well as his feeling of betrayal over Xavier’s secrets. Xavier sends the rest of the team to the Savage Land yet again to recover the body of Magneto, but their plane crashes and Jean supposedly perishes, but they soon learn she was sent to the Land of the Dead and the team stops Nhu’Ghari from enslaving the natives while Jean learns Magneto is still alive and they defeat and capture Magneto. Meanwhile, Iceman, Havok and Polaris receive a mental call from Xavier to seek out the others that have gone missing so Lorna and Alex receive help from Ka-Zar while Iceman fails to reach the Savage Land. A storm hits the craft while traveling home and Magneto escapes while Angel and a native named Avia are lost at sea. The remaining X-Men arrive at Kenya where they meet Ororo Munroe and they assist her in stopping Deluge while Iceman is found with amnesia by Lykos, and Angel and Avia are rescued by a barge.
When Lorna and Alex pick up Bobby’s mutant signature, they seek him out while Angel and Avia are sold to Krueger. When the rest of the team returns home, they are attacked by the Fantastic Four and are made aware although they prevented the Z’Nox from invading Earth, the force attacked another world so the X-Men teamed with the Fantastic Four to deal with the Z’Nox. While in space, Jean’s mind is contacted and briefly possessed by the Phoenix Force, but the contact was erased from everyone’s mind and both teams worked together to send the Z’Nox home world into the Negative Zone. After returning to Earth, Jean has a secret screening session with Moira Mactaggart while Xavier and Hank travel to Illinois in order to investigate a new mutant detected by Cerebro and they meet Ashley Martin, who has gained mental control of a damaged Sentinel. The Sentinel then regains its original programming and attempts to kill the trio, but Ashley shuts it down and turns against Hank and Xavier so Xavier is forced to use his mental powers to delay Ashley’s and he stays behind to monitor the girl’s recovery. Meanwhile Scott, Jean and Candy Southern search for Warren which leads them to Krueger’s freak show and, becoming captured and depowered and then sold to the Brotherhood, but later defeat them.
Later when Candy warns Angel his uncle Burt is attempting to marry his mother, the X-Men arrive to stop the wedding, but are too late to prevent her from dying of the poisoning Burt was administering to her. Alex, Lorna and Bobby return to find the mansion empty and Cerebro detecting a new mutant in the Himalayas so they depart to later find the hidden realm of the Inhumans. After returning, Lorna is compelled to leave after being put under mental control of Tad Carter and the X-Men discover Tad is a member of the Promise who later takes Havok, Lorna and Angel while sending the rest of the team to the realm of the Mole Man. While the team is battling Mole Man, Angel is freed by a member of the Promise and he freed Alex and Lorna while also helping the Fantastic Four in stopping Magneto and Namor’s attack on Earth. After escaping the Mole Man, the X-Men reunite with Warren and Iceman decides he’s not ready to rejoin the group, but is briefly conned by Sam Bullit to pursue Spider-Man and rejoined the group shortly after. After returning, Bobby comes into conflict over Lorna and is injured so Alex leaves the team and Lorna follows where they get into a battle with Hulk shortly after.
After the battle, the duo decide to return to the X-Men, but are captured by the Secret Empire while Hank leaves the team for a position at the Brand Corporation where he further mutates himself and ignores any calls by the X-Men due to his shame at his transformation. The remaining X-Men investigate a series of murders caused by Morbius and aid Spider-Man in capturing him. Meanwhile Beast is aided in battling the Brotherhood, Quasimodo, Juggernaut and the Griffin by Warren, later coming to aid Vera Cantor to save Mimic from radiation poisoning after mimicking Hulk’s powers and is captured by the Secret Empire along with Bobby and Warren. The remaining X-Men aid the Hulk defeat Juggernaut before learning the Secret Empire is responsible for disappearance of other mutants, eventually teaming up with Captain America and Falcon to fight the Empire and free their friends. Iceman later helped Human Torch catch Equinox before departing on a mission with his team and Xavier aided the Defenders stop Magneto and the Brotherhood. When the X-Men were sent to investigate a large mutant energy signature on Krakoa, they learned the entire island is alive and become captured as the island fed on their life-force, but Scott is set free to gather more mutants.
Xavier then gathers a group of mutants who were taken in by Moira to form a new team of X-Men and Scott departs with them to Krakoa, but are overpowered with Petra and Sway being killed in the process. Darwin and Vulcan were saved when they were drawn into the Earth and Darwin absorbed Sway and Petra’s powers which converted him into energy so he merged with Vulcan. When Scott believed everyone was dead, he returned to Xavier who used his powers to wipe out all memory of the group and began recruiting a new team to face Krakoa. This new group consisted of Banshee, Sunfire, Storm, Nightcrawler, Colossus, Wolverine and Thunderbird, and the new team succeeded in freeing the original X-Men. After returning, the original team left with the exception of Scott while Thunderbird is killed during the second mission and Sunfire abruptly quits. While entering Earth’s atmosphere after a space mission, Jean saves her teammates from intense radiation and is believed dead upon crashing, but she suddenly rises from the ocean and calls herself Phoenix while wielding more power than before. It’s unknown by all that Jean was replaced by the Phoenix Force while Jean is placed in a cocoon at the bottom of the bay while her body healed from radiation poisoning.
