The Mythical Pokémon Mew is said to possess incredible abilities and eternal life. In an attempt to create the world's strongest Pokémon, scientists manage to find a fossil containing one of Mew's eyelashes and extract the DNA from the sample, successfully developing the Legendary Pokémon Mewtwo. But not long after its birth, the creature destroys the lab and plans to retaliate against humanity—all for its existential search for purpose.

Meanwhile, Satoshi, Kasumi, and Takeshi receive a mysterious invitation to a castle on New Island, where they can supposedly meet the greatest Pokémon trainer. Satoshi eagerly accepts, and upon arrival, the gang soon meets three other trainers who were also invited for their potential: Sorao, Umio, and Sweet. Unbeknownst to them, their host and the trainer they were all waiting for reveals itself to be Mewtwo, who challenges its guests with clone Pokémon of its own!

[Written by MAL Rewrite]