As Shaymin tumbles down the river, she meets Ash and his friends, who were on their way to the Flower Garden. Shaymin becomes friends with them and hitches a ride on their journey. However, Shaymin keeps getting ill as she needs Gracidea Flowers to stay healthy. The group learns that the Gracidea Flowers grow in the Flower Garden, and they journey there to help Shaymin. However, the Flower Garden is no ordinary place; it has a mystical guardian called the "Chikorita Guardians," who protect the Garden and the Gracidea Flowers. The Guardians capture the group, and they are interrogated. Finally, the Guardians agree to help Shaymin with the promise that the group would return one of the Guardians to the Garden.
Meanwhile, Giratina, enraged by being trapped in the Reverse World, breaks the time loop and sets out to find Dialga. Giratina's rage causes massive earthquakes, creating several portals to the Real World. Zero uses this opportunity to capture Giratina, taking her to his spacecraft.
The group reaches the Garden, and Shaymin is cured. However, as they head back to the Real World, they see Zero's spacecraft. Ash confronts Zero as the rest of the group fights his henchmen. Using the Gracidea Flower, Shaymin transforms and helps battle. Zero detaches the spacecraft, making it plummet to the ground. Dialga appears at the last minute and saves everyone. Shaymin uses Seed Flare to destroy the spacecraft, and Ash and Dialga work together to send Giratina back to the Reverse World. In the end, the group returns the Chikorita Guardian to the Garden, keeping their promise.
The movie concludes with Shaymin parting ways with the group, but promising that they will meet again. The final scene shows Dialga and Giratina reconciling, ending their feud.