The team returns to space to aid Lilandra of the Shi’ar in order to help stop K’Ken from using the power of the M’Kraan Crystal to take over the universe so the Phoenix uses her power to fuse the crystal back together after it is about to shatter and the X-Men return to Earth with Lilandra. After a fight with Mesmero and Magneto, most of the team find themselves in the Savage Land, becoming separated from Phoenix and Beast who believe their teammates dead so they return to Xavier to report the news and he departs Earth with Lilandra to Shi’ar space. The remaining team members eventually return home and are later ambushed by Alpha Flight on the way back, taking Wolverine into custody but he escapes and the team finds Xavier gone and the phone disconnected. The X-Men and Phoenix reunite on Muir Island where they battle Proteus and a powerless Banshee stays behind with Moira, while Xavier returns and recruits Kitty Pryde and defeats Emma Frost which alerts the X-Men’s existence of the Hellfire Club. Phoenix catches the attention of Mastermind and is easily convinced by illusions in her mind to become Black Queen, but breaks free of his control and unleashes the Dark Phoenix and abruptly departing Earth, destroying a distant star and absorbing its energy, ultimately killing over five billion inhabitants of the nearby planets.
Upon her return, Hank designs a neutralizer to subdue the entity and Xavier places mental blocks in her mind, allowing Jean to regain control, and the Shi’ar arrive on Earth demanding the death of Dark Phoenix. Xavier then invokes a duel of honor and Lilandra allows the Imperial Guard to battle the X-Men but start to fall on the Blue Area of the Moon, which lead to the re-emerging of Dark Phoenix and after Jean regains control, ultimately sacrifices herself. After Jean’s funeral, Kitty arrives to live at the school while Scott leaves due to Jean’s death, leaving Storm as the leader in his absence and after a battle with Magneto who nearly kills Kitty, he comes to terms with the fact he’s become what he has always hated while Scott returns to the team. When Corsair returns to Earth seeking the X-Men’s aid in stopping a rebellion against Lilandra, its discovered Deathbird is in league with the Brood and the team assists in stopping the threat while Scott discovers Corsair is his father who was believed dead. After returning, Carol Danvers, Logan and Storm infiltrate the Pentagon and upload an open-ended virus erasing all references to the X-Men and its members, encountering Mystique, Rogue and the Brotherhood during the mission.
The Brood later resurface and abduct the X-Men, Lilandra and Danvers, implanting embryos inside them, but Storm is saved by the Acanti who were used as starships so the team frees the Acanti and the X-Men are healed, but before killing the Brood Queen, Kitty finds Lockheed and he follows her back to Earth. While abducted by the Brood, Xavier believed his team was killed so Moira convinced him to form a new team with the exception it is only to train them in their abilities rather than sending them into combat, later being named the New Mutants and aiding the X-Men in many battles after their return. The X-Men later learn one Brood embryo had not been destroyed and was planted inside Xavier during their initial contact, finding he had been transformed into one of the Brood, but he was defeated, leaving his mind implanted inside a cloned body. After their return to Earth, Scott leaves the team and meets Madelyne Pryor during a trip to meet his grandparents and falls in love, is married and has a child named Nathan. Warren later rejoins the team, but is captured by the Morlocks and taken into their tunnels to be Callisto’s groom so Storm challenges her to combat without the use of her powers and wins, securing her leadership of the Morlocks and Angel’s freedom.
Rogue later joined the group after leaving the Brotherhood and Danvers became furious when they allowed her to join after she had absorbed her powers so she left with the Starjammers, but Rogue gained the team’s trust when she nearly died protecting Logan and infiltrated the S.H.I.E.D. helicarrier to rescue Michael Rossi. Later, Rachel Summers joined the team as well after arriving from an alternate timeline. Magneto also becomes an ally to the team and is captured by Freedom Force while attending a Holocaust memorial, but is exonerated after being put on trial, but it was interrupted by the Fenris twins, who sent Xavier and Magneto into the Parisian sewers. Xavier convinced Magneto to take his place as the school’s Headmaster after being half-drowned and near-death and Lilandra took Xavier from Earth to recuperate from his injuries. Magneto became Headmaster for a long time under the alias Michael Xavier and was later invited to join the Inner Circle of the Hellfire Club so he accepted. When Scott returned, he attempted to regain leadership of the team but was opposed by Storm and she defeated him without powers and he left the team again. Shortly after, Warren contacted the original team to include a revived Jean Grey and they became X-Factor while Rachel departs to the Mojoverse.
