The fateful mission would cause the premature end of the superhero team, if Jean Grey hadn't done anything. Afraid of losing the only home she had left, she used her telepathic powers to suppress the existence and fate of all the deceased members in the minds of everyone involved in the mission. Petra, Sway, and Darwin would no longer be mentioned, because their identities were erased from the minds of all who had known them. Scott was unable to mourn his brother and, for a long time, awaited his return, believing he had been abandoned at the X-Institute. 

Notable Missions 

• In the team's first official mission, the X-Men dealt with the presence of the mutant terrorist Magneto, who kidnapped an Eastern European city to shed light on the mutant containment camps in Genosha. The heroes easily managed to rescue all the civilians, but they were unable to deal with Magneto without the help of Xavier, who mentally connected with the villain and destabilized him. The X-Men triumphed but were curious; there seemed to be something unspoken between the two mutants leaders. 

• While trying to stop the series of robberies led by the mutant Vanisher, the X-Men encountered a secret Interpol division focused on dealing with mutant threats: Factor Three. But when their paths intertwined with the superhero team, the heroes began to share information with the infiltrated agent Sean Cassidy, a mutant juvenile delinquent who claimed to have been forced to act as a member of Factor Three. 

• The young heroes located Magneto again as he invaded a communication center in Antarctica, but now, accompanied by his own team of allies to deal with the X-Men. The Acolytes of Magneto were formed by Mastermind, Toad, Phantazia, and his son, Quicksilver. The battle became arduous, and Magneto managed to complete his plan, sending a televised message across the globe, inviting any and all mutants to join his group of Acolytes. 

• Before leaving Antarctica, the X-Men were warned by the group of scientists that Magneto may have caused a serious communication failure with another information center located in the center of the Arctic. The heroes agreed to resolve the issue, but upon delving into the search, they ended up finding something much bigger. In the center of the Arctic, behind powerful, endless ice storms, they found an isolated world, registered by the group of researchers as the Savage Land, but they were not yet able to reach it. 

• In an attempt to frustrate Xavier's presence in his plans, Magneto freed the mutant's half-brother from a maximum-security prison in Australia. Cain Marko also received his mystical helmet, which made him capable of resuming his identity as the Juggernaut. The villain proceeded unstoppably to the X-Institute, destroying everything in his path, and the X-Men did everything they could to stop him. In the end, he could only be defeated when finally face-to-face with his half-brother, who, combining his telepathic abilities with Jean's mind, was able to put him into an induced coma. In Cain's mind, Jean managed to understand the true magnitude of her powers and gained access to some secrets of Professor Xavier's dark past, such as the fact that Cain was responsible for leaving him paralyzed. But... how did Magneto know about Charles's relationship with the Juggernaut? 

• A wave of crimes across the country seemed to have been organized to incriminate the X-Men, with their abilities being used to commit terrorist acts. The heroes discovered that it was the young Mimic, who was used by the American government to commit such attacks, in order to encourage the approval of the Red Code Act, which was indeed concretized. 

• The Red Code Act was established in 78 out of 150 countries belonging to the UN. It implemented a curfew across the globe so that automatons, known as Sentinels, focused on capturing criminal mutants, could spread through the streets and keep their states safe. The First Class was formed, but the celebratory mood still seemed bitter, because the future now looked even scarier.

• For the team's last mission, before each member went their separate ways after graduation, the X-Men traveled into the stratosphere to deal with a mysterious UFO signal captured by Cerebro. It was Asteroid M, the new base of operations founded by Magneto to house his new army of Acolytes. At the center of the facility was The Cauldron, a chamber capable of enhancing the mutation of anyone who entered it to its ultimate evolutionary state. The X-Men did everything to try and deactivate the machine, but it required a sacrifice from Hank McCoy to succeed, as he locked himself inside the machinery to shut it down. The Cauldron was permanently destroyed, but Hank was terribly affected by the machine's effects and would never be the same again.

Nightcrawler was being persecuted in Germany for his "invasion" of religious temples and agreed to join the team. Banshee was an Irish teenager who was rescued from the Factor Three operation by the X-Men and joined the team as a way to return the favor. Psylocke was a Japanese assassin-for-hire hired to kill Charles Xavier, but the Professor offered her another possibility for the future. James Proudstar began operating as a vigilante after being trained by his older brother, taking up his heroic mantle as the native hero Warpath. Colossus was raised in the Soviet countryside as a very humble farmer and agreed to leave his family to protect the world from a greater threat.

