Karen, along with Will, Green, Silver, Chermaine, and Keane, is one of the children kidnapped by the Masked Man and raised to be his servants. Karen was one of the leaders of the new Team Rocket formed in Johto. Unlike Silver and Green, she and Will were willing members of the evil man's cohorts, having been inducted as one of his followers at the age of eleven, and continuously trained. They expected a surefire victory against Green, which seemed feasible with Ho-Oh and Lugia under their command. However, with the resistance of Green and her friends Red and Blue each commanding one of the legendary birds of Kanto, and the help of many other Pokemon sent from all across Johto and Kanto, Ho-Oh and Lugia were freed. Karen then fled with Will.
After the Masked Man was defeated, Karen formed an alliance with Bruno, Will, and Koga; the four of them are all ex-members of various criminal organizations. They later reappear in the HeartGold & SoulSilver chapter.