In a magical water city of canals and mazes, Ash, Pikachu and the rest of the gang face off against a slick pair of thieves who plan to steal and awesome and dangerous jewel guarded by Latios and latias. To save the city from total destruction, our heroes must defeat the evil duo and overcome impossible obstacles, but time is running out.
Giovanni, the leader of Team Rocket, had ambitious plans to take over the world, involving his latest experiment, a powerful clone of Mew Mewtwo. Mewtwo is very powerful, and also very smart-smart, enough to not want to be controlled by Giovanni. It escaped from the lab, and now Mewtwo begins to concoct its own scheme, clandestinely inviting a number of Pokemon Trainers to the ultimate test.