When the Marauders appear, they kill most of the Morlocks living in an alley and paralyze Colossus during their first fight, put Nightcrawler into a coma and trap Kitty with her own power. Magneto manages to heal Colossus, but couldn’t do anything to help the other two so Havok, Longshot, Dazzler and Psylocke take the injured members’ place while Nightcrawler and Kitty leave to form Excalibur after healing. While in Texas, the X-Men battle the Adversary and appear to die saving the Earth but were resurrected by Roma and made them undetectable to electronics, still believed to be dead in order to protect their friends and family. The team relocates to the Australian Outback after defeating the Reavers and take in Madelyne Pryor to protect her from the Marauders. The team is soon lured back to New York during Inferno where Madelyne is discovered to be a clone of Jean by Mr. Sinister that part of the Phoenix Force entered after committing suicide on the moon. Madelyne strikes a deal with N’Astirh to become Goblin Queen out of anger at Scott and his intentions are to sacrifice Nathan to allow demons to freely travel to Earth, but are ultimately defeated by X-Factor and the X-Men and Madelyne commits suicide while Jean absorbs the remaining Phoenix essence.
Rogue is later presumed dead when a merged Nimrod/Mastermold drags her into the portal made by the Siege Perilous and other members leave the team, leaving only Havok, Dazzler, Colossus and Psylocke who later return to the Savage Land to rescue Lorna, but are teleported back to the Outback by Gateway while the Reavers approach. Meanwhile Lorna boards a freighter to travel home and her powers are stolen by Zaladane and replaced by awkward size changing and invulnerability so she contacted Muir Island, leading to an interim group of X-Men to defend the research center and the Reavers were stopped. Rogue later returns to be attacked by Danvers and joins Magneto in the Savage Land while allying with Ka-Zar against Zaladane, becoming attracted to one another, but it ended quickly once Magneto killed Zaladane. After the Reaver assault, Forge and Banshee began looking for the missing X-Men and find Colossus in New York under the guise Peter Nicholas and his powers gone and no memory so they leave him alone. Psylocke is found as a naked amnesiac by the agents of the Hand so her mind and soul were transformed into the Asian body of Kwannon and is brainwashed into becoming Lady Mandarin, but when she faced Logan, her psychic knife backlashed her memories and she broke free from the Hand’s control.
Storm is found as a de-aged pre-teen, losing her memories of her adult life and framed for murders by the Shadow King, but she eventually met Gambit and the two later went to the X-Mansion, reuniting with Forge and Banshee while Dazzler was discovered on a beach by Guido, but is later trapped in Mojoverse while trying to save Longshot from Spiral. Soon after the partial reunion, Genoshan Magistrates arrive and capture the team for crimes committed on their island and brought to Cameron Hodge who made a deal with N’Astirh to become immortal and took control of Genosha. X-Factor joins the New Mutants and interim X-Men on a rescue mission to save their friends while Logan, Psylocke and Jubilee save Boom-Boom and Rictor. Jubilee tends to the two while Logan and Psylocke infiltrate Hodge’s citadel to be discovered by an amnesiac Havok who later regains his memory and the two are captured. The mutants are put on trial and found guilty, but they eventually escaped before being put to death, stopping Hodge and destroying the citadel while burying his body beneath it. Eventually the Magistrates were able to seize power from the Genoshan government while Havok and Wolfsbane stayed behind to make sure mutants were given fair treatment and the world learned the X-Men were still alive so they returned to the school and began rebuilding the team.
Soon after Xavier returned to Earth the Shadow King began spreading waves of hate around the globe and used Lorna to absorb the negative emotional energy to empower himself so Xavier used Cerebro to identify the source and sent the X-Men to Muir Island, but were defeated by the island’s Shadow King-controlled residents. Back at the mansion, a possessed Colossus attacked so Xavier had to erase the Peter Nicholas persona completely, and then asked X-Factor to rescue the X-Men while Shadow King possessed Legion as his new host. The remaining heroes divided into three teams by an attack on the astral plane, defending Xavier from physical attacks and freeing Lorna, disrupting the Farouk’s nexus. Forge used a neuro-synaptic weapon on Psylocke so she could use her psychic knife on Lorna and Xavier was badly wounded during the battle, but Shadow King was defeated and X-Factor returned to the fold along with Rogue and Colossus to form a new team. To remain effective as a group, the X-Men divided into a Blue and Gold squad and the Blue Squad battled Magneto and his Acolytes in Genosha where he forced Moira to brainwash the Blue Squad into joining his Acolytes on Asteroid M so the Gold Squad snuck on board to rescue their teammates.
When the Asteroid is destroyed, Magneto and his Acolytes chose to stay behind rather than escaping and seemingly perished in the explosion. After the battle with Magneto, the Gold Squad attended a party at the Hellfire Club thrown by Emma Frost who explained her and other members were targets of assassination and sought help, but before long, Trevor Fitzroy arrived and began attacking Frost. Donald Pierce was also attacked by Fitzroy’s Sentinels so Gateway teleported Pierce to New York along with three of the attacking Sentinels, seemingly killing Emma, Pierce and Jean, but Xavier learns Jean’s consciousness had been relocated to Emma’s body and awakens in the custody of Fitzroy and Shinobi Shaw. Jean surprised both men by using her telekinesis and helping the X-Men escape so Fitzroy opened a portal to the future to bring allies, but Bishop arrived instead to later join the X-Men and Jean is rejoined with her comatose body. The two teams are later brought together again when Xavier is shot while giving a speech by Stryfe who was disguised as Cable, infecting him with the techno-organic virus. Both Scott and Jean are also abducted by the Horsemen of Apocalypse and delivered to Mr. Sinister, who was disguised as Apocalypse and handed the two over to Stryfe in exchange for a mysterious container.
