Distressed due to the loss of their homeland, the Genesect Army attacks New Tork City. Coincidentally, Ash and his friends are visiting the city to see the park called Pokémon Hills. When the Genesect begin rampaging in the city, Ash is protected by the sudden appearance of a familiar Pokémon Mewtwo. Despite sympathizing with the plight of the Genesect, Mewtwo attempts to convince them to leave New Tork City and go somewhere else where artificial Pokémon can belong, only to get into a conflict with the Red Genesect that leads the team. Can Mewtwo overcome the Genesect to save New Tork City or is the city doomed to be destroyed and changed into the nest of a Pokémon left behind by history?