12-year-old Oriko Seki, who lost her parents in a car accident, ended up living in her grandmother's Onsen Ryokan "Haru no Ya." With the ghost "Uribou" cohabitating with her and all the other odds, she ended up training to be a young female innkeeper. At first, she didn't like the training, but gradually felt her admiration for her title and began to train seriously. Thus, the growth of the young warrior Oriko begins.

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.