The remaining members of Freedom Force (the Blob, Crimson Commando, Silver Sabre, Pyro, and Avalanche) were sent on a mission to retrieve a nuclear physicist named Harvey Kurtzman, who was being held captive in Kuwait during the Gulf War. The mission went unsuccessfully, Pyro killed Kurtzman, and the super team Desert Sword killed Silver Sabre and Crimson Commando. Avalanche escaped with American soldiers, leaving Blob and Pyro as prisoners of the Iraqi army (Blob and Pyro eventually escaped or were released by unknown means).

The Toad, who allied with the Morlock Masque (Callisto) and the mutants Blob, Pyro, Thornn, Sauron, and Phantazia, eventually reformed another Brotherhood. The new Brotherhood's mission was to kill Cable, leader of X-Force and retrieve the mutant Feral, who had escaped from the Morlocks. The Brotherhood battled X-Force led by Cable and Domino, and was defeated, resulting in the death of Masque and the apparent death of Sauron (who later reappeared). The Brotherhood disbanded soon afterward. Phantazia's whereabouts are unknown, the Toad was last seen living in a mansion abandoned by Emma Frost, Pyro is currently suffering from the Legacy Virus, and Sauron returned to the Savage Land.

The Blob received an increase in his powers from the entity known as Onslaught, and recently encountered the members of X-Force known as Meltdown, Domino, and Siryn.

Most of the Heroes on Earth came to battle him including Rogue who brought with her a man named Joseph. Together the X-Men, Fantastic Four, and The Avengers and other heroes defeated Onslaught. The X-Men and Quicksilver were the only one's to walk away from the battle.

Onslaught was a sentient psionic entity created from the consciousness of two mutants: Professor Charles Xavier, telepathic founder of the heroic X-Men, and the charismatic subversive known as Magneto, Master of Magnetism. Possessed the combined mutant abilities of progenitors Professor X and Magneto. He could induce illusions, temporary mental or physical paralysis, loss of specific memories, or total amnesia; project mind-numbing mental bolts; and sense the presence of mutants within a small radius.

X-Man (Nathan "Nate" Grey) is a mutant possessing vast psionic abilities. Nate has so far shown telekinetic ability rivaling that of Phoenix, creating destructive psionic spikes, and lifting objects of at least 10 tons or more. Nate is also a telepath of the first order, able to create psionic illusions, read, probe and control the minds of others, and to pull a psionic entity out of the astral plane. It is possible that, with practice, Nate Grey could be the most powerful psionic on the planet.

The X-Men, the Fantastic Four and the Avengers, Earth's Mightiest Heroes, challenged Onslaught. Their first confrontation with the entity and his minions resulted in the rescue of a now-powerless Xavier, who retained his usual benevolent personality. Onslaught now existed as psionic energy contained within his armor. A second and final confrontation occurred at his Central Park citadel. After a number of attempts to free Franklin Richard and X-Man from Onslaught's seemingly impervious armor, the heroes regrouped. During their next assault, Jean Grey used her telepathy to turn off the part of the monstrous Hulk's mind that contained the rationality of his alter ego, Dr. Bruce Banner. The now-savage Hulk, possessed of a nearly animalistic intelligence and unbelievable strength, battled Onslaught and tore apart his armor. The resulting explosion of psionic energy separated Banner and the Hulk, and Onslaught was left as an energy being, immune to most physical harm. Onslaught then used Franklin's powers to create a second sun that would destroy the heroes and Manhattan.

The Avenger known as Thor, Asgardian God of Thunder, master of the storm and lightning, flew into the energy being, disrupting Onslaught's form. Realizing that Thor's efforts alone were insufficient to destroy their adversary, the non-mutant members of the Avengers and the Fantastic Four entered the energy field. The X-Men were unable to do likewise, as it was theorized that if Onslaught, a being of mutant origin, came to possess a mutant host, he would become unstoppable. Onslaught dissolved, seemingly destroyed, along with the heroes who had thrown themselves into the rift. The remaining Sentinels were disabled, Franklin and X-Man were rescued, and Manhattan was returned to normal.

