Thousands of years ago, Arceus, a Pokémon believed to have created entire worlds, saved this world from a meteor storm and nearly died with the loss of its sixteen Life Plates. Arceus was saved by a man named Damos, from the wasteland town of Michina, when he returned the plates to Arceus. Feeling pity for the town, Arceus fused five of its plates into the Jewel of Life, which made the land rich and fertile. Arceus asked Damos to return the jewel to him, but Damos, hypnotized by a Bronzong belonging to Damos’s lieutenant Marcus, betrayed Arceus and attacked it, as Marcus believed the town would again become a wasteland. Arceus destroyed the temple which was built as a shrine dedicated to it and was forced to go into a long slumber. Arceus intended to judge humanity when it awakened.
When Arceus began to awaken, massive whirlpools of energy formed around it. These distortions brought together the dimensions of two Pokémon that should never have met: Dialga, which rules time, and Palkia, which rules space. Dialga and Palkia then collided with one another in Alamos Town, both mistakenly assuming the other had threatened their territory. This battle affected the Reverse World, the dimension ruled by the Pokémon Giratina, bringing Giratina into the conflict.
In the present, the Pokémon trainers Ash Ketchum, Dawn, and Brock arrive at a lake near the ruined temple. A whirlpool strikes up, threatening the lives of Ash’s Pikachu and Dawn’s Piplup. Sheena, a descendant of Damos who investigates disruptions in time and space, summons Dialga, who saves Pikachu and Piplup. Giratina arrives, but Ash, who Giratina remembers from their previous encounter,[d] calms Giratina’s rage. Sheena believes that Pikachu and Ash are the thunder creature and its master from legend, said to have changed the fate of the town long ago. Palkia arrives to save Dialga from another whirlpool, before the two return to their own dimensions.
Arceus arrives. Sheena offers it the Jewel of Life to calm its wrath, only to discover that the jewel is a fake. Dialga, Palkia, and Giratina arrive to stop Arceus from destroying humanity. Dialga sends Ash, Dawn, Brock, and Sheena back in time to the day when Damos was manipulated into betraying Arceus, where Damos and Marcus fall to their deaths in the collapsing temple. Upon Sheena’s request, Dialga sends her and the others further back.
Unaware of Marcus’s true role, Sheena tells him everything about the future. Arceus arrives to collect the Jewel of Life from Marcus’s scepter, but Sheena is fooled into betraying Arceus when the scepter is empty. Arceus is forced into a pit and is wounded by silver water and electrical attacks, which Arceus became vulnerable to after it gave Damos the jewel. Marcus’ intention is to kill Arceus himself to save the future. Sheena and Damos use their abilities to communicate with the other Pokémon to stop the Pokémon under Marcus’s control from electrocuting Arceus.
Ash obtains the Jewel of Life. Calmed by Damos’s ability, Arceus absorbs the jewel, restoring its own life force, and reversing the time paradox that nearly killed Ash, Dawn, Brock, Sheena, and their Pokémon. Arceus rescues the people and Pokémon from the collapse of the temple. Ash, Dawn, Brock, and Sheena are transported to the present, only to discover that Arceus is still furious and has defeated Dialga, Palkia, and Giratina. Arceus spots Ash and recognizes him due to history’s alterations, and reverses the destruction it caused and heals its former adversaries. Ash and the others discover Damos has put them on a mural, thanking them for their help in saving the world and seeing that even without the Jewel of Life, Michina is still fertile due to the people and Pokémon cultivating the land. Dialga, Palkia, Giratina, and Arceus depart for their dimensions, with Arceus realizing that it is truly a part of this world.