The story begins with the voice of Stan Lee: "Look around you... you never know who could be a mutant, a person born with strange and wondrous powers..." It is the desert. The X-Men’s archenemy Magneto is being transported by a military convoy, unable to use his powers, trapped in a force field. That is, until the White Queen appears. A member of his "Brotherhood of Mutant Terrorists", she scatters the escort and dismantles the field restricting Magneto, allowing him to use his magnetic powers to tear apart his portable prison.

Los X-Men ayudan a Júbilo, después que sus padres adoptivos la ofrecen al registro de mutantes. Ella es atacada por los Centinelas. Los X-men la salvan y la integran al grupo. Allí, ella aprende un poco sobre ellos. Los X-Men descubren que el grupo que ejecuta el Programa de Registro de Mutantes tienen la intención de realizar un seguimiento y eliminar a los mutantes, así que deciden entrar a la sede y destruir todos los datos.

Después de la destrucción de los archivos mutantes, los X-Men se escapan, pero son detenidos por los Centinelas. Durante la lucha con los Centinelas, Morfo es asesinado y Bestia capturado y encarcelado por el gobierno. Los X-men logran localizar la sede de los Centinelas y rescatan a Júbilo. Ella decide unirse a la academia de Charles Xavier.

Magneto intenta liberar a Bestia de la prisión, pero Bestia prefiere esperar su juicio. Leónidas [Sabretooth] exige que Bestia sea liberado y se deja llevar por una ira destructiva, haciendo que los guardias le disparen y lo lastimen. Cíclope ayuda a Leónidas y lo lleva a la enfermería de la Mansión, lo cual no le agrada a Guepardo [Wolverine]. Más tarde, Magneto ataca una bodega militar de misiles.

El Profesor X trata de curar a Leónidas [Sabretooth] contra las advertencias de Wolverine, mientras Magneto ataca una planta química para atraer la atención de Charles.

Cíclope y Jean son capturado por un grupo de mutantes llamados los "Morlocks" (mutantes demasiado deformados para pasar por humanos ordinarios, lo que impide que vivan en la superficie) cuando intentaban tener una cita romántica, lo que lastimaba los sentimientos de Logan. Tormenta lucha contra su líder Callisto para controlar al grupo de Morlocks.

Wolverine encuentra a Sabretooth en el Ártico, mientras Tormenta, Gambito y Júbilo se dirigen a la isla paradisíaca de Genosha "amiga de los mutantes".

Los X-MEN descubren la verdad detrás de Genosha pues Gambito, Júbilo y Tormenta, junto con otro grupo de mutantes, son obligados a trabajar como esclavos para completar una represa con la cual dar energía a la fábrica de Centinelas. Mientras tanto, Gambito conoce al misterioso Cable.

Cuando la Mansión X es destruida, los X-Men culpan primeramente al mutante ruso Colossus, antes de descubrir que el verdadero culpable es Leviatán.

Titania va a la Isla Muir por un tratamiento experimental para librarse de sus poderes mutantes y escapa por poco de convertirse en una esclava de Apocalypse.

Apocalipsis convierte a los mutantes que viajan a la Isla Muir buscando la supuesta cura en Jinetes. Apocalypse y sus Cuatro Jinetes atacan la Conferencia de la Paz en París. Titania absorbe el lado maligno de Arcángel.

En un futuro controlado por Centinelas, Bishop es enviado atrás en el tiempo para evitar que un miembro de los X-MEN asesine a una importante figura política.

Aparecen las lápidas de las tumbas de Cyclops (2032), Rogue (2033), Storm (2021) y Jubilee (2010).

Bishop y los X-Men viajan a Washington e impiden el asesinato del senador Robert Kelly; pero Bishop regresa para darse cuenta que el futuro no ha cambiado.

Los X-Men y Magneto se unen para detener a Master Mold que intenta reemplazar el cerebro del Senador Kelly con un computador, e involucrarse en una fuerte batalla contra una tropa de Centinelas. Kelly retira su campaña anti-mutante y Beast es liberado de la prisión

Luego de que Scott y Jean se casen, Morph logra infiltrarse en la Mansión X dispuesto a vengarse de todos los X-Men por haberlo abandonado en el ataque contra los Centinelas en el Cuartel General del Registro de Mutantes. Morph, disfrazado de los X-Men, logra causar el caos en la Mansión mientras Jean y Scott se dirigen a una trampa mortal…

El Rey Sombra logra llegar al lugar de nacimiento de Tormenta, Kilimanjaro, y logra poseer el cuerpo del hijo espiritual, Mjnari, por lo cual Rogue y Tormenta deben viajar a Kilimanjaro para encontrarlo y salvarlo cueste lo que cueste.

