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.

40 years ago, a Celebi was being attacked by a Pokemon Hunter. Luckily, a young boy named Sammy saved Celebi. Using its Time Traveling power, Celebi transported himself and Sammy 40 years into the future. There, Ash, Misty, and Brock assist Sammy to the healing lake in the forest so they can heal the wounded Celebi. Unfortunately an evil Team Rocket member, Viscious a.k.a. "The Iron Masked Marauder", tries to capture Celebi using his technology. As Ash and Co. try to get away from Viscious, they also run into Jessie, James, and Meowth, who also want to capture Celebi. Soon it becomes a race against time to get Celebi and Sammy back to the forest before Celebi is caught and is used to destroy the forest and themselves.