A group of scientists funded by the head of Team Rocket, Giovanni, have worked for years to prove their scientific theories by cloning the rarest of pokémon, Mew. They finally successfully managed to clone the pokémon while genetically improving the DNA – resulting in Mewtwo! The scientists make the mistake of underestimating Mewtwo’s ability to feel and reason. They congratulate each other on a job well done while Mewtwo struggles with the idea that his destiny may be that of a laboratory experiment. Mewtwo releases his frustration on the scientists. Giovanni arrives in his helicopter to a destroyed research facility. He greets Mewtwo as an ally and promises to teach him to control his powers. Mewtwo continues to struggle with the meaning of his existence and his purpose in life. He quickly comes to the realization that he is being used by Giovanni who sees him as a creature he owns – one that should fight for him. Mewtwo determines that he will serve no human master. He leaves Giovanni in search of his purpose and the answer to his ultimate questions.
Shortly later, Ash, Misty, and Brock receive an invitation from a mysterious pokémon trainer requesting that they attend a special gathering at his palace on New Island. They readily agree to meet this mysterious pokémon trainer. Upon arriving at the ferry that was to take them to New Island, the friends learn that due to a major storm the ferry has been cancelled. Not only has the ferry been cancelled by Officer Jenny states that the local Pokemon Center is closed due to the sudden disappearance of Nurse Joy one month ago. Our friends along with several other trainers decide to weather the storm and try to reach the island even against the advice of Officer Jenny.
Arriving on the island, a mysterious woman instructs the friends and the other trainers who arrived through the storm to release their pokémon. She then proceeds to introduce the mysterious pokémon trainer who happens to also be the most powerful pokémon – Mewtwo! Mewtwo declares himself the master of humans and pokémon alike. The pokémon trainers challenge Mewtwo. Mewtwo calls to his pokémon clones and a battle begins. It is pokémon versus cloned pokemon in a battle to determine which is better. What will it take to show Mewtwo that fighting over differences that do not exist is a senseless battle?