El Rey Sombra logra llegar al lugar de nacimiento de Tormenta, Kilimanjaro, y logra poseer el cuerpo del hijo espiritual, Mjnari, por lo cual Rogue y Tormenta deben viajar a Kilimanjaro para encontrarlo y salvarlo cueste lo que cueste.

Omega Rojo es resucitado por tres oficiales corruptos que planean restaurar y dirigir la Unión Soviética. Coloso va por ayuda hacia los X-Men para que le ayuden a evitar la destrucción de su país natal a manos de Omega Rojo.

Vindicator y el Escuadrón Alfa capturan a Guepardo para conocer el secreto de su esqueleto de adamantium.

Gambito se ve obligado a volver a sus raíces del sur por un antiguo diezmo, una vieja disputa familiar y el secuestro de su hermano, Bobby.

Cable usa su dispositivo de tiempo y ve que el Bishop viajó desde 2055 DC hasta el presente para detener una plaga que comenzó Apocalipsis.

Cable llega hasta el presente para detener a Bishop y salvar su propio futuro.

Mística, madre adoptiva de Titania, la obliga a volver a su propio pasado.

Bestia se enamora de Carly, una paciente ciego. El padre de Carly es un enemigo mutante y manda a los Amigos de la Humanidad a secuestrar a Carly.

Un extraterreste, Mojo, secuestra a los X-Men (excepto Gambit y Jubilee) como su más reciente éxito de televisión de toda la galaxia.

Xavier y Magneto son secuestrado por Mr. Siniestro para atraer a los otros X-Men a su fortaleza en la Tierra Salvaje.

Al momento del aterrizaje en la Tierra Salvaje, los poderes mutantes de los X-Men han sido neutralizados por las máquinas del siniestro y son capturados por aliados de Siniestro excepto Guepardo que tendrá que rescatar a los otros.

A group of cyborg mercenaries, led by a woman from Wolverine's past, seek his forced help in unlocking the secrets of a long buried alien spacecraft.

An alien being called the Spirit Drinker drains the life-force of Jubilee and the Reavers, making strained allies of Wolverine and Lady Deathstrike.

Following visions from recent dreams, Professor Xavier sends his X-Men on a mission to the Eagle One Space-Station, putting them in the middle of an interstellar conflict.

The X-Men barely survive their return trip from space, Jean Grey discovering herself changed by the experience. Professor Xavier's dark half is given form, and proceeds to attack his students.

Professor Xavier's claims of the capture of his alien soulmate Lilandra by Juggernaut and Black Tom Cassidy are met with skepticism.

Lilandra seeks to protect the M'Kraan Crystal from her wicked brother, the Emperor D'Ken. But the interstellar pirates known as the Starjammers capture it, and Cyclops, in an effort to enact their own revenge scheme on the emperor.

Shi'ar Emperor D'Ken's rise to power via the M'Kraan Crystal is causing a universal implosion. The X-Men, Imperial Guard, and Starjammers find themselves overpowered and unable to stop it. Jean Grey must unleash her destiny as the host of the Phoenix, even at a most personal cost.

Mutant-draining, pterodactyl-man Sauron is persuaded into capturing Storm by Zaladane, the high priestess of Savage Land Sun God Garokk, unaware of her ulterior motives for unleashing the mutant's full potential.

Storm's unfettered weather-fury continues setting the stage for the rise of Garokk. Even if Storm can be brought back under control, the Sun God's geothermal rejuvenation will spell an end to the Antarctic paradise known as the Savage Land.

Fueled on by his desire to seek vengeance against the immortal mutant that changed him into a weapon of evil, Archangel persaudes Rogue into helping him hunt down and destroy Apocalypse.

The flirtation between Cyclops and a mutant singer named Dazzler exacerbates the Phoenix-controlled side of Jean Grey, leaving her open for manipulation by a secret sect of mutants coveting her immense powers for their own evil designs.

The Circle Club makes the Phoenix-controlled Jean Grey their new Queen, but finds two factors opposing it: her mental bond with Cyclops, and the presumed-dead Wolverine stalking after them.

As the Dark Phoenix grows increasingly hostile, even destroying an entire star system, the X-Men struggle to figure out a way to stop her without harming their teammate Jean Grey.

The X-Men face the Shi'ar Imperial Guard in a trial by combat to spare the life of Jean Grey, though even they begin to question the safety of the universe as long as the Dark Phoenix remains alive inside her.

