Following Professor X's arrest for crimes committed as the evil psionic entity Onslaught, Scott assumed the role of leadership of the X-Men once more. Soon after, the government sponsored mutant-hunting operation known as "Zero Tolerance" took effect, and the villainous Bastion captured the X-Men. In his attempt to destroy mutantkind, Bastion placed a nanotech bomb inside Scott's body. The X-Men escaped, and the mutant doctor named Cecilia Reyes saved Scott's life. Scott and his wife soon took a leave of absence from the X-Men for a period of recuperation.

Not long after returning to the team, Scott and Jean soon found themselves embroiled in Apocalypse's bid for cosmic power by assembling "The Twelve" - a group of mutants who would determine the fate of their kind that included Scott, Jean, and Cable. They were wired to a machine that would channel their awesome energies into Apocalypse, allowing him to absorb the body of the time-tossed powerful mutant teenager known as X-Man. As his teammates fell around him, a powerless Scott saved X-Man and merged with the would-be conqueror to create a new evil entity. Jean detected Scott's psyche inside Apocalypse and prevented the X-Men from destroying him, however he was presumed dead by most of his teammates. Only Jean and Cable refused to believe Scott had perished. Investigating rumors he was alive, the pair found him in the birthplace of Apocalypse in Akkaba, Egypt, struggling to reassert his mind over the villain's psyche. Ultimately, Jean was able to physically rip Apocalypse's essence from Scott's body using her mental powers, and Cable destroyed it with his own powers.