In a secluded part of the Johto region, Giovanni, the leader of Team Rocket, stumbles upon the powerful Mewtwo. As Giovanni schemes to reclaim Mewtwo, Ash and his companions fall into the clutches of Domino, a fresh face in Team Rocket, during their attempt to rescue Pikachu from the clutches of Jessie and James. The cloned Pokemon are ensnared and become pawns in the quest to lure Mewtwo. What ensues is a clash of ideologies between Mewtwo and Giovanni, with Mewtwo grappling with the existential question of purpose for itself and the clones, creations of scientific experimentation.