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One day, while searching for bugs in the woods, a boy named Nate (Keita in Japan) comes across a peculiar capsule machine next to a sacred tree. When he opens one of the capsules up, it brings forth the Yo-Kai Whisper, who gives Nate a device known as the Yo-Kai Watch.

A group of scientists obtain a fossilised eyelash of the legendary Pokémon, Mew, and clone it to create a supersoldier named Mewtwo. The project is successful as it awakens, but upon learning the scientists plan to treat him as an experiment, Mewtwo unleashes his psychic powers and destroys the laboratory Giovanni, leader of Team Rocket and the project’s benefactor, convinces Mewtwo to work with him to hone his powers.