The Gold Squad searched for Scott and Jean while the Blue Team joined X-Factor in hunting down X-Force for information on Cable’s whereabouts, but he convinced Logan and Bishop it was Stryfe, also revealing both men were from the future. When Apocalypse awakens from his rejuvenation, he is quickly defeated by Stryfe so he aids Hank and Moira with the cure to Xavier’s virus. Logan later receives a subconscious telepathic message from Jean, hinting she’s being held captive on the moon so the X-Men head to Stryfe’s base and launch an attack, rescuing Scott and Jean and Cable disappears with Stryfe into the time-stream. Meanwhile, Sinister opened his container to find nothing inside and soon discovering he opened a Pandora’s Box with the mutant infecting Legacy Virus. Magneto later resurfaces with Exodus and starts to prepare an all-out war upon humanity with Colossus joining his cause after losing faith in Xavier’s due to Illyana’s death by the Legacy Virus. The rest of the X-Men attacked Magneto on Avalon with Jean and Xavier attacking telepathically while Logan defended Quicksilver, so a wounded and furious Magneto ripped the Adamantium out of his body, leaving him near death and Xavier shut down Magneto’s mind, leaving him in a vegetative state.
Logan leaves the team following his injuries and Sabretooth comes to stay for rehabilitation while Scott and Jean finally gets married, raising their son Nathan in the future during their honeymoon. Not long after, the X-Men face the Phalanx after taking over the X-Mansion and assuming the form of various team members, but Banshee manages to escape along with Sabretooth, Emma Frost and Jubilee. Banshee learns the Phalanx are after the next generation of mutants, hoping to experiment and eventually absorbing them into their collective, but they are saved by Emma and Banshee, later becoming Generation X and are taught to use their powers at the Massachusetts Academy. The Blue and Gold Squads later become one large team and Legion awakens to make amends he caused his father by killing Magneto in the past, but as he fired a powerful psi-blast at Magneto, Xavier sacrificed himself and Legion faded away along with the rest of the X-Men, except for Bishop who was a temporal anomaly and a crystalline wave emerged from the M’Kraan Crystal, eliminating all reality. Learning of the battle against Haller, Apocalypse began his world domination a decade earlier than planned and rather than being defeated by X-Factor, conquered all of North America along with his Horsemen known as the Age of Apocalypse (AoA).
Apocalypse erected a citadel on Manhattan Island with breeding pens and experiments run by Sinister and Dark Beast so humans fled to Europe where they were frequently massacred by Sentinels. In this reality, the X-Men are created by Magneto and acted as freedom fighters, eventually being able to send Bishop back in time to stop Legion and restore reality to normal, but four AoA individuals crossed over to the Earth-616 reality (X-Man, Sugar-Man, Dark Beast and Holocaust), while Blink and Sabretooth joined the Exiles. When Xavier shut down Magneto’s mind, his anger and Xavier’s repressed negativity resulted in the birth of a psychic being which lay dormant in Xavier’s increased frustration with anti-mutant sentiment, Legacy Virus deaths and the fall of his own students and awakened Onslaught. Rogue simultaneously discovered Joseph, who was an amnesiac Magneto, and he was brought to the X-Men. Onslaught aimed to turn the human race into a collective so he absorbed Franklin Richard and Nate Grey and erected a citadel on Manhattan Island while using Sentinels and mutant minions to battle the rebellious heroes and a first strike from the Avengers, Fantastic Four and X-Men freed Xavier from the entity’s control, leaving him as psionic energy contained within special armor.
Jean Grey aided the Hulk in destroying Onslaught’s armor and Thor flew into the energy which damaged him so the other non-mutant heroes followed and successfully destroyed the entity while seemingly sacrificing their own lives, but in actuality, Franklin used his reality warping powers to transport them to a pocket universe and their fate was undiscovered while Xavier was taken into custody. Bastion used the Onslaught crisis to push his anti-mutant agenda to the US government and his Prime Sentinels to hunt down and eliminate mutants across the country under Operation: Zero Tolerance. Cannonball, Logan, Scott, Jean and Storm were captured along with members of Generation X, but all of them managed to escape while in New York, Iceman managed to save Dr. Cecelia Reyes from termination. Marrow and Sabra also joined the duo and took the fight to Bastion, but before matters were worse, Senator Kelly put an end to the operation and S.H.I.E.L.D. arrived to arrest Bastion who is revealed to be the Nimrod/Mastermind robot. Meanwhile the other X-Men return from a space mission and Bishop is separated along with Deathbird while the other members become prisoner of Nanny and brought before Erik the Red who put Gambit on trial for past crimes.