Later, it was revealed that the Avengers and the Fantastic Four did not die, as had been surmised. Rather, the heroes were reborn in a pocket universe created by Franklin. The Avengers and the Fantastic Four returned to their rightful home months later, possessing only hazy memories of their time on Counter-Earth.

This time it was revealed that Nathan Grey a.k.a. X-Man is the genetic son of Jean Grey and Scott Summers when they were captured in the Savage Island. He was the result of the experiment by Mister Sinister.

Joseph joined the X-Men; Iceman soon took another leave of absence to spend time with his father after he was almost killed by man trying to get to him. Xavier was then taken into government Custody. While in New York when Archangel and Psylocke have their own leave in for recovery they met a young Mutant named Maggot while he is looking for Joseph. He is also from a place where Joseph was found. Later he end-up in joining the X-Men when Archangel and Psylocke went back to the mansion.

Operation: Zero Tolerance

Wolverine and Professor Xavier are sitting in the early morning rain, amongst the ruins of the mansion. Charles is feeling sorry for himself, and Wolverine has taken it upon himself to deliver a pep talk. Charles feels the guilt of Onslaught weighing heavily upon his shoulders. Wolverine’s duty there is to reaffirm Charles’s belief in what the X-Men are all about.

Meanwhile, Graydon Creed makes an impassioned speech for the cameras at the site of Onslaught’s defeat. Watching on television, J. Jonah Jameson feels there’s more to Creed than meets the eye, and wants information on him, fast. At the mansion, Cyclops tells Beast it’s good to have him back, after inadvertently blasting him with his optic beam. Iceman’s intervention and the resulting jocularity make Jean to smile. A week ago, she could never have conceived that they would enjoy laughter again. Quicksilver is with her, struggling to get over the loss of his wife and sister. He must go on, he informs Jean, if only for the sake of his daughter. He hears the door handle turn, and prepares the table before Psylocke even enters the kitchen. She is a little distant, but Jean puts this down to changes of late. They’ve all been confronted by change. Logan and Charles continue their conversation; with Logan reminding him that he is the sole reason he stayed with the X-Men. A lot of others feel the same way too, and they’d hate to think that Charles pulled one over one it. He joins the others at the breakfast table and, for the time being, things appear to be looking up. Meanwhile, at Operation: Zero Tolerance, Bastion overlooks the ongoing plans for mutantkind’s downfall, telling Harper that they will all be very sorry if they fail.

Archangel mysteriously molts his metal wings and gains feathered ones, and ends up helping the X-men subdue an out-of-control Pyro at a church. Meanwhile, Iceman and Cannonball infiltrate Graydon Creed’s campaign, posing as volunteers.

However, Havok had a nervous breakdown and he leaves the X-Factor after the Onslaught Saga. Random also came with him. In an explained circumstance, the Dark Beast managed to escape from the Age of Apocalypse timeline through the M’Kraan Crystal. He is an evil mad scientist working for Mister Sinister. He kidnapped the real Beast and managed to brain washed Havok and formed the New Brotherhood of Evil Mutants.  It was later known that he is responsible for the existence of the Morlocks. They recruited Random, Fatale, Nate Grey (X-Man), Ever and Aurora of Alpha Flight.

The X-Men, alerted by Spider-man about Jameson’s recent activities, tail the Daily Bugle owner to a jet just in time to prevent Havok and his Brotherhood of Mutants from destroying the plane and everyone on it. The X-Men saved the Beast and Dark Beast was given parole by Professor Charles Xavier in Genosha. Meanwhile, a Daily Bugle reporter, who uncovered Creed’s true heritage, is killed by Bastion and Mystique is making plans against the presidential candidate Graydon Creed. Iceman’s cover in Creed’s campaign is blown and his father is almost killed by Creed’s men. The X-Men comfort Iceman at the hospital; Bobby resigns from active duty since he wants to oversee his father’s recovery. Despite of the danger Cannonball decides to stay in the campaign as an undercover operative.

