While investigating the legend of the mythical Pokémon Arceus, Ash, Goh and Dawn uncover a plot by Team Galactic that threatens the world.

Ash, Pikachu, and their friends come to a desert city by the sea. Here they meet the Mythical Pokémon Hoopa, which has the ability to summon things—including people and Pokémon—through its magic rings. After a scary incident, they learn of a story about a brave hero who stopped the rampage of a terrifying Pokémon long ago. Now, the threat that has been bottled up for years is in danger of breaking loose again.

The film opens with Shaymin as Dialga appears. Then, in the Reverse or Distortion World Giratina senses Dialga's presence, and flies up to the Real World to capture him. Dialga drinks, just as Giratina's portal opens up. Giratina then drags Dialga into the Reverse World. Shaymin is also catapulted into the Reverse World. As Dialga and Giratina fight, Zero observes the battle in his ship. Shaymin absorbs a dark gas and uses "Seed Flare," tearing a hole in the Reverse World and escaping. Dialga fires a laser at Giratina, enveloping her in a time loop and trapping her in the Reverse World. As Dialga escapes, Shaymin falls into a river.

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.

The adventure explodes into action with the debut of Mewtwo, a bio-engineered Pokemon created from the DNA of Mew, the rarest of all Pokemon. Determined to prove its superiority, Mewtwo lures Ash, Pikachu and others into a Pokemon match like none before. Mewtwo vs. Mew. Super-clones vs. Pokemon. It's the ultimate showdown ... with the very future of the world at stake!