It’s revealed Gambit led the Marauders to the Morlocks during the Mutant Massacre, which repulsed his teammates and they abandoned Gambit in Antarctica and returned to help Scott from a bomb planted in his chest. Dr. Reyes, Marrow and Maggott joined the team and the Summers’ left for Alaska in order for Scott to recover from his wounds, leaving Storm and Logan in charge. The new team battled Alpha Flight and extra-dimensional demons and the Shadow King also returned to trick Psylocke into giving him control over every mind on Earth, but Betsy managed to defeat him. After Excalibur disbanded, Kitty, Nightcrawler and Colossus returned to the team and Dr. Reyes set up operation in the school as a doctor while Maggott briefly joined Generation X. Magneto later resurfaced once again, holding the Earth hostage with the planet’s electromagnetic field in his control so the X-Men traveled to Antarctica and Joseph discovers he’s a clone, later sacrificing himself to stop Magneto, who later gains control of Genosha. Logan is then kidnapped by Apocalypse and forced to fight Sabretooth for the mantle of Death, defeating his nemesis in the hopes he may be able to resist Apocalypse’s programming and his Adamantium is replaced inside his body while a Skrull poses as him on the team.
After a fight with the X-Men, Logan’s teammates eventually break him free of Apocalypse’s control and his secret of the Twelve is revealed, who are prophesized to defeat En Sabah Nur. The team attempts to round up the mutants listed, but with the help of the Skrulls and his Horsemen, Apocalypse manages to capture them first, revealing his plans to absorb their powers instead to become invincible and unveil the AoA. Using Nate Grey as a vessel, the Living Monolith acts as a power conduit, but Apocalypse failed to factor in Magneto’s weakened powers, which broke the machine and the twelve were freed, but Nate was still in danger of being possessed so Scott freed him and took his place and Apocalypse was destroyed while Cyclops was presumed dead. Cable then joined the X-Men to honor his father while the High Evolutionary was manipulated by Sinister to revert all mutants back into humans, but their powers returned shortly after and the Neo appeared six months later claiming to be the next stage in the evolution, but eventually yielded to Magneto who was preparing to wage war on humanity. When Mystique and the Brotherhood attempted to attack Senator Kelly, Pyro prevented the act and begged the Senator to stop the circle of violence, but its later revealed Mystique tampered with the Legacy Virus to only affect humans.
Mystique and Sabretooth then attacked Muir Island where Moira had finally discovered a cure, but was mortally wounded and Rogue subdued Mystique while Xavier absorbed the knowledge of the virus into his mind before Moira died. Senator Kelly was also killed by a human angry by his change of stance and Hank used Moira’s data to create the Legacy Virus cure, but a mutant power signature had to be activated for the cure to disperse around the world and Colossus injected himself and activated his mutant power, killing himself and saving the lives of countless mutants. Jean left on a quest with Cable to discover whether or not Scott had truly died and eventually found him in the Middle East so Cable used his powers to cleave Apocalypse’s final hold on his father and Scott returned, but more distant and self-conscious due to his insecurities of being possessed. With the Legacy Virus gone, the Mutates on Genosha were amassed into a huge army by Magneto who then went after Xavier, capturing him and bringing him back to Genosha. Scott and Logan infiltrated the island as Jean recruited an interim team and managed to free Xavier who mentally stopped Magneto from ripping out Logan’s Adamantium a second time while Logan impaled him with his claws.
The team divided yet again with Storm gathering a secret squad to obtain prophetic diaries of Destiny but later abandoned the search after realizing the prophecies only came true if they chose to let the diary control their action. The X-Men also had to deal with Banshee’s paramilitary X-Corp which was founded after Moira’s death, but Mystique infiltrated X-Corps and slit Banshee’s throat, which ended the organization. Later, Cassandra Nova surfaced and activated a forgotten Master Mold to manufacture immense Sentinels to attack Genosha while a paralyzed Magneto could do nothing but watch as the entire island was exterminated along with sixteen million mutants except for Emma Frost due to her sudden mutation of diamond-hard skin. Many mutants also started gaining Secondary Mutations and Cassandra was brought into custody by Scott and Logan, but managed to break free and switched bodies with Xavier, shooting her previous body to near death. Emma joined the team and the school was reopened to students while Cassandra (as Xavier) admitted to the world he and the school’s residents were all mutants while Hank suspected something was wrong with Xavier and was put into a coma by a mind-controlled Beak before leaving for space so Jean assumed the role of Headmistress and immediately drove off an attack by the U-Men.
Hank finally awoke from his coma to warn his teammates and Xorn accepted an invitation to join the team in time for another fight with Cassandra who had tricked the Imperial Guard into attacking the school and the X-Men were weakened by nano-sentinels Cassandra planted but were cured by Xorn. Jean managed to fragment Xavier’s mind with the help of Cerebra and placed a tiny part in every mutant mind on Earth so when Cassandra attempted to use Cerebra to eliminate every mutant, Xavier’s mind reformed and resumed control of his body and Cassandra became trapped inside Imperial Guard member Stuff. When Storm’s team returned, Rogue and Gambit took a leave of absence after losing their powers and Cannonball joined the team just before facing Reverend Stryker and Lady Deathstrike while Storm was asked to lead the X-Treme Sanctions Executive (XSE), while Rachel, Logan and Magma joined the X-Men as well as Storm’s team. Xavier then created the X-Corporation in order to improve mutant/human relations while Quentin Quire and his Omega Gang pushed Magneto’s policies during Open Day as humans visited the mansion, but were stopped by Sophie Cuckoo as she sacrificed her life while her sister Esme revealed Emma and Scott’s psychic affair and shot Frost in her diamond form, splintering her into thousands of pieces.