Rogue, Bishop, Gambit, Joseph, Beast and Patricia Trish Tilby were abducted into space by the Shi’Ar to do battle with the Phalanx again. After the X-Men beat the Phalanx they head back to Earth with the Shi’Ar empress Deathbird. When their ship was destroyed in coming back to the planet, some how they were transported to Antarctica, all but Bishop and Deathbird who were believed dead.

While In Antarctica the X-Men along with Psylocke, Archangel and Maggot learned of Gambit's role in the Mutant Massacre. Xavier officially recruited his old student Samuel Guthrie to become the youngest X-men from the team of Cable.

Deathbird recovers from her injuries and alerts the X-Men that the Phalanx is the villains responsible for the massacre. Some of them already try to infiltrate the team by posing as Joseph and Gambit, but the Team managed to drive the off. Facing overwhelming odds, the team decides to let the Phalanx destroy their ship while they use an escape pod to escape to a nearby mining station. Once there they use a teleportation chamber to make their way to the Shi’Ar homeworld.

Back on Earth, Bastion’s plans are furthered with his custody of Jubilee.

The X-Men arrive in the Shi’Ar royal palace, which is already in the Phalanx’s hands. Bishop and Deathbird try to safeguard the hatching chamber to ensure the survival of the entire next generation of Shi’Ar and feelings develop between the two. The others work on a device to separate the technological and organic components of the alien race. Seeing hundreds of slaughtered Shi’Ar, Joseph remembers to have lived during the Holocaust and outrage attacks the techno-organic aliens endangering the whole mission, yet Gambit and Rogue distract the Phalanx long enough for the Beast’s plan to work, all Phalanx in the area perish.

On earth Senator Kelly begins having doubts about Bastion Creed and his Operation: Zero Tolerance.

At night Gambit helps digging graves for the fallen Shi’Ar to atone for some sin in the past. The X-Men celebrate the defeat of the Phalanx with the Shi’Ar, and then head home, only to be caught in the explosion of a stargate collision. Maggott is introduced as a mutant following Joseph’s trail.

Storm, Wolverine, Cyclops, Phoenix and Cannonball were attacked and captured by Operation: Zero Tolerance, They were then taken to A Hulkbuster Base. This time X-Men met the next anti-mutant name Bastion Creed. They later escaped not knowing that their escape would not have been possible with out the help of Jubilee, who was also being held there in the base. Jubilee was captured earlier when they attacked the Generation X institution. It wasn't till on their way home the X-Men discovered Cyclops had a bomb in his chest.

Iceman went to protect a mutant woman named Dr. Cecilia Reyes, while trying to escape the Sentinels with the help of Marrow they met Sabra an agent for the Israeli Government, They joined force's to help take down Bastion the leader of Operation: Zero Tolerance. After Bastion was defeated Sabra headed back to her Israeli Government, while Iceman, Marrow and Dr. Cecilia Reyes went back to the school after committing herself to be part of the X-Men team, where Cecilia removed the bomb from Cyclops's chest. From Morlocks, Marrow became an active member of the X-men. Gambit also made the first leave in the group.

Dr. Cecilia Reyes, a Puerto Rican, who can generate a translucent psioplasmic bio-field around herself as a protective force shield or reshape it into a variety of patterns and forms

Callisto and Marrow try to attack Henry Peter Gyrich. Spiderman gets involved and prevents the two Morlocks from murdering Gyrich. Suddenly Gyrich’s bodyguard turns into Prime Sentinels and fight the two mutants. Callisto intercepts an almost lethal blast meant for marrow. Gyrich realizes that these Prime Sentinels are as much a threat as the mutants themselves and shoots both bodyguards.

Meanwhile, Bastion tries to make a deal with J. Jonah Jameson, but Jonah refuses and continues to do research on Bastion. After last issue’s accident in space, Gambit has crash landed on an unknown planet.

