The story is about a group of crazy scientists who, for their dream, developed a machine that can replicate Pokémon with only a few genes, and copied the world's strongest Pokémon they discovered into Mewtwo, which has stronger abilities than Mew. But when Mewtwo wakes up, he goes berserk because he can't find his true self. The boss of Team Rocket appears in front of Mewtwo and uses sweet words to win over the lost Mewtwo to work for him, but it doesn't take long for Mewtwo to feel confused about himself again. Mewtwo returns to the island where it was copied and decides to start its revenge.