Sage and Bishop’s investigation found the culprit, but Esme fled and Jean reformed Emma’s broken body despite being furious at her and Xorn began pushing Magneto’s theories on his special class of mutants, but when Xavier confronted him about it, it is discovered Xorn is Magneto in disguise. Magneto then traps Logan and Jean on the remnants of Asteroid M and incapacitates the other X-Men, destroys the Institute and takes over Manhattan. While Asteroid M drifts closer to the sun, Logan kills Jean in order to unlock the power of the Phoenix and Scott leads a last ditch effort on Magneto as Phoenix arrives to defeat him, but he manages to give Phoenix a stroke and Logan decapitates Magneto in a berserker rage as Jean dies in the arms of Scott. Due to the loss, Scott and leaves the school and leave it to Hank who begins taking the drug Kick to deal with the stress, but its discovered the drug is an aerosol form of an ancient parasitic bacteria and he’s possessed into creating a chain reaction which destroys civilization. Jean is then reborn years later as Phoenix and her memory is restored, but after destroying Sublime, White Phoenix travels through the time-stream and pushes Scott towards Emma and averts a disastrous future.
Scott and Jean then become co-Headmasters and rebuild the school while Xavier leaves for Genosha to begin rebuilding with the real Magneto due to Xorn being an imposter and the X-Teams are rearranged and Colossus is later discovered alive by Kitty who also rejoins the team while the Danger Room becomes sentient and tries to murder the group. When Scarlet Witch loses control of her reality warping abilities and destroys the Avengers, Magneto takes her to Genosha where Quicksilver manipulates her into creating House of M, but even though the world seemed perfect, Logan suspected something is wrong so with the help of Layla Miller, the heroes begin remembering their past lives and commence an attack on Magneto’s Genoshan headquarters to find Xavier. After learning how her mutant heritage and father’s choices nearly destroy her family, Wanda utters “No more mutants” which returned the world as it was, but erased the X-Gene from many mutants, drastically reducing their population to an estimated 198. The Xavier Institute then became a sanctuary for mutants while Valerie Cooper dispatched Sentinel Squad O*N*E* to protect the swelling population at the mansion and Apocalypse returns with Horsemen with the plan to eliminate most of humankind but is stopped by the X-Men and Sentinel Squad O*N*E*.
Vulcan also returns and reveals himself to be Alex and Scott’s brother along with a revelation about Krakoa and after the Superhuman Registration Act is passed, Ms. Marvel and Tony Stark attempt to recruit the X-Men into the Act but are quickly turned down when Emma reminded them how the non-mutant heroes turned their backs in the past and mutants were not required to register. Rogue was then assigned her own team to make and they battled the multiple adversaries until facing the Marauders so they disbanded after Iceman became the only member active. Xavier then recruited a team to participate in a space mission to stop Vulcan where Alex witnessed him kill their father, Corsair and decided to stay in space along with Rachel and Lorna to join the Starjammers and their resistance against Vulcan and Deathbird. When the first mutant birth occurs following M Day, it blew out Cerebra and most telepaths at the mansion so the team jumped to Alaska to find the Purifiers and Marauders and battled for the life of the mutant baby with Scott ultimately agreeing to hand the child over to Cable so he could take her to the future and protect her, but Bishop betrays the X-Men and attempts to kill the child, accidentally shooting Xavier in the head while aiming for the baby.
With the X-Men disbanded and mansion destroyed, Hank returns to destroy the last remaining records of the team and its students, but Xavier is discovered to be alive thanks to the intervention of the remaining Acolytes, but his mind is badly damaged and only had contact with Gambit so X-Force and X-Factor relocate while a Young X-Men team is established. Scott and Emma investigate the sudden loss of contact from other team members and travel to San Francisco where Goddess had manipulated the city into thinking it was living in the 1960s, but she is defeated and the mayor of the city is rescued who then offers the X-Men safe-haven. Scott, Ororo, Hank and other various team members established and built a home base for all mutant-kind, sending a message to all mutants around the world they would now have a place to call home. After fighting off the Skrull Invasion, the X-Men marched through the streets of San Francisco, being welcomed and thanked by the people of the city. Soon after, Simon Trask helped propose a ban on mutant reproduction to control the mutant population and led his supporters on a march across the state, arriving in San Francisco and met by many of the new mutants in the city which erupted into a riot.
Emma was asked by Norman Osborn to keep the mutant population under control but she failed to do so and the Dark Avengers, along with H.A.M.M.E.R. soldiers deployed to quell the riots, resulting in Hank’s arrest. Osborn also contacted Emma and placed her in charge of her very own group of X-Men while Mystique (posing as Xavier) asked Scott to surrender, but he resisted and retreated, later being forced to battle the Dark Avengers while Emma is introduced to the Dark X-Men. Hank became imprisoned and the real Xavier contacted him, stating the prison was a place where they planned on depowering mutants. Cable and Hope also returned which prompted Bastion to order a strike force to kill Hope and the X-Men came to their aid. Rogue and Nightcrawler escaped with Hope and Bastion brutally beat Rogue, but just as he was about to kill Hope, Nightcrawler teleported between them and was impaled through the chest and teleported her to Utopia where he died. A large energy dome was activated over the Bay Area to cut off the X-Men from escape or help and Bastion opened a dimensional portal to allow more Nimrod Sentinels so Cable used his last time jump to take X-Force to the future where they shut down all the Nimrods in the present and future.
