Bastion's attack occurs when an entourage of X-Men has traveled

The consequences of the saga of Onslaught are manifested when the government of the United States authorizes the villain Bastion to begin a hunt for mutants. Professor X is put in prison, and Mansion X is taken by the government. To make matters worse, Bastion's attack occurs when an entourage of X-Men has traveled into space to fight the Phalanx in the Shi'Ar Empire. Cyclops, Wolverine, Storm, Jean Gray and Cannonball form a resistance against Bastion. Iceman is in charge of rescuing several mutants attacked by Prime Sentinels, a new generation of sentinels created by Bastion. Cable also plays a crucial role in freeing Mansion X from Bastion control. In the end, it is discovered that Bastion is actually a sentinel, reincarnation in only one of Nimrod and Master Mold. The government cancels its operation and the villain is put in prison. Two mutants rescued by Iceman are accepted in the group: Marrow, a former member of the Morlocks, and Puerto Rican surgeon Cecilia Reyes.

The X-Men who were in space are stranded in Antarctica. There they discover that Joseph is not Magneto, but an impostor Cosplay UK
. The real Magneto confronts the X-Men and brings out the murky past of Gambito, who is abandoned in Antarctica. The X-Men return home taking with them a young South African mutant Maggot, who is briefly attached to the group.

With these new members of the group, some members like Cyclops, Jean Gray, Iceman, Psylocke and Archangel, decide to take a break time. Colossus, Nightcrawler and Kitty Pryde return to the group when Excalibur disintegrates. The same fate will suffer X-Factor, which is canceled by the government. Gambit is forgiven and accepted back into the team a little later.v

Professor X will return with his disciples, ironically with the help of the Brotherhood of devilish mutants. Magneto reappears after a long absence and threatens to blow up a nuclear bomb if he is not given diplomatic control of the island of Genosha. Joseph sacrifices his life by disabling Magneto's bomb, but the villain manages to be given control of the Island of Genosha, which is named absolute king and the Acolytes as his cabinet.

After a long absence, Apocalypse returns. The villain challenges the twelve most powerful and dangerous mutants to his ascent (Magneto, Polaris, Storm, Solar Fire, Iceman, Cyclops, Jean Gray, Cable, Bishop, Mikhail Rasputin, Professor X and the Living Monolith) Ant-man Costumes
. The X-Men and Magneto join forces to combat this threat. Wolverine is kidnapped by Apocalypse, who names him his new Death Rider and replaces the skeleton with the metal Adamantium. In a brutal battle in Egypt, the X-Men fight Apocalypse, their Four Horsemen and their allies, the Skrull aliens. Wolverine manages to save himself from the control of Apocalypse with the help of Jubilee and Psylocke. Apocalypse kidnaps X-Man and tries to take over his body, but Cyclops intervenes and in the end, is merged with the villain. When defeated, the Cyclops-Apocalypse escapes.

After the defeat of Apocalypse, the team reappears with a new lineup: Storm, Wolverine, Colossus, Jean Gray, Psylocke, Archangel, Kitty Pryde, Cable, Beast, Nightcrawler, Rogue and Gambit. In their first mission the X-Men fight a group of new villains known as the Neo. Also reappears Mysticism and the Brotherhood of Diabolical Mutants, who finally assassinate Senator Robert Kelly. Cable and Jean Gray are successful in finding Cyclops fused with Apocalypse. Cable manages to separate them and eventually destroys the essence of Apocalypse. New members join the group: the Indian mutant Bird of Thunder II (Neal Shaara), Danielle Moonstar of X-Force and Sage, the ancient and mysterious assistant of Sebastian Shaw (who was always a secret agent controlled by Xavier). They make their appearance the mysterious diaries of the mutant visionary Destiny, who supposedly detail the future of the X-Men and the mutant race Arrow Costumes
. It is precisely the search of these journals which leads Professor X to entrust Storm with the creation of a special team to find them. Thus emerges the X-Treme X-Men. At this stage is very important the discovery of the awaited cure of Virus Stryfe Legacy, thanks to Beast and Moira MacTaggert. Unfortunately MacTaggert and Colossus themselves had to give their lives to propagate this cure. With the death of Colossus, Kitty Pryde leaves the group, and without the Storm team, only Cyclops, Wolverine, Jean Gray and Professor X remain in the mansion.