Whilce Portacio's UXM run in 1991 opened with the members of the Hellfire Club, Hellions and Reavers being attacked by the Upstarts and their Sentinels, Emma was in a coma until 1994, and the X-Men were treating her at the mansion to protect her from further attacks because reasons. The X-Cutioner was basically the Punisher if he only targeted killer mutants, and the X-Men protected the comatose Emma from him.
Despite having been explicitly indoctrinating the Hellions as her child soldiers and assassins, when Emma woke up and learned most of them were dead, she was retconned into genuinely caring about them and being broken by their deaths. The X-Men allowed her to basically retire from being a villain, and work alongside Banshee as a teacher to the Generation X kids. When Generation X ended, she moved up to the main X-Men cast, on justification of "she hadn't been a villain in years", even though her characterization backslid, she talked and acted more like a villain than she had in years, abused her telepathy, taught openly mutant supremacist views to kids, and seduced Cyclops just to hurt Jean, but that's supposed to be OK because she actually fell in love with him.
By the time Morrison's X-Men run was over, she was entrenched as the most popular X-woman with readers and with other writers, some of whom tried very hard to make excuses for her past as a villain, and retcon a narrative of everything she ever did being to protect the children.