A founding member of the X-Men, named Iceman, breaks into a government facility. He refuses to trust his former teammates about his reasons for doing so, but when Jubilee aids him in his quest, it leads to the team going up against another group of mutants, known as X-Factor.

Cyclops discovers that Corsair, the leader of the interstellar band of pirates known as the Starjammers, is his father. He's a fugitive on the run from the Shi'ar empire, and seeks his help in proving his innocence. But can the man who abandoned him as a child truly be trusted?

Professor Xavier's step-brother, and sworn enemy, the Juggernaut loses his powers to a bumbling archeologist. He must overcome the pain of their childhood together, and have the powers restored to him to save his life.

Gambit, Rogue, and Wolverine take a ski trip in Germany. While Gambit and Rogue seem to be enjoying themselves, Wolverine is restless, and longs for some action. When he hears reports of a demon hiding in a local monastery, his investigation reveals not a demon, but a mutant, Nightcrawler, whose devilish appearance is in stark contrast to his peaceful and deeply philosophical nature. Later the townsfolk attack and burn the monastery. The X-Men convince the townsfolk not to fear what they do not understand, Wolverine, too, learns something about the nature of faith.

A cryptic postcard unleashes a flood of maddening and painful memories in Wolverine that threaten to drive him insane. To keep his mind from being torn apart, Wolverine and Beast travel to the one location that may hold the answers to his hidden past: the ruins of the top-secret Weapon X lab where Wolverine's bones were laced with adamantium. There he encounters other former 'test subjects'—Sabretooth, Maverick and Silver Fox—who are suffering similar mental breakdowns. Later they find out that many of their memories were implanted, and their true memories are destroyed with the lab.

Bishop & Shard recruit Wolverine & Storm for a time travel mission to save Professor Xavier's life. Except they're from the parallel timeline where he died before founding the X-Men, a world where humans and mutants are in a constant war with one another. Not only do they pair lack a connection to him, but correcting history may put an end to their marriage.

Bishop, Shard, and the alternate-present versions of Wolverine & Storm, will have one more chance to save Xavier from being killed before he founded the X-Men... if they can survive the alternate-future ruled entirely unopposed by Mastermold.

Morph feels he's finally ready to return to the X-Men. But his homecoming is interrupted by the return of the Sentinels, the robotic mutant-hunters who nearly killed him the last time he faced them. Will history repeat itself?

The long hidden secret patient of Muir Island, a reality-warping mutant teen known as Proteus, escapes from his 15 year long captivity, and wreaks havoc across Scotland searching out his father.

Tracking down his father, who is now a candidate for Secretary of State, Proteus continues threatening lives with his uncontrolable powers. It's up to Professor X alone to try to stop the boy who brought even Wolverine to his knees.

Magneto builds a home strictly for mutants on the orbiting base known as Asteroid M. The message goes out worldwide of initial exodus, and he finds just as many eager to join him, as those anxious to destroy him.

With Magneto seemingly dead, Fabian Cortez takes over Asteroid M, and initiates a nuclear war with Earth. The X-Men attempt to sabotage his warhead stockpile, and rescue Gambit, finding assistance in the most unlikely of places.

Apocalypse steals Cable's computer in the year 3999, allowing him to time travel to the past, where he schemes to bring an end to his struggle against inferior mutants once and for all. This leads to Bishop becoming trapped amid the timestream, and brings

When Oracle, the psychic member of the Imperial Guard is kidnapped by Apocalypse, Professor Xavier deduces his scheme involves capturing mutants with telepathic abilities. The X-Men are split up to track them down before the villains can, which puts Wolverine & Shard in the middle of a scuffle between Archangel and a ninja named Psylocke.

After swiping the government's own time machine, Cable ends up recruiting the X-Men on his mission to destroy Apocalypse's source of immortality at its creation.

Two of Apocalypse's former evil allies, the captive Wolverine, the loose cannon Cable, and the exiled Bishop, come together to free the kidnapped psychics and save reality from being rewritten.

Jubilee's first Christmas with the X-Men doesn't go exactly as she expected, when she, Storm, and Wolverine become involved with a mission to save the Morlock child known as Leech.

Finding himself continually losing control, Wolverine takes a sabbatical to Japan, in an effort to find inner peace in temple-building. Instead, he faces a village under siege by a group of bandits, and struggles to help them without compromising his search for his true nature.

In a New Mexico desert, Wolverine witnesses the crash of a spaceship carrying horrific, alien bug-like creatures—the Family—which overwhelm him. Rogue reunites with her first boyfriend, Cody, who ends up being a part of the Family's plot to have Rogue become their new leader. The X-Men defeat the Family.

