Apocalypse finally revealed the secret of "The Twelve", a dozen mutants prophesied to defeat him. The X-Men tried to round up the mutants listed as the twelve according to one of Destiny's diaries. With the help of Skrulls and his new Horseman, Apocalypse managed to capture them first and admited he was the one who started the rumor of mutant saviors; He instead planned to absorb the powers of "The Twelve" to become invincible and unveil the Age of Apocalypse. Using Nate Grey as a vessel for intense energy, the Living Monolith acted as a power conduit transferring the power of the other mutants: Storm, Sunfire, and Iceman (the forces of nature); Magneto and Polaris (opposing magnetic poles); Bishop and Mikhail Rasputin (time and space); Cyclops, Cable, and Jean Grey (familial unit); and Xavier (mind). Apocalypse did not factor in Magneto's weakened powers, which broke the machine used for the power transfer and freed the twelve. Nate Grey was still in danger of being possessed by Apocalypse, so Cyclops decided to free Nate and take his place. With no sign of their former friend, the X-Men destroyed Apocalypse and Scott was presumed dead. Cable joined the X-Men following his father's apparent death.
Soon after, the High Evolutionary was manipulated by Sinister to revert all mutants back into humans. The X-Men temporarily enjoyed normal life, but their powers returned shortly. Six months passed, and the Neo emerged. Claiming to be the next stage in evolution after homo sapiens superior, they were also effected by the High Evolutionary's actions and suffered casualties. The Neo battled the X-Men several times. Dr. Reyes was brought back into the X-World temporarily. The Neo eventually yielded to Magneto, who was preparing to wage war on humanity.
Meanwhile, Senator Robert Kelly was running for President on an anti-mutant platform. Sage attempted to persuade him from causing a race war, but he remained headstrong. Mystique again attempted an assassination along with her Brotherhood, but made her actions much more obvious. The Brotherhood's attack on Kelly was prevented by a dying Pyro, who begged the Senator to stop the circle of violence. Kelly began to think twice.
Mystique's real intentions were more sinister; she had tampered with the Legacy Virus to release a strain that would only infect regular humans. During the attempt on Kelly's life, Mystique and Sabretooth attacked Muir Island where Dr. MacTaggart had finally discovered a cure of the virus. Mystique neutralized Wolfsbane's powers as she tried to defend her mother, whom Mystique mortally wounded. Mystique even stabbed her own foster daughter Rogue attempting to keep the cure hidden, yet Rogue recovered quickly enough and subdued her. Professor Xavier was able to transfer Moira's knowledge of the virus to his mind before she died. As Cable aided his mentor, a human angry at Senator Kelly's change of stance on mutants shot and killed him.
Beast used Moira's data to create the Legacy Virus cure. Unfortunately, a mutant power signature had to be activated for the cure to disperse around the world. Impatient for Dr. McCoy to discover another way, Colossus injected himself with the cure and activated his mutant power; killing himself but saving the lives of countless mutants.
Jean Grey still couldn't believe Cyclops was truly dead, and went on a journey with Cable to discover the truth. The two eventually found Scott in the Middle East using Jean's rapport with her husband. Cable used his psimitar to cleave Apocalypse's final hold on his father. Returned to his friends, Cyclops became more distant and self-conscious due to insecurities from being possessed. His marriage deteriorated, and eventually led to him seeking comfort from Emma Frost.
With the Legacy Virus cured, the mutates on Genosha were healthy enough for Magneto to amass a superpowered army. At a time when Storm was away, leading a squad of the X-Men in search of Destiny's diaries, and many others having left for personal reasons, Magneto went after Xavier. Without enough powerful X-men around to stop him, Magneto was sucessful in his attempt to capture Xavier, whom he brought to Genosha on the eve of his invasion. Cyclops and Wolverine infiltrated the island nation as Jean Grey recruited ex-Alpha Flight member Northstar, along with Wraith, Paulie Provenzano, and Sunfire's sister Sunpyre, convincing them to join an interim X-Men team. Dazzler showed up seeking help but also joined the group, and Jean mentally controlled the Acolyte Joanna Cargill to aid the team. On Genosha, the team managed to free Xavier who mentally stopped Magneto from ripping out Wolverine's adamantium a second time. Convinced there was no other way, Logan impaled Magneto.
Uncanny X-Men:
Gambit
Phoenix
Beast
Storm
Cable
X-Men:
Rogue
Wolverine
Colossus
Nightcrawler
Archangel
Psylocke
Thunderbird III