In order to return, Cable had to sacrifice himself to hold the portal open and allow X-Force to return while Hope drew upon the mutant powers of the X-Men and eradicated Bastion along with the dome surrounding the city. Later, when the Young Avengers find Scarlet Witch and restore her memories, they convince her to start re-powering former mutants and she’s taken into custody by the X-Men and a confrontation arises between the X-Men, Avengers, and X-Factor. The fight is cut short when Wanda proceeds to put them all asleep and the X-Men agree to leave Wanda alone but state she would never be forgiven. After Kid Omega’s attack on the United Nations, anti-mutant sentiment begins rising and world leaders begin reactivating Sentinels, while Mayor Sinclair expedites the grand opening of the Mutant History Museum. Kade Kilgore and the Hellfire Club use this opportunity to attack the X-Men and despite Logan’s objections, Scott orders Idie to stop the Club by killing them, which leads to a giant super-Sentinel nearly destroying Utopia while Scott and Logan part ways due to their beliefs after a savage fight. However, the two men agree Idie would be better off away from Utopia so she leaves with Logan to rebuild the school, while each team member is forced to choose to remain on Utopia with Scott or rebuild the school with Logan.
Logan than founds the Jean Grey School for Higher Learning and on the first day, its attacked by the Hellfire Club, but saved by Kid Omega and the Club is defeated and later served papers by Matt Murdock, having being sued by Logan so the Club contracted Sabretooth to torment the school. Scott then assembled his Extinction Team, which consisted of the world’s most powerful mutants to act as a nuclear deterrent for enemies of Utopia, their first foe being Mr. Sinister who had taken over the Dreaming Celestial. Sinister transformed a section of the city into an all-Sinister zone which was a hive mind of Sinisters and Scott was alerted of an incoming threat by Agent Brand that the Celestials were heading to Earth. Sinister offered a truce in order to open a dialogue with the X-Men and revealed his plans, then took control of the Extinction Team using mind control except for Emma who was in her diamond form while Hope shot Sinister in the head to free the team. Sinister then possessed one of his doppelgangers and told Scott he couldn’t kill him because there was no real him as Sinister, but the Extinction Team fought the doppelganger while being protected from his mental attacks by Hope.
Sinister’s body and his clones were then destroyed by Danger, but while regrouping for another fight with Essex, they discovered he was already prepared and revealed he was using Scott’s mind as a map for his own mind which allowed Emma to return the Dreaming Celestial head to its body and destroyed Sinister’s body along with the clones except for one. Sinister congratulated the heroes and revealed all the data of their failures had been gathered, processed and integrated, then teleported and stated the next time he would meet the X-Men, they would be more hated then he was. Sinister then took a gun and shot himself and when the other Celestials arrived, Scott and his team told them the Earth, to include their friend the Dreaming Celestial was under their protection. While waiting for the Celestials to respond, the Dreaming Celestial gave a sign for the others to leave. Following the Dark Angel Saga, Fantomex decided to enroll Genesis in the Jean Grey School and Logan brought Warren as well in the hopes his memories would return, but failed to work due to his childish behavior and his belief he’s a real angel so he was enrolled in the school by Iceman.
After bringing a device back that restored the use of Logan’s legs, Warren and Evan became friend and Warren eventually came to realize he was indeed a mutant and not an angel after an attempt to fly to heaven and being saved by Evan. It is revealed that his energy levels and skills are growing rapidly and he has the power to see the essence in other people so when Evan asks to see his essence, Warren tells him he can see only the good inside him, despite the fact he only saw nothing but Apocalypse. When Sinister returns to one of his own labs and activates the self-destruct, he is unaware a member of the Phalanx had captured the lab long ago and was a strain of Phalanx Sinister performed experiments on. In order to be cured, the Phalanx attempted to contact the rest of the Phalanx from his strain and to do so, it had to assimilate a whole town so Scott and his team arrived to fight it and when the Phalanx knew it was the last of its strain, it lowered its shield and allowed the team to destroy it. Back at the school, Kitty began throwing up more and more and then started having pain in her stomach.
Once in the ladies room, Kitty found she seemed to be in her eighth month of pregnancy so she locked herself in her room for two days. Meanwhile, Warren’s money was cut off due to being mentally unfit which left the school without funding so Logan took Kid Omega to the galactic casino with him in order to win enough money to fund the school, leaving Bobby as Headmaster. Back at the school, Hank and Rachel went to check on Kitty while she called Colossus thinking he was the father, but he had no idea on the matter. When they finally see Kitty, they see her at being eight months pregnant so they attempt to determine the gender of the child, but discover Kitty is actually under attack by microscopic Brood that came from an egg sac residing in her womb. All the students were then sent to the safe room except for Broo who could hear the Brood telepathically and Kid Gladiator also stayed behind after sneaking into the lab and entering Kitty’s body in order to prove he can’t be defeated. Hank, Bobby, Lockheed, Rachel and Warbird then enter Kitty’s body to discover Kid Gladiator while the school is attacked by Brood and an unknown alien who defeats Krakoa.
