Ash and friends arrive in the beautiful ancient Michina Town. Although the town seems peaceful, Pikachu and Piplup are suddenly sucked into a vortex. A girl named Sheena arrives and uses her powers to summon Dialga to save them. Then, Sheena’s friend Kevin tells everyone that Dialga and Palkia’s battle in Alamos Town has caused the Legendary Arceus to start awakening, and she also tells everyone about how her ancestor betrayed Arceus, and she hopes to correct his mistake. When Dialga falls prey to one of Arceus’s vortexes, Sheena summons Palkia to save it. This in turn alerts Giratina, and the three continue their vicious battle. Sheena uses her power to quell the fighting, and the three finally resolve their differences. However, Arceus eventually awakens and begins to destroy Michina Town. Sheena summons Dialga, Palkia, and Giratina to defend the town, and when it is revealed that the Jewel of Life she posses is fake, she and the others decide to travel back into the past in order to get the real Jewel of Life and make sure Sheena’s ancestor does not betray Arceus.

Due to the disastrous battle between Dialga and Palkia in Alamos Town, the Reverse World, where the legendary Giratina lives, has become more corrupted than usual. Dark and ominous clouds have appeared which enrages Giratina. As a form of revenge, Giratina tries to lure Dialga into its world. Meanwhile, the small, but legendary Shaymin appears before Ash and friends and guides them to the flower paradise of Gracidea, but what is its intention? There’s also the villain Zero on the loose who wants to control Giratina and use it for his evil plan.

Ash and the others arrive in Alamos Town, where Dawn will take part in a contest. However the sudden appearance of the legendary pokemon Darkrai sends the town’s citizens into nightmares and a force to stop Darkrai is formed. However, the town is soon warped to another dimension where a battle between the legendary pokemon Dialga and Palkia is occurring. The battle is threating the safety of the town and its citizens and it is up to Ash, Dawn, Brock, Alice, and Darkrai to stop the two from destroying the town.