Scientist Dr. Fuji is hired by Giovanni, leader of Team Rocket, to utilize his expertise in cloning in order to create a living weapon based on an eyelash from legendary Pokémon Mew. Soon after the weapon is created, it gains sentience and is named Mewtwo.
Several years later, Mewtwo has fully awakened from a long slumber in a laboratory on New Island, and learns of his origin as Mew’s clone from Dr. Fuji. Infuriated that Fuji and his colleagues see him as nothing more than an experiment, he unleashes his psychic powers and destroys the laboratory, killing Fuji and the rest of the scientists. Giovanni, witnessing the carnage afar, approaches and convinces Mewtwo to work with him to hone his powers. However, after Mewtwo learns of his purpose to be a weapon for Giovanni’s benefit, he escapes back to New Island where he plots his revenge against humanity.
After Mewtwo rebuilds the laboratory and establishes a base there, he invites several trainers with hologram messages to battle the world’s greatest Pokémon trainer at New Island. Ash, Misty, and Brock receive a message and accept the invitation, but when they arrive at the port city, Old Shore Wharf, Mewtwo creates a storm, causing the boats on the wharf to be closed off for safety. As a result, Ash’s group are picked up by Team Rocket disguised as captains on a Lapras-shaped sailboat. After the storm sinks their vessel in the middle of the ocean, Ash and his friends use their Pokémon instead to reach New Island.
Directed by: Kunihiko Yuyama, Motonori Sakakibara
Screenplay: Takeshi Shudo