In the Forest of Okoya, Koko is a feral child who has been raised as a Pokémon by the Mythical Pokémon Zarude. Koko has grown up never doubting that he is a Pokémon even though he can’t really use any sort of moves. Ash Ketchum and Pikachu meet Koko and help him protect the Great Tree from the crooked scientist Dr. Zed.

After a scientific experiment leads to the creation of Mewtwo, he sets out to destroy the world. Satoshi and his friends then decide to thwart Mewtwo’s evil plans.

On their way through the Battle Frontier, Ash and friends meet up with a Pokémon Ranger who’s mission is to deliever the egg of Manaphy to a temple on the ocean’s floor. However, a greedy pirate wants the power of Manaphy to himself.

The Struggle for Time and Space Begins Again…! The legendary Arceus. Long ago Arceus granted a fragment of its awesome power as the Jewel of Life to help Michina in the town’s hour of need only to be betrayed when it was time for that power to be returned. After so many years Arceus is about to return to reclaim its power – enraged vengeful and seemingly unstoppable. Not even the combined might of Dialga, Palkia and Giratina can stop Arceus from devastating all existence across multiple dimensions. But Ash and his companions joining forces with their new friend Sheena, may have discovered the only way to redeem that ancient betrayal. Their journey will be both dangerous and uncertain: even if Ash and his friends can set an old wrong right again will there be time to return the Jewel of Life before Arceus destroys everything and everyone they’ve ever known?

Pikachu and his friends have gathered to listen to a song performed by Meloetta at the melody tree. Meloetta is soon interrupted by a Sandstorm attack which breaks the tree and causes the Melody Berries to scatter. Before the performance can continue the Pokémon must retrieve the lost berries.

A group of five Genesect have invaded the big city and pose a threat to the supply of electricity, which attracts the attention of the legendary Pokémon Mewtwo. Ash, Pikachu and his friends must come to the rescue when the powerful leader, a red Genesect, faces Mewtwo.