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.

Jubilee atakują roboty Sentinele w centrum, ale ratują ją Storm i zabierają do X-Mansion. Grupa Programu Rejestracji Mutantów zamierza tropić i eliminować mutantów. X-Meni odnajdują bazę Sentineli i chcą zniszczyć akta mutantów. Odcinek kończy się cliffhangerem, gdy Storm otwiera drzwi do pomieszczenia, gdzie żołnierze robią zasadzkę na X-Menów.

Wolverine wyczuwa olej z broni żołnierzy i szybko zamyka drzwi, zanim ci zdążą wystrzelić. Storm zmiata strażników swoją siłą wiatru. Po zniszczeniu akt dotyczących mutantów X-Men uciekają do Blackbirda, ale zostają zatrzymani przez Sentinele. Podczas walki z Sentinelami Morph zostaje postrzelony i uznany za zmarłego. Podczas gdy Beast zostaje uderzony w ogrodzenie, porażony prądem i schwytany, reszta na rozkaz Cyclopsa wycofuje się do Blackbirda. Jubilee decyduje, że najlepiej będzie zostać w X-Mansion.

Po procesie Beasta, Sabretooth żąda uwolnienia go, co powoduje, że strażnicy strzelają do Sabretootha i ranią go. Cyclops pomaga Sabretoothowi i przenosi go do ambulatorium Mansions. Później Magneto atakuje wojskowy ośrodek rakietowy. Gdy X-Meni przybywają na miejsce, Magneto przygotowuje się do wystrzelenia pocisków nuklearnych, aby doprowadzić do wojny między mutantami a ludźmi. Cyclops, Storm i Wolverine ścierają się z Magneto, ale nie są w stanie go powstrzymać. Później Storm wykorzystuje swój wiatr i błyskawice, aby spowodować zwarcie w pociskach, dezaktywując je i zrzucając do wody. Zapobiegłszy wojnie nuklearnej, X-Meni wracają do rezydencji, poznając pełną moc Magneto.

Magneto niszczy fabrykę chemiczną, aby przyciągnąć Profesora X. Cyclops, Rogue, Storm i Profesor X udają się do fabryki chemicznej, podczas gdy Jubilee zostaje, aby pilnować Sabretootha. Profesor X wchodzi do zakładu chemicznego, aby zmierzyć się z Magneto. W momencie, gdy Magneto wydaje się pokonywać Profesora X, Profesor X telepatycznie zmusza Magneto do przypomnienia sobie swoich młodych lat. Magneto wycofuje się w popłochu. W X-Mansion Sabretooth warczy z obrzydzeniem na senatora w telewizji, a Jubilee zauważa problem z jego wiązaniami na nadgarstkach. Jubilee rozluźnia więzy i Sabretooth chwyta Jubilee, lecz Wolverine wyskakuje z cienia i atakuje go. Ich walkę przerywa powrót Profesora X i pozostałych X-Men.

Grupa mutantów zwanych Morlokami porywa Jean i Cyclopsa, gdy ci wychodzą z domu. Przywódczyni Morloków, Callisto, porwała Cyclopsa, aby ten rządził Morlokami u jej boku. Jean używa swoich telepatycznych mocy i mówi profesorowi, że zostali schwytani. Wolverine, Gambit, Rogue i Storm wyruszają na ich poszukiwanie. Gdy X-Men odnajdują Jean i Cyclopsa, Storm wyzywa Callisto na przywódczynię Morlocków, aby ocaliła Cyclopsa i Jean. Callisto nie ma innego wyboru, jak tylko przyjąć wyzwanie. Po krótkiej walce Storm pokonuje Callisto i staje się nową przywódczynią Morlocków, ale po uratowaniu Jean i Cyclopsa czyni Callisto przywódczynią pod swoją nieobecność.

