Koko grows up in the jungle with a solitary Zarude. When he meets Ash and Pikachu, he discovers the human world — and a plot threatening his home!

Usagi Tsukino is chosen to be a guardian of justice and is sent on a quest to locate a Silver Crystal before the Dark Kingdom invades the Earth.

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 Kingdom of the People of the Vale once ruled over the land, but now all that remains is the Sword of the Vale. in the city of Eindoak. Ash, Iris, and Cilan arrive in Eindoak during a harvest festival's Pokémon Tournament and meet the legendary Pokémon Victini who wishes to share its powers of victory to someone. Elsewhere in the city, a descendant of the People of the Vale named Damon has arrived who seeks to revive the kingdom's power with the Sword of the Vale, bringing them back into power over the land, and Ash and his friends must stop him before he destroys the land along with Victini.

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.