Cyclops heads solo to the desert town of Skull Mesa, where humans and mutants live in harmony, to visit an old mentor from his youth. But he not only finds himself powerless when he arrives, but discovers the place under the rule of a maniacal mutant, with none of the citizens willing to take a stand.

Trapped on the astral plane after suffering a concussion, Professor Xavier is at the mercy of the Shadow King, and in desperate need of help from his X-Men, who are unable to hear him.

X-Factor's Quicksilver, and his sister, the Avenger called Scarlet Witch, seek revenge against Magneto when they learn that he was responsible for their birth mother's death. But the trio is unaware of the common bond between them, nor the true purposes of the mysterious man who brought them all together.

Rushing to investigate a disturbance downtown, the X-Men find Sabretooth on the rampage again, but realize too late that it isn't really Sabretooth at all. It is the Phalanx, a voracious alien life-form that can assume the guise of anything or anyone. Before long, the X-Men are all captured, except for Beast, who must find a way to stop the alien horror from devouring the entire Earth.

Snatched from the jaws of the Phalanx by the villainous Mr. Sinister, Beast and Forge search for allies to help them battle the alien threat. Gathering assistance from such unlikely sources as Magneto and Sinister himself, they embark upon a daring and risky plan to free the planet from the clutches of the Phalanx by traveling straight into the belly of the beast.

The former Soviet Union's living weapon, Omega Red, is thawed out by the US Military to deal with an abandoned Soviet nuclear submarine near Hawaii. He asks for his old enemy, Wolverine, and the woman responsible for freezing him most recently, Storm, to accompany him on the mission. Omega Red is offered restored humanity, but once aboard the warhead-filled sub, he reveals his true, deadly intentions.

Cyclops, still in mourning after Jean Grey's "death", quits the X-men and returns to his orphanage home and encounters his friend Sarah. She tells him that a wealthy man has decided to adopt all the mutant children, especially Rusty, but his intentions are to make them his army to destroy all humans in the world so that mutants are accepted. It's up to Cyclops to stop him and save the mutant children. Later, Cyclops returns to the mansion and he and the other X-men discover that Jean Grey hasn't died after all.

Longshot, a rebel from another world, tumbles into this world with no memory and a murderous gang led by the six-armed woman warrior Spiral hot on his trail. It turns out that Longshot is on the run from Mojo, maniacal inter-dimensional TV executive. Using Jubilee as the 'prize', Mojo and his minions lure Longshot and the X-Men into a deadly contest which Mojo broadcasts 'live' to up his ratings.

Nightcrawler gets a mysterious message. He is informed that his birth mother (whom he never knew) is in trouble. He turns to the X-Men for assistance. Jubilee is baffled that Nightcrawler wants to help the mother who abandoned him -- she has never known her birth parents and feels pretty hostile toward them, whoever they are. Nightcrawler admits there has been pain, but his faith in God has helped him overcome her rejection. The plot thickens when one of the team members recognizes Nightcrawler's mother's voice. There are more 'bloodlines' here than anyone imagined, including the Friends of Humanity who arranged this 'reunion' in the first place.

The dashing alien, Arkon, unleashes terrible weather conditions over Washington D.C. to get Storm's attention. It works, he begs her to return with him to his planet, Corsus, to save it from meteorological chaos which threatens his people. After much pleading, Arkon convinces Storm. Intrigued by this dynamic leader but slightly suspicious, Storm departs but leaves a clue for the other X-Men to follow. The X-Men travel through an inter-dimensional portal and arrive to 'rescue' Storm, just as she is in the midst of restoring the planet's raging eco-system. Once successful, Storm is proclaimed savior throughout this universe. What's more, Arkon asks her to marry him.

Spectacular preparations for Storm's wedding to Arkon proceed quickly. But as Jubilee helps Storm, the new queen, prepare for the wedding, Jubilee can't help notice how badly the palace workers are treated. When Storm mentions this to Arkon, he reminds her she is new to his world, and asks her for her trust. meanwhile Wolverine, Cyclops and Beast discover there are fleet ships bringing slaves from the neighboring planet. Arkon, it seems, is a ruthless tyrant. Storm must know the truth. Back at the castle, Storm has been making a few discoveries of her own.

Jubilee tells children her own fairy tale having herself, her fellow X-Men and their greatest enemies be the characters in it.

Fabian Cortez helps Apocalypse escape from the astral plane.

Wolverine thinks back to the time when he fought during World War II and teamed up with Captain America.

The origin of Mr. Sinister is revealed.

When the army learns of Sam Guthrie's cannonball power, they try to enlist him in their ranks.

At a Mutant/Human Relations Summit, Henry Peter Gyrich attacks.