Wolverine ucieka do Kanady, by szukać odosobnienia na kanadyjskim pustkowiu. Odnajduje spokój wśród grupy Inuitów z Wyspy Baffina, ale odkrywa, że Sabertooth prześladuje go, a także bierze do niewoli mieszkańców wioski i planuje ich wszystkich zabić. Wolverine'owi udaje się pokonać Sabertootha i uratować mieszkańców wioski. W rezydencji X-Men Gambit mówi X-Men, że słyszał, iż mieszkańcy Genoshy chętnie przyjmują mutantów i chciałby, aby drużyna spędzała tam wakacje. Profesor Xavier wysyła Storm, Gambita i Jubilee do Genoshy jako turystów. Podczas pobytu w Genoshy Storm, Gambit i Jubilee zostają zaatakowani i schwytani przez Sentinela.

Gambit, Storm, Jubilee i wielu innych mutantów zostaje zmuszonych do pracy jako niewolnicy w Genoshy, aby dokończyć budowę tamy, która ma zasilić fabrykę Sentineli. Specjalne obroże na szyjach mutantów uniemożliwiają im używanie swoich mocy, ale Gambitowi udaje się uciec. Podczas ucieczki Gambit odnajduje Cable'a, który poszukuje osoby odpowiedzialnej za zniewolenie mutantów. Cable daje Gambitowi klucz do odblokowania obroży, po czym atakuje fabrykę Sentineli. Tymczasem Gambit uwalnia pozostałych mutantów. Mutanci rozpoczynają walkę ze strażnikami i Sentinelami, po czym uciekają. Storm wykorzystuje swoje moce, by zburzyć tamę, powodując powódź, która niszczy całą fabrykę Sentineli. X-Men wracają do domu, do zniszczonej posiadłości.

Po tym, jak X-Men odkrywają, że posiadłość została zniszczona, Wolverine wyrusza na poszukiwanie podejrzanego, a za nim Storm, Rogue i Jubilee. Później Jubilee znajduje mutanta wykonanego z czystej stali. Myśląc, że to on jest odpowiedzialny za zdemolowanie szkoły, Jubilee rusza za nim, ale Wolverine stwierdza, że to nie on zniszczył rezydencję, ponieważ inaczej pachniał. Jubilee i Wolverine znajdują Juggernauta napadającego na bank i próbują go schwytać, ale Juggernaut jest zbyt silny. Wkrótce na miejscu zjawiają się pozostali X-Men. Jean wyjaśnia, że nie może mentalnie zaatakować Juggernauta, dopóki jego hełm jest na głowie. Cyclops uważa, że mogą go pokonać, jeśli tylko będą pracować jako zespół.

Lekarz z Centrum Badań nad Mutantami na Wyspie Muir twierdzi, że znalazł lekarstwo na gen mutacji. Rogue udaje się na wyspę w poszukiwaniu tego lekarstwa. Rogue odwiedza doktora Adlera i opowiada mu o tym, jak rozważa leczenie. Dr Adler wysyła ją w drogę i pojawia się Apocalypse. Dr Adler zmienia się w Mystique i rozmawiają o mocach Rogue. Później Cable atakuje doktora Adlera, ale X-Men pokonują go, a Rogue zmienia zdanie na temat leczenia i odchodzi. Pod koniec Warren (Angel) przychodzi na leczenie i wchodzi do laboratorium doktora Adlera. Później Mystique odnajduje Apocalypse'a i mówi mu o Warrenie, na co ten odpowiada, że planuje zniszczyć świat.

Nieśmiertelny mutant Apocalypse zmienia mutantów, którzy udali się na wyspę Muir w poszukiwaniu fikcyjnego lekarstwa, w Jeźdźców Głodu, Zarazy, Wojny i Śmierci. Jeźdźcy zaczynają niszczyć wszystko na całej planecie. Na miejsce przybywają X-Men i walczą z Jeźdźcami. Rogue w końcu chwyta Archangela i pochłania jego pamięć, wysysając z niego moc Apocalypse'a. Archangel, przerażony tym, czym się stał, rozwala pozostałych Jeźdźców. Apocalypse ucieka statkiem kosmicznym, a odwrócenie uwagi pozwala uciec także pozostałym Jeźdźcom.

Mutant o imieniu Bishop podróżuje w czasie z roku 2055 do teraźniejszości, aby powstrzymać członka X-Menów przed zamordowaniem kogoś. Po powrocie do teraźniejszości nie pamięta, kim jest zabójca. Później zwraca się o pomoc do X-Men. Odcinek kończy się cliffhangerem, w którym okazuje się, że podejrzanym jest Gambit.