Notable Missions 

• In their first mission, the X-Men must contain the Japanese mutant wanted throughout the United States, Sunfire, who has been causing immense natural disasters in the area, with the promise that they are only warnings of an even more destructive future event. They eventually manage to contain him and discover that the teenager had just gained access to his opulent gifts, almost as great as his hatred for the United States of America, motivated by the actions that triggered the Hiroshima attack, which directly affected Shiro Yoshida's family, who never recovered from the attack. The X-Men offer him shelter at the X-Institute, where he would be kept hidden from the government while learning how to truly deal with his powers, so that in the future, he could decide for himself what to do with them. 

• The team returns to the Savage Land, now able to cross the barrier of devastating icy storms with the help of their own Storm. They discover that the place is like a Jurassic vivarium kept untouched by global transformation, a place where dinosaurs cross the skies and vegetation dominates the entire view. The first human they encounter is Ka-Zar, a man who grew up alone in that dense forest and never left it. He is not surprised by the mutant nature of the heroes, as mutants are the majority there and live in riverine societies around the Great River, which is being threatened by the presence of local flora and fauna manifestations, such as Sauron and Stegron, who want to put an end to the little human presence still scattered in the area. The X-Men easily protect them, and Xavier adds the Savage Land to his list of possible habitats, whatever that means... 

• The X-Men receive a call from Dr. Moira MacTaggert and travel to Muir Island in Scotland, where they find her laboratory completely overturned. They discover that Magneto invaded the place and, with the help of his Acolytes, reached the containment cell of the young Proteus, Dr. MacTaggert's mutant son who must remain contained. The political leader offers the confused youth a possibility to live alongside him in a true mutant paradise, but the X-Men defeat him before he is able to finish his proposal. Xavier and Magneto battle through their speeches to convince Proteus to join their ideals, but instead, it is Moira who manages to console and contain her own son. Magneto leaves the place, but only after saying goodbye to Charles Xavier with a kiss. 

• The X-Men follow the wave of crimes in England committed by the group of mutant smugglers known as the Marauders and discover the team's connection to the brilliant and millionaire geneticist Nathaniel Essex. However, the X-Men begin to receive contact attempts from an unknown mutant who claims to know everything about the operation involving the Essex Corp. Invading the scientist's secret base, where he was conducting genetic experiments to manipulate the X-Gene, the X-Men discover that their infiltrated agent is Alex Summers, who turned against his boss to help Lorna Dane, a prisoner who had been held captive to serve as a form of blackmail against Magneto, the mutant's father. 

• Polaris and Havok are kept safe by the X-Men so they cannot be located. The team tries to contact Scott Summers to warn him of his younger brother's whereabouts but is unsuccessful. The X-Men then accompany Banshee to Ireland, where he must attend a family meeting to secure his part of the inheritance. But the heroes discover that a terrible evil has spread its vines through the walls of Cassidy Keep, when the isolated relative, Black Tom Cassidy, uses occultism to manipulate his family. The X-Men try to face the sorcerer, but first, they must deal with his newest crime partner, the Juggernaut. 

• The X-Men go to a facility in Canada that seems to be linked to the secret projects of the Essex Corp but are stopped by Alpha Flight, governmental heroes who claim to control the entire territory of the country. The group must then act stealthily but end up crossing paths with another mutant who is also leading his own investigation in the area, Wolverine. Charles explains that the mutant is an old acquaintance of his and that he offered him a place alongside the X-Men, but never received an answer. The team works together with the vigilante, even against his will, and discovers that he is looking for the place's connection to his origin. They even offer for Wolverine to join the mutant cause, but he says he still has things to resolve before playing superhero. 

• Genosha Island is attacked by Magneto and his Acolytes. The place is completely taken over, and the mutant prison that was located there is dismantled. A new political era frightens the platforms, and the polarization of the mutant population becomes extreme with the rise of a third front, anarchism. The Brotherhood of Mutants led by Mystique begin assassinating anti-mutant activists across the globe and spread messages that humanity's days are numbered. The team decides to stop the terrorist group's actions but is unable to deal with the global revolt headed by Mystique and Destiny, at least until they receive help from the couple's daughter, Rogue, who believes her mothers' plan has gone too far.