The X-Men believe themselves to be scattered around a strange world, but really have crash landed on earth. The alien landscape is cast up by an illusionist belonging to a small bounty hunters group (Spat, Grovel, Landscape) that tries to bring in Gambit, who was partially responsible for a past accident of Spat. They run into Rogue and Joseph, but before a fight starts all are surprised by the Nanny, a robot designed by Magneto.

In the United States Maggott continues his search for Joseph, and the badly injured Callisto sends Marrow to find and help the X-Men.

Spat and Grovel bring Gambit to a fortress in the middle of Antarctica. Rogue, Beast, Joseph and Trish assemble follow them and explore the huge structure. In New York Betsy Braddock is determined to investigate Maggott’s darkness and shadow-teleports him, herself and Archangel away. Strangely all emerge in the same Antarctican fortress, where all X-Men are attacked and defeated by an unseen foe. Maggott seems to know the attacker and as part of an old debt he agrees to play along.

All X-Men are chained and put into a courtroom, where Gambit is put on trial by Eric the Red (actually Magneto in disguise). It is revealed that before joining the X-Men Gambit occasionally worked for Mister Sinister, he also assembled the Marauders and helped them enter the Morlocks tunnels before the Mutant Massacre. The X-Men free themselves and try to fight Eric the Red, but he causes the building to collapse and escapes. Rogue helps Gambit to get out of the fortress in time, but then abandons him in the Antarctic, while Psylocke teleports the X-Men back to New York.

Dr. Cecilia Reyes tries to regain her life as a doctor at a hospital in New York, and confronts much anti-mutant bigotry; still there is enough work for her. One of her patients is Pyro who has been shot trying to rob a bank, and later Daredevil sneaks into the hospital with an infected gunshot wound. He tries to convince her that as a hero she could even save more lives than as a doctor. Later Pyro lures Cecilia into loosening his straps and he escapes from the hospital, resulting in her being fired. She goes back to the X-Men. During their flight to Alaska, Scott and Jean recognize a danger among the plane.

AIM Agents burst into the plane carrying Scott and Jean, wanting possession of an otherworldly being onboard known as Entity. Scott and Jean help stop them without the use of their powers, and the Entity helps to absolve all onboard of the panic resulting from the incident, ensuring a safe landing. Wolverine rebukes Archangel for not being part of the team, while Cannonball departs to meet up with X-Force.

After Operation: Zero Tolerance the X-Men weren't so much a team as a group of people trying to pick up the pieces Cyclops and Jean Grey left to give Cyclops some time to recover from his injures. Iceman went back home to be with his father again. Archangel and Psylocke went back to the City to work on their relationship saying they would help where they could. Leaving an unsure team. With the effort of Jean Grey in helping Betsy's abilities, she was able to heighten her powers. At one point Psylocke did return to battle the Shadow King, she beat the Shadow King by locking him in her mind. Although she won she can no longer use her mental powers for fear of releasing him. By this time she is not allowing herself to use her telepathy and teleportation. Forge went to Muir Isle to help Moira in her laboratory. And Dr. Cecilia went back to her career as an attending physician in her clinic.

The X-Men go out for a day by the pond, which is interrupted by an inspector from the board of education. While she is shown around she witnesses Rogue acting strangely and Joseph having a seizure, which is why she put the school on probation. Later the X-Men discover the original Blackbird in the pond. Wolverine is attacked alone in the woods. The others hear him cry and find Rogue sitting over him, assuming she just absorbed him. All of a sudden Sauron, the real villain, attacks.

Outside the mansion the X-Men have a long battle with Sauron, while Rogue is forced to do mouth-to-mouth on Joseph. The scene is observed by Marrow who assumes that Rogue caused Joseph’s seizure by kissing him. Rogue runs away and confronts her inner demons, eventually leaving to the Agee Institute to attempt to rid herself of her powers.

