Determined to prove its superiority, a bio-engineered Pokémon called Mewtwo lures Ash, Pikachu and others into a Pokemon match like none before.

Pikachu and the gang learn responsibility, teamwork as well as cooperation during their Summer vacation at Pokemon Island.

The devious leader of Team Rocket Organization, Giovanni, has a fervent ambition to take control of the Pokémon world through both financial and military means. To achieve his military needs, he covets a Pokémon stronger and more adept than any other, a veritable living war weapon, so he enlists a scientist named Doctor Fuji to create this being from the DNA of the ancestor of all Pokémon and most powerful of Pokémon, Mew, which Fuji had found on a previous jungle expedition. Fuji accepts, for he is heavily into the prospect of cloning to create and restore life itself, because of his love for his deceased daughter, Amber.