After a scientific experiment leads to the creation of a clone of Mewtwo, he sets out to destroy the world. Ash and his friends then decide to thwart Mewtwo's evil plans.

Ash, Pikachu and his friends try and stop a pair of thieves hiding out in the canals and alleyways of Alto Mare, the age-old water capital. Joining the adventure are two new legendary Pokémon, a pair of siblings named Latias and Latios, who serve as peacekeepers and protectors of the Soul Dew - a priceless treasure with a mysterious power.

When Molly Hale's sadness of her father's disappearance get to her, she unknowingly uses the Unown to create her own dream world along with Entei, who she believes to be her father. When Entei kidnaps Ash's mom, Ash along with Misty & Brock invade the mansion looking for his mom and trying to stop the mysteries of Molly's Dream World and Entei!