Giovanni, the boss of Team Rocket, uncovers Mewtwo in an isolated part of the Johto region. Ash and his buddies fall into the clutches of a greenhorn Team Rocket member named Domino when they attempt to recapture the formidable Pokemon. Amidst this madness, Jessie and James snatch Pikachu, further complicating things. The capture of Clone Pokemon entices Mewtwo into a confrontation with Giovanni concerning control of the clones. In the meantime, Mewtwo is plagued by thoughts of purpose and self-identity as a scientific creation.