The Brood begins attacking Kitty and Broo while the faculty is inside her body and she orders a force field to protect him while she fights off the Brood, but is taken by surprise when the other alien reveals he’s the one who implanted the Brood inside her in order to target Broo. On Planet Sin, Logan and Quire are stopped by security as they are leaving due to them cheating and back on Earth, the faculty finds Kid Gladiator but he’s been changed into a Brood. Outside Kitty’s body, the alien reveals himself as Professor Xanto Starblood who has come to Earth to kill Broo, believing him to be a mindless killer while back inside the team struggle to restrain Kid Gladiator while Hank finds the egg sac and attempts to plant a bomb. Meanwhile, the Bamfs find Kitty and teleport her away while Logan and Quire fight for their lives and Xanto is still trying to kill Broo. The Bamfs return to teleport Xanto outside where he then has to face an angry Krakoa while inside Kitty, Iceman freezes Kid Gladiator while Hank plants the bomb and sets the timer, which explodes and makes Kitty feel sick. Broo then becomes enraged and savagely attacks Xanto who is ultimately saved by the team that returned from Kitty’s body and he is arrested by S.W.O.R.D. and takes Kid Gladiator to be cured.
That night the team finds out Krakoa has the ability to grow diamonds the size of grapefruits which solves their financial issues while in space, Logan awakens after being knocked unconscious. During Avengers vs. X-Men, Nova crashes in New York with a warning to the Avengers that the Phoenix Force is returning to Earth while Scott is sparring with Hope and when she asks why, he is cryptic with his answers so Hope flares up with the power of the Phoenix. The Avengers detect her power and Captain America consults with Logan, finding out the source is Hope Summers. Scott is convinced the coming of the Phoenix would herald the rebirth of mutant-kind as a species while Cap sees it as Earth’s destruction so he arrives on Utopia with the intent of taking Hope into protective custody. After an argument, Scott refuses and blasts him into the ocean, which results in a response by the Avengers when a S.H.I.E.L.D. Helicarrier uncloaks and the invasion on Utopia beings. After a brief battle, Scott fabricated surrender to the Avengers, but then teleported out of Utopia together with several powerful X-Men, resulting in a head start in the search for Hope who had escaped. Scott then contacted Rachel at the school and convinced her to feed the Avengers false information in order to throw them off the trail.
Since Hope scattered her signal, various teams of both X-Men and Avengers traveled around the globe to find her and Scott later traveled to the school in order to recruit more people in his fight against the Avengers. After discovering Hope’s location on the Blue Area of the Moon, the X-Men pursued her and encountered a team of Avengers there, but before a fight breaks out, a badly injured Thor crashes on the moon, followed by the Phoenix Force. Both teams then descend into a brawl while the power of the Phoenix Force increases within Hope, finding herself unable to control it. She then asks Logan to kill her, but Scott prevents him from doing so and as the Phoenix descends upon the moon, Iron Man uses a specially designed suit to try and destroy the entity, but instead splinters it and it takes five other X-Men present as hosts. The Phoenix Five then go about making the world a better place while the Avengers continue to oppose them by staging guerilla assaults and eventually convince Hope to join their cause. Meanwhile Namor loses his patience and attacks the Avengers in Wakanda and the Avengers narrowly manage to defeat him so his portion of the Phoenix Force leaves him and enters the remaining four.
Some of the other hosts then begin acting erratically and start losing control so after a prison break is staged; Colossus and Magik lose their portions after knocking each other out thanks to Spider-Man pitting them against each other, resulting in Scott and Emma becoming sole hosts. Emma begins losing control and starts killing people and also rules Utopia with an iron fist, threatening those whose thoughts displease her, prompting many of its inhabitants to seek sanctuary at the Jean Grey School. The Avengers are then attacked by Scott and makes quick work of anyone opposing him, but is defeated by Hope after combining her powers with Iron Fist, Scarlet Witch and Shao-Lao’s flames to teleport Scott to the moon. Several X-Men then team up with the Avengers after realizing Scott and Emma are losing control and attack the duo, gaining the upper hand until Scott is forced to take the final piece of the entity from Emma, eventually turning him into the Dark Phoenix. Both teams then fight Scott worldwide while trying to also contain the chaos the entity has produced and in a moment, Scott begs Wanda and Hope to kill him, but not before he kills Xavier. The Phoenix is eventually extracted from Scott and possesses Hope who dissipates the entity with the help of Wanda and uses it to create new mutants.
Scott is brought into custody and Captain America visits him where he accepts full responsibility for everything and asks Steve not to hunt the X-Men that went missing. After Scott learns mutant-kind has been reborn, he states even though he regrets his actions, he would do it all over again and Steve accepts the Avengers should’ve done more to help mutants and promised Scott he would change that.