•  The X-Men discover that the disappearance of the First Class members was not accidental, and they seem to have been kidnapped as part of some political plot. Jean Grey is able to send a telepathic signal to Charles Xavier, pointing to the group's location, now contained in cells under the power of Bolivar Trask and used to train a new generation of Sentinels. The two generations of X-Men unite to destroy the facility while exposing the true face of the anti-mutant policy headed by Bolivar Trask to the public. At the same time, Magneto decrees the creation of the illegitimate state of Genosha, his own mutant paradise, at a UN meeting.

The X-Men find themselves being pursued by a teenager who wants the team’s attention; she reveals herself to be Kitty Pryde, a member of the X-Men who isn’t yet part of the team. It turns out her mind has come from the future and was sent into that young body to warn them, but she won’t be able to maintain the connection for long. The X-Men aren’t sure if they should believe her, and Jean tries to enter the girl’s mind with her telepathic powers, but every time she does, she ends up scrambling the signal and bringing Kitty’s teenage mind back into her body. 

Notable Missions 

• The team is guided by the girl to a television network, where Reverend William Stryker is hosting, and where she claims that widespread chaos is about to erupt between mutant protesters and the Reverend’s followers, who will arrive armed against the crowd. Everything unfolds exactly as described, and the X-Men defend the protest when a group of “vigilantes” known as the Purifiers, led by the masked X-Cutioner, arrive armed. The heroes are applauded by the protesters and draw attention from outside, causing the fight to be broadcast live, until William Stryker invites them onto the stage. Storm accepts, believing it will serve as positive publicity for the team, but when they begin to speak, the Reverend uses the opportunity to attack them, declaring them children of sin and humiliating them publicly. Storm considers reacting, but Jean reassures her that it is better to let the Reverend drown in his own ignorance.

• Proving her right, Kitty tells her full story to her teammates. The future she comes from is one where the Sentinels dominate everything, and it all spiraled out of control after they began patrolling the country full-time, monitoring mutant activity, all due to a desperate act by world governments in response to the assassination of Senator Kelly by Mystique and her Brotherhood. Storm decides that the team should locate the mutant responsible and convince her to reconsider her actions before it is too late. However, the group must balance this mission with their ongoing responsibilities, such as helping the Morlocks, an isolated group of alternative mutants who feel unfit to live in society. They are approached by Caliban, who asks for help stopping a civil war brewing in the sewers of New York. Despite initial tension with Storm, the Morlocks’ leader, Callisto, accepts the X-Men’s help, explaining that they have been threatened by the team of billionaire Warren Worthington to vacate the land beneath one of his recently acquired abandoned properties.

• Madame Marvel and Iceman stay behind to assist the Morlocks, contacting a past ally, Angel, to secure legal aid for them. Meanwhile, Storm and Nightcrawler track Mystique’s whereabouts, while Colossus introduces Shadowcat to the X-Mansion. The two grow closer while training in the Danger Room, something that clearly means a lot to both teenagers. Nightcrawler begins receiving mysterious letters from someone claiming to be from his past and wishing to contact him. As if things could not get stranger, an unexpected visitor arrives at the X-Mansion: the imposing Bishop.

• The time traveler comes from the same future as Kitty and claims to be there to help complete the mission, as temporal instability is affecting her mind, causing memory lapses. He claims to know Mystique’s location, an abandoned mansion near Detroit, which matches the same address Nightcrawler received in his letter, a detail he keeps secret. The team easily locates the place and sends Nightcrawler for reconnaissance, but upon teleporting in, he is spotted by Mystique. The internationally wanted criminal presents a new side of herself, claiming to be his biological mother, having conceived him as an experiment alongside her partner Destiny, but abandoning him when they were both hunted by an angry mob. Nightcrawler hesitates to believe her, until her true intentions become clear when she states he would be useful to her cause, seeing him more as a pawn than a son, just as she once did with Rogue, who had been taken in by the X-Men.

• Nightcrawler chooses where to place his trust and reveals Mystique’s location, but he is attacked by members of the Brotherhood of Mutants, which continues to grow, gaining new followers to its anarchist movement every day. Mystique forces the mutant Phantazia to manipulate her son’s senses, causing the teleporter to bring the entire group exactly where they need to be: the White House, where senators are gathered for a conference that will decide on the Mutant Registration Act.

