Sinister, with his helpful but untrustworthy henchman, Sage, began investigating "metamutants," like Sage herself, mutants with mutations that seem highly advantaged to living among mutants, proof that the X-gene is self-referential. In the initial stages of his research, he cloned a metamutant of his own, using material from the mutant Mimic. His project was a controlled weapon, capable of absorbing the powers of others, and already carrying copies of mutant powers from other sources. Sinister's first act was to turn this monstrosity loose upon the mansion.

The mutant was defeated and destroyed, but not before Rogue had touched it. The multiple genetic copies spliced into the mutant came into Rogue all at once, and the overload fractured her mind. Xavier, suspecting the invading mutant's creator was still nearby, brought Catalyst with him into Cerebro. The teenager boosted Xavier's powers and traveled with him on the astral plane to seek out and engage Sinister, and unwittingly exposed her existence to Essex when she did. Sinister did not forget her, or Rogue, although he did escape the mansion and Xavier.

While Rogue recovered slowly under the care of Xavier, Beast, and also Garou (who it appeared was capable of touching Rogue with his fur to guard him from her deadly skin), Sinister put new plans into effect. He sent a message to Catalyst, posing as her brother, and met her in the city. He took her, drugged and unconscious, to his own small hideout, where he could conduct experiments on her powers as necessary. The intense experiments left Catalyst psychologically damaged, and her brief contact with Sage evolved her own power to the point that she could not only increase powers but also to decrease them. The X-Men searched for her, but Sage took steps first to arrange a rescue for Catalyst herself, in the form of Catalyst's old friend, Pyro. The former student, now a member of the Brotherhood, received a drawing of himself he immediately recognized as Catalyst's along with a cryptic message bidding him to save her. Sinister's powers were heightened by Catalyst's effects, and he was able to see Sage's betrayal. He was prepared when Pyro arrived.

Sage quietly made her own exit as Pyro arrived to rescue Catalyst. He entered Sinister's lab, but was gassed unconscious before he could make a move to help Pyro. Sinister destroyed his own lab, faked his death with the body of a spare clone of himself, and implanted false memories of a heroic, fiery rescue into Pyro's mind. Pyro left the scene with a shattered Catalyst, though the X-Men were close behind. They caught up to Catalyst hiding in a motel room with Pyro, and almost took her back with no conflict. At the last moment, Pyro, angry at being abandoned after rescuing Catalyst, attempted to use his fire against Beast. Catalyst used her new powers for the first time, shutting down Pyro's power temporarily and causing him great pain.

Catalyst remained drastically changed by her experiences even when she had been returned to the mansion...as did Rogue. Sinister reached out to her mind, tempting her with promises of control over her powers. At first she pushed his messages away, but then she discovered Gambit's new relationship with Eclipse, and in her unsteady state imagined the worst of both of them, suspected the affair of having gone on longer than it seemed. She attacked Eclipse in the mansion hall, nearly killing her, before she regained some control over herself. She fled to Sinister, joining his Marauders, leaving the X-Men to worry and wait for her return and never guessing that she might have taken up with Dr. Nathaniel Essex.

Catalyst meanwhile struggled to control her emotional state, her new powers, and her surfacing memories of her torture at the hands of Sinister. When Garou tried to reach out to her, she hurt him with her new ability, and inadvertently discovered he felt more than friendship for her. Professor Xavier was ultimately the one who was able to rescue her sanity, but the close friendships of Catalyst, Iceman, and Garou might never be the same.