Ash and friends (this time accompanied by newcomer Dawn) arrive at an idyllic village on their way to their next Pokemon contest, where chaos will soon erupt with the prophecy of two Pokemon Gods (Dialga and Palkia) and the arrival of a mysterious, seemingly deadly Pokemon named Darkrai, which has the power to distort space and time.

When Giratina is discovered to be able to create parallel dimensions, it's up to Ash and his friends to stop a mysterious stranger from using its powers for evil.

When the creator of the world, Arceus, comes to pass judgement on humanity for the theft of the legendary Jewel of Life, Ash and his friends are sent back in time to possibly reverse the events that led to Arceus' vendetta.

Ash and his friends must stop a greedy media mogul from using the shape-shifting Zoroark to capture the time-travelling Celebi.