• Storm and Bishop lead the X-Men to the White House, even without government authorization. Upon entering, they are confronted by authorities unaware that the Brotherhood is already inside. A massive battle erupts between the three groups, seemingly endless and bound to end in tragedy. However, Jean enters Senator Kelly’s mind and speaks with him without interference, pleading for him to revoke the Registration Act and offering a chance for Mystique to see him differently and spare his life. He agrees, but upon returning to the physical world, he declares he will remain true to his values and that the law will pass. Before Mystique can fire the fatal shot, Nightcrawler teleports in front of him, taking the bullet in his place.

• Mystique is then apprehended by authorities, while the Brotherhood flees to avoid capture. Nightcrawler is treated by paramedics, and Senator Kelly votes against his own bill, but the majority of senators vote in favor, and the law passes. Kitty’s mind is finally freed from her future self, signaling to Bishop that they have succeeded, that future no longer exists, and he has nowhere to return to. Storm offers him a place with the team.

• Just as things seem resolved, the media begins reporting on what they call the “Mutant Virus,” a potentially pandemic disease affecting only mutants. The first cases are confirmed worldwide, and the consequences appear severe. Colossus receives a call from his family, fearing that his younger sister, Illyana, has been infected. The X-Men immediately offer to treat her at their laboratory.

• Beast leads research on Muir Island alongside Dr. McTaggert and Cecilia Reyes. The X-Mansion students are placed in quarantine, and strict health protocols are enforced. However, humanity shows little urgency, and world governments delay investing in a cure, prompting Magneto and his Acolytes to seize laboratories worldwide, forcing scientists to work on a solution. The Brotherhood orchestrates Mystique’s escape, informing her that Destiny has succumbed to the disease.

• The X-Men are forced to deal with multiple crises at once. Jean and Professor Xavier appeal to the U.S. Senate, but newly elected politician Graydon Creed turns public opinion against the cure, claiming the disease poses little threat, while Reverend Stryker declares it divine punishment on live television. The crisis leads to the beginning of Operation Zero Tolerance, enforcing segregation protocols between humans and mutants.

• When Illyana Rasputin dies during treatment, it becomes the breaking point for Colossus and many others. He abandons the X-Men and joins Magneto as an Acolyte, setting the facility ablaze and cremating his sister’s body. Now enemies of humanity, they help Mystique and the Brotherhood access the seized laboratories, where she leads the creation of a new strain of the Legacy Virus, now capable of infecting humans. The X-Men attempt to stop the process but seem like mere bystanders in this war between species.

• Mystique and Magneto infect Graydon Creed as patient zero, forcing him to publicly admit he carries a recessive X-gene or die without a cure. Cowardly, he chooses to confess and reverses his public stance. Beast finally receives government support to develop a cure and, with the new strain, manages to create a vaccine. However, it requires a test subject to activate it, a body capable of reabsorbing protective cells.

• Colossus, filled with guilt, volunteers, but Storm, driven by hope, steps forward instead. The vaccine is a success and is distributed worldwide. The consequences, however, are devastating for Storm, who completely loses her mutant abilities as a side effect. Even knowing the answer, she is left wondering if she made the right choice.

Notable Missions 

•  The X-Men investigate the identity of the new U.S. Secretary of Defense, referred to in official documents only by the alias “Bastion.” He appears to be at the forefront of the U.S. Senate, encouraging Senator Kelly to propose the Mutant Registration Act, which would require all mutants to have their identities and histories logged in a system easily accessible to the government. This system would operate alongside the Sentinel Program, with robots equipped to patrol countries 24/7, intervening only when they detect an unregistered mutant.

•   Rogue and Gambit travel to Louisiana after separating from the group to learn more about each other and their pasts. There, they discover a Brotherhood of Mutants outpost led by Toad, a former teammate of Rogue when she served under her mothers. The Brotherhood is attempting to form an alliance with the League of Thieves, offering mutant operatives in exchange for financial support to fund their terrorist activities. The conflict becomes personal when Gambit realizes the League is now led by Belladonna, a haunting figure from his past who manipulated him since childhood to become her husband.

•   Wolverine leads the team to explore an abandoned Weapon X facility in search of clues about Bastion’s origins, only to discover they are not alone. Omega Red leads a group of mutants forced to collaborate with Weapon X, searching the facility for leftover energy sources. Meanwhile, Psylocke encounters Lady Deathstrike, a member of the Reavers who had previously crossed paths with her in Madripoor. By the end of the operation, the X-Men free both Lady Deathstrike and Sabretooth from Weapon X’s control, allowing them to turn against the organization. 

