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

A year after losing her mother, a young girl learns that she must journey across Japan to the annual gathering of gods in the sacred land of Izumo.

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.

Join Ash Ketchum, accompanied by his partner Pikachu, as he travels through many regions, meets new friends and faces new challenges on his quest to become a Pokémon Master.

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.