The story of the Twelve begins with a young mutant by the name of Tanya Trask, who would later become Madam Sanctity. Adrift in the timestream, Tanya was rescued by Rachel Summers, in her guise of Mother Askani, and took her to the future, where she healed her mind. The future, under the rule of Apocalypse, was somber and grim, and Tanya sought to change it. She traveled back in time, three years before the formation of the X-Men, despite Mother Askani's warnings not to do so, and attempted to contact her father, Bolivar Trask. Rachel followed her and stopped her from revealing herself to her father, but not before Tanya could tamper with her father's creation, Master Mold, and upload a program called "The Twelve".
Years later, as Cyclops pondered his relationship with Madelyne Pryor in Alaska, he was attacked by Master Mold, who claimed Cyclops was one of the "strong" one of the Twelve and had to be killed. Master Mold was stopped, but not before revealing several other possible members of the Twelve, such as Charles Xavier, Apocalypse, Storm, Jean Grey, and Franklin Richards among others.
Master Mold survived the encounter and later faced Power Pack in an attempt to kill Franklin Richards. As the youngsters fought the demented robot, he revealed the nature of the Twelve: "The dozen mutant humans who will one day rise up and lead all of mutantkind in war against Homo sapiens in the twilight of earth." He was stopped, but not before revealing several other possible candidates, including Danielle Moonstar, Cannonball and Psylocke.
The subsequent mention of the Twelve came from Apocalypse himself, claiming that not only he was one of the "fabled Twelve" but so too were all five original X-Men, Charles Xavier, Storm, Cannonball and Cable.
As the new millennium approached, a series of events led to the return of Apocalypse. Cable was witness to said events-- the darkening of New York City, the arrival of the Harbinger of Apocalypse, and several other signs. Mother Askani's astral form revealed herself to Cable, implanting the knowledge of who the Twelve were. Sadly, he never had the opportunity to find them.
Apocalypse began his attack by planting a fake Wolverine among the ranks of the X-Men. This led Xavier, who suspected of infiltration, to disband the X-Men. The X-Men parted ways, and soon after, Rogue and Shadowcat found themselves protecting Mystique from Japan's military, the Yakiba. As Rogue fought Sunfire and his men, Kitty "babysat" Mystique and found, unwillingly, Destiny's diary. The diary itself had a very cryptic description of a "thirteenth" and told that the Twelve would be involved in the destruction of the world.
With the death of Wolverine's impostor, the X-Men reunited at the mansion, only to discover it wasn't truly Wolverine who had died, but a Skrull. The infiltrator had been found. To save Polaris from abduction, Cyclops took her place using an image inducer, and the X-Men followed him to the Skrulls' lair, where they were attacked by Death, Apocalypse's most lethal and fiercest Horseman, the same person responsible for the death of the fake Wolverine. After a heavy battle, Death was unmasked by Colossus. The X-Men were surprised to see their newest enemy was in truth the real Wolverine. Death escaped, leaving the X-Men with half-truths and enigmas that needed solving.
Soon after, Xavier revealed the "List of Twelve", for it was clearly written in Destiny's Diary. The Twelve were: Cyclops, Phoenix, Storm, Magneto, Polaris, Living Monolith, Bishop, Cable, Xavier, Iceman, Mikhail Rasputin and Sunfire. But whatever part they had to play was not revealed.
The Horsemen of Apocalypse kidnapped Cable, Mikhail Rasputin, Iceman, Sunfire and the Living Monolith. The X-Men, with Magneto's help, rushed to Egypt, to Apocalypse's lair. They were soon attacked by an army of Skrulls and followers of Apocalypse. Amidst the battle, Bishop, who had been trapped in an alternate future reality, appeared out of thin air, furthering the confusion. Thanks to illusions and lies, the agents of Apocalypse were able to kidnap all remaining members of the Twelve. Their true role was then explained at last. Placing the Twelve inside containment cells, part of an ages-old Celestial machine, Apocalypse revealed his plan was to siphon the energies of the "Eleven of Power" through the Living Monolith to start the machine, which would grant him omnipotence. The role of each mutant was clearly explained by Apocalypse. Polaris and Magneto were opposing magnetic poles. Storm, Iceman and Sunfire were extreme forces of nature. Cyclops, Jean, and Cable represented the unity of family. Bishop and Mikhail provided control over time and space, and Xavier provided the power of pure thought. However, Apocalypse knew his frail, centuries-old body would not be able to withstand such power. And that's when he revealed the thirteenth mutant, the X-Man, Nate Grey. He intended to transfer his consciousness into Nate's young body and then use the energies of the Twelve to evolve.
He began the process, but Magneto's then-recent power loss was something Apocalypse had not counted, and soon his energies were depleted, creating a break in the chain of power. Apocalypse increased the flow of energies, attempting to bypass the break, but this drove the Living Monolith insane, destroying his containment unit and starting a rampage that unwillingly released the X-Men. While half of the team battled the Monolith, the other half attempted to stop Apocalypse. Jean Grey exposed the true nature of Apocalypse, showing his rotting body inside his armor. As he tried to enter Nate Grey's body, Cyclops took his place, sacrificing himself to save Nate. Jean attempted to contact her husband's mind, but Xavier claimed there was nothing of Cyclops left inside Apocalypse. Using the energies of the Twelve, Apocalypse re-made reality twice, attempting to re-create the process once more and finish his transformation. He was unable to do so, for the X-Men fought him both times, in the past and the future. His energies spent, he and the Living Monolith escaped. The X-Men had prevented Apocalypse from becoming a god, at the seeming expense of Cyclops' life.