•  Jubilee, the team’s newest member, joins a mission due to her connection to the orphanage where Sebastian Gilberti (Bastion’s civilian identity) was raised. The X-Men discover the orphanage is run by the religious extremist group Purifiers, secretly organized by televangelist William Stryker. The team dismantles the operation and offers full scholarships to the mutant children at the Xavier School for Gifted Youngsters. 

•  Cyclops and his fiancée, Madame Marvel, undertake a covert mission to investigate Sebastian Gilberti’s adoptive home. Disguised as social workers, they question his adoptive mother, who proves uncooperative. Madame Marvel probes her mind but finds only metallic interference. The woman’s body contorts, revealing she is actually an android that attacks them. After a difficult fight, they subdue it, encountering technology unlike anything they have seen before. 

•  Beast attends a Senate hearing as a representative of mutantkind, secretly accompanied by Dr. Moira McTaggert. There, they meet Bastion for the first time, standing beside President Henry Gyrich and Senator Kelly. Political tensions rise, with billionaire Norman Osborn emerging as a likely presidential candidate. Moira manages to get close enough to Bastion to collect a strand of his hair for DNA analysis. 

•  Back at the X-Mansion, the arrival of time traveler Bishop clarifies the situation. He identifies Bastion’s genetic pattern as that of a Prime Sentinel, like those from his dystopian future. It is revealed that Bastion is not a mutant, but a form of advanced bioengineering sent back in time and implanted into a human zygote. He is, or once was, Nimrod, the most advanced Sentinel, responsible for devastating both humans and mutants in the future. 

•  The X-Men are contacted by Valerie Cooper, head of the Pentagon, who reveals the Operation Zero Tolerance initiative. This program implants Sentinel technology into human volunteers, effectively turning them into sleeper anti-mutant soldiers capable of taking control of their own bodies when activated. The program recruits prisoners and civilians alike, creating a hidden army that threatens mutant survival. As the Legacy Virus spreads across the country, Bastion’s security measures gain support, enforcing segregation between humans and mutants. 

•  While Beast focuses on developing a cure, the X-Men track Bastion to Asteroid M, Magneto’s former base, now under government control. A full-scale conflict erupts as the X-Men, government forces, and Magneto’s Acolytes clash. Through uneasy cooperation, the mutant factions manage to stop Bastion before the Prime Sentinels can be activated. The X-Men offer him a chance at redemption, but Magneto kills him brutally. 

•  Enraged, Magneto attempts to reclaim Asteroid M and reprogram it to amplify his powers, intending to reverse Earth’s magnetic poles and cause global catastrophe. Wolverine stops him by impaling him, though Magneto retaliates by violently ripping the adamantium from Wolverine’s skeleton, leaving both gravely wounded. 

•  Returning to Earth, the X-Men discover that the Legacy Virus has been cured. However, Bastion left behind a dossier exposing the X-Men and the Xavier Institute to the government, forcing a public hearing to determine their future. In the end, an agreement is reached: the Xavier School may remain open, but the X-Men must disband. To mark the end of an era, one final event is held at the mansion: The wedding of Scott Summers and Jean Grey.

During these five years apart, much has changed in the lives of the X-Men. 

• Gambit and Rogue experienced ups and downs in their married life, but are more in love than ever.

• Cyclops and Phoenix separated after secrets from the past came to light, and Jean assumed the identity of the Phoenix following a space expedition to aid the Shi’ar Empire. 

• Storm regained her powers thanks to Forge, but she was changed by the five years she lived without them. 

• Wolverine lived in Madripoor under a new identity, attempting a fresh start after coming close to death at the hands of Magneto, but has now returned to action as Wolverine after making a pact with his greatest enemy: Project Weapon X. He offered his body as a test subject for one final experiment in exchange for restoring his adamantium. His body was used as the blueprint to create a new weapon, the agent Cyber, a human who volunteered for the project. 

• But Wolverine was never going to let things be that simple. He used the invitation as an opportunity to finally come face-to-face with The Director. Malcolm Colcord, the man who kidnapped and experimented on Wolverine in the past, now lies dissected on a surgical table. Unfortunately for him, he does not share the mutant’s healing factor.