Professor Charles Xavier founded the Xavier Institute for Gifted Youngsters, intended to shelter and educate young mutants while secretly training them as a covert task force to act as agents protecting both humanity and mutantkind.
The first student at the institute was young Jean Grey, adopted by Charles Xavier after the death of her parents. But the first X-Man was the student Scott Summers, who demonstrated an aspiration to fight for the mutant cause.
Soon, more students were also chosen to be part of the program, thus forming the First Class: the eldest was the scholarly Beast, with unbreakable bones and powerful physiology. Warren Worthington III, a young man from high society secretly sent to the X-Institute by his father, a billionaire who was ashamed of his son's mutant origin. Bobby Drake (Iceman), the youngest, but also the heart of the team. And finally, Cecilia Reyes, the shy and isolationist recruit.
There were more members on the team, such as Petra, Sway, Darwin, and Vulcan, the latter being Gabriel Summers, Cyclops' older brother, who brought the young boy to the institute. But none of them survived the team's first mission, a disastrous visit to Krakoa Island, whose territory was entirely occupied due to the exploitation of the billionaire Warren Worthington II.
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.
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.
A new group of X-Men is assembled by Charles Xavier, now featuring international students from all over the globe. Their mission is to operate in the 78 countries that have submitted to the Red Code Act and prove that they were wrong in their decision.
The team's leader is Ororo Munroe, a princess from Kenya who is worshipped as a deity in her community but who met Charles Xavier in her childhood and maintained contact with him.
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.
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.
Storm leads Madame Marvel and Iceman from the First Class, who unite with Nightcrawler and Colossus from the Second Generation, while welcoming Kitty Pryde (Shadowcat) and Bishop as new members.
This new task force exists because the X-Men must now answer to world governments for their actions, thus operating through diplomacy as vigilantes.
Cyclops leads Beast from the First Class, who unites with Psylocke from the Second Generation, while welcoming Rogue, Wolverine, Gambit, and Jubilee as new members.
This new secret task force exists because the X-Men must operate in parallel with global governments, thus acting in secret, stealthily, and without diplomatic constraints.
After the end of the X-Men thanks to Operation Zero Tolerance, Charles Xavier gathers his most promising students for a new iteration of the team.
But this time the group is meant to act as full-time superheroes, to strengthen the relationship between mutankind and humankind, and to guide the world toward a new era of reconciliation.