Bishop strzela do Gambita, X-Men powstrzymują go. Jadą do Waszyngtonu, gdzie Bractwo Mutantów planuje zamach na senatora Roberta Kelly'ego. Mystique podaje się za Gambita i próbuje zabić Kelly'ego, ale prawdziwy Gambit ratuje go. Bishop wraca do swoich czasów. Profesor X odkrywa, że Magneto porwał senatora Kelly'ego, co prowadzi do cliffhangera.

Magneto przyprowadza senatora Kelly'ego na zatopiony statek, aby go zabić, dzięki czemu mutanci i ludzie wypowiedzą sobie wojnę. Sentinele atakują Magneto i porywają senatora Kelly'ego. Kiedy X-Men w końcu znajdują miejsce, gdzie jest Magneto, Sentineli już nie ma wraz z senatorem. Sentinele zabierają senator Kelly do Master Molda. Master Mold chce zastąpić mózgi wszystkich światowych przywódców komputerami, aby Sentinele mogły kontrolować świat. X-Men udają się do bazy Sentineli i ratują senatora. Kelly uświadamia sobie, że niektórzy mutanci mogą być dobrzy. Cyclops i Jean zaręczają się. Pojawia się też wskazówka, że wkrótce poznamy postać o imieniu Sinister.

Trwa ślub Jean Grey i Cyclopsa. Mister Sinister poddaje Morpha praniu mózgu, a następnie wysyła go do Nowego Jorku, gdzie Kevin zaczyna eliminować X-Menów jednego po drugim. Tymczasem Graydon Creed wprowadza w życie swój projekt eksterminacji mutantów.

Udający Magneta Morph zwabia Profesora X na Antarktykę. Mister Sinister porywa Cyclops i Jean. X-Meni wyruszają w pościg za Sinisterem. Tymczasem Profesor X wraz z Magnetem zostają zasypani pod lawiną.

W szeregi X-Menów powraca Storm. Tymczasem coś dziwnego zaczyna się dziać w Afryce. Storm i Rogue wyruszają do Afryki żeby zbadać sprawę. W tym samym czasie pozostali X-Meni szukają Profesora X. Charles i Magneto trafiają do Dzikiej doliny.

Profesor X i Magneto zostają zaatakowani przez dinozaury. Jubilee wraz z Colossusem łapią złodziei, którzy obrabowali sklep. Tymczasem w Rosji trzej skorumpowani generałowie przywracają do życia Omegę Reda.

Jean Grey nadal szuka Profesora X. Tymczasem Vindicator wraz z pozostałymi członkami Alpha Flight chwytają Wolverinea. Chcą żeby wyjawił im sekret swojego szkieletu z adamantium. Vindicator postanawia przeprowadzić eksperymenty na Loganie.

Gambit must come face to face with the past he's been running from for years, as he returns to Louisiana to save his brother from the woman he left at the altar.

Bishop returns from the future to again attempt to fix his world, this time trying to stop a plague from infecting mutants. But his noble actions lead to a far greater tragedy.

To stablize his own timeline, Cable comes to the present to prevent Bishop from saving mutant-kind from Apocalypse's plague.

Haunted by visions of a strange woman, Rogue must come to grips with the dark secrets of her past prior to joining the X-Men.

Beast falls in love with his patient, a blind woman named Carly, and though the feelings are mutual, her mutant-hating father and anti-mutant sentiment drive a split between the pair. Meanwhile, Wolverine seeks to take down the Friends of Humanity from the inside out.

An alien being named Mojo abducts the X-Men to use as forced action stars of television programming.

Professor Xavier and Magneto gain a native ally, as they finally come face to face with the new ruler of the Savage Land. A lead from Morph sets up a rematch between Wolverine, Cyclops, Jean Grey and Mister Sinister & his Nasty Boys.

The X-Men find themselves powerless in the Savage Land, and become fodder for Mr. Sinister's experiments. It's up to Wolverine and Ka-Zar to initiate a rescue.

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.