In space, Bishop realizes that he is not paralyzed at all, but held in stasis by Deathbird’s medi-lab devices. Their ship is shot and crashes to a planet. In Alaska Jean shocks Scott with wearing the green Phoenix costume.

At this point the X-Men went through some major changes, Cannonball left the team to go take care of his bother's and sister's when he's mother fell ill; Dr. Cecilia left to open a Clinic in Salem Center, Joseph left the team to try to find out who he was, Beast left so he could spend more time looking for a cure for the Legacy Virus.

The Hunt for Xavier

In Alaska, Jean tries to explain to Scott that she is wearing the Phoenix costume as a symbol of rebirth, as she no longer wants to hold back with her powers. Scott is not convinced and considers calling the X-Men for help.

Warren, Bobby, and Hank are in Anchorage to visit Scott and Jean after receiving a message from Scott. After they arrive, Scott tells Hank that he thinks Jean may be turning into Dark Phoenix. The original X-Men discuss things until a big bird clogs the chimney. As they go to dinner, Inuits are holding a riot in the streets. Scott states that maybe the Xavier’s dream should be reconsidered as crows begin to fill the sky. SHIELD picks up the defeated Sauron from the mansion, and in New York, Rogue meets with Dr. Agee, the man who claims to be able to cure mutants.

The original X-Men are at dinner when a human stampede rush by. A murder of crows is waiting outside. Each of the X-Men does their own part in defeating the crows, and they split up to find the reason for the birds’ odd behavior. Cyclops eventually releases a powerful optic blast that destroys all the birds. The true reason remains a mystery, Iceman still believes that the Indian guy caused the bird’s madness, Beast suspect’s pollutants, and Phoenix discovered a mechanical crow amidst the other birds. In Dr. Agee’s lab in New York, we discover that he knows Rogue is a member of the X-Men and we see the deformed image of his “cured” sister.

A universe away, aboard Deathbird’s ship, she finally releases Bishop, as they are about to crash-land. Bishop and Deathbird have crashed on a planet and are attacked by locals. Another off-worlder named Karel saves them. Other aliens called Chnitt attack Bishop, Deathbird, and Karel and an alien mothership come down on the planet. Bishop destroys the mothership but the gateway they were to escape through closes before Bishop and Deathbird make it through.

Back in Ptarmigan Creek, the original X-Men are packing up to go back to New York when Jean experiences a psychic attack and goes catatonic.

Meanwhile, in Dr. Agee’s clinic Rogue was scheduled for her operation believing that he can cure her.  Inside a hidden room, Dr Agee is working with Peter Gyrich. She was saved by Mystique disguising as the nurse making a gunshot to Dr. Agee. They have a long discussion, which ends with Rogue touching Mystique. Using Mystique’s power, Rogue infiltrates Mutopia and destroys the “curing machine.” She would like to use it, but Rogue knows that she has to make sure that it would never use on a mutant against his will. In Anchorage, Jean gets a check-up by Michael Twoyoungmen, Alpha Flight’s Shaman. Her psi-powers are gone, and Scott tries to comfort her as well as he can.

However, recently Magneto has reappeared and made another bid for political power by creating another Earth-wide electromagnetic pulse and then merge with the so-called magnetosphere to gain ultimate power. The X-Men, Joseph and Astra confronted Magneto, and Joseph sacrificed himself to stop Magneto's schemes, an action which left Magneto without his powers.

As these entire member's were leaving; Shadowcat, and Nightcrawler returned to the X-Men after Excalibur had disbanded. Also Pete Wisdom joined the X-Men while continuing his love affair with Kitty Pride.  And Colossus also returned after the incident in Avalon.

Sunfire and Gambit soon re-joined the team to mixed emotion. The X-Men then went in looking for Xavier. Once he was found he disbanded the X-Men felling they had turned away from his dream he and Storm then went looking for a new group of X-Men.

Shadowcat and Storm are in South Korea to meet Black Tom Cassidy. Some warriors attack them before their meeting, where Black Tom says Juggernaut is dying because his power was leeched into a second, powerless Ruby of Cytorrak. Juggernaut is rampaging through the city when Gambit arrives and knocks him down. Shadowcat, Storm, and Gambit follow a map to find a secret island where Gambit finally retrieves the ruby. In Westchester, Wolverine discovers Rogue searching the world for Gambit, while Marrow steals Colossus’s sketchbook because she likes one of the pictures. Colossus discovers Marrow’s secret wall of pictures of beautiful pictures, and gives her a portrait of herself.

In Nebraska a frightened Pyro is running about, setting crops on fire, mumbling about Xavier. SHIELD is called in, and Nick Fury calls the X-Men to deal with it, as they might be able to help more. The X-Men try to stop Pyro, but his powers are spiraling out of control due to the Legacy Virus, and he is running from something very, very bad.

While this is happening Marrow is wondering what the point is in searching for Xavier, and clashes with Storm on the subject. But it is Gambit who brings it home for her; Xavier is just a man, a man who would risk anything to save their lives. When it looks as though stopping Pyro will be impossible something emerges from the flames trailing behind him; something metallic, and the reason he was fleeing, trying to warn Xavier. It attacks Pyro, taking him out, but not killing him. Kitty gets a glimpse of this thing. Later, SHIELD takes Pyro away. Kitty uses the Cerebro sent over by Moira MacTaggert, and discovers two mutant energy signatures belonging to Professor Xavier. Then some outside source shorts out the machine, ruining it. The X-Men decide to split up into two groups to investigate the mutant signatures. One group will head to Russia, and the other to San Francisco. Meanwhile, something crashes into San Francisco, and it is looking for Xavier...

Cerebrite Beta crashes into San Francisco. Professor Xavier is revealed to be on Alcatraz Island, apparently a prisoner of the Newest Brotherhood of Mutants. The X-Men, consisting of Wolverine, Nightcrawler, Shadowcat and Marrow are looking for one of the bio-signatures of Xavier in San Francisco (the other X-Men are looking for the other one in Russia). Logan tracks his scent, but loses it, and has to ask the advice of Black Crane, possible a mutant mystic. They are directed to Alcatraz Island.

Meanwhile Cerebro breaks into a secret government complex to steal the technology it needs to carry out its objectives. The X-Men arrive on Alcatraz Island and are immediately engaged in battle by the Newest Brotherhood of Mutants (Blob, Post, Mimic and Toad). But the X-Men find this difficult. Their enemies know their tactics and training. It becomes evident why when they find Xavier, who turns out to be not their prisoner, but their teacher. A powerless Xavier tells them that enemies can be bound together by the need to fight a mutual foe. A foe which has gained sentience because of Bastion; a foe called Cerebro. At that moment a unit of Cerebro crashes in, calling itself Cerebrite Beta. It has come for Xavier, and to catalogue the mutants with him...

Cerebro Prime is checking over current activities concerning mutants when his current base is detected. He quits the base, taking his files with him, and ordering the discorporation of his fake X-Men as he leaves. His base explodes due to the self-destruct. On Alcatraz Island the X-Men and Brotherhood battle Cerebrite Beta. Kitty tries to help Xavier to safety as the thing is clearly after him. The creature apparently kills Toad. The battle rages on, but Kitty is killed too, as Blob explains that Cerebrite Beta is a unit commanded by Cerebro, who was created by Bastion during Operation: Zero Tolerance. He isn't sure what it's up to. Suddenly Cerebrite Alpha blasts the brainwashed Mimic as he flies away with the professor, vaporizing him. Xavier falls to the ground, explaining that Kitty, and Toad, and Mimi, were not killed, just moved somewhere else. He feels the only to get Kitty back is to be "moved" by Cerebrite Beta too, much to Marrow's horror. As Nightcrawler, who had gone back to the jet, flies over-head, he sees the X-Men vanish. He decides to go to Tajikistan to find the other X-Men, thinking they can help him find his teammates if they are even alive.