Long ago, when Earth was on a collision path with a meteor, the Legendary Pokémon Arceus used its power to prevent the disaster. This act caused the 16 Plates surrounding it to spread across the world. Without the Plates providing Arceus with life energy, it began to die. A human named Damon managed to find one of the Plates and returned it to the dying Pokémon, helping it recover. As a reward, Arceus created the Jewel of Life and gave it to the people of Michina Town, requiring that it be returned, but the humans refused, keeping the Jewel for themselves. In the battle that followed, Damon was killed and Arceus went into slumber, swearing to punish humanity upon its return.
Satoshi and his companions arrive in Michina Town where they meet Sheena, a descendant of Damon, who claims to have the Jewel of Life and intends to give it back to Arceus when it awakens.
The situation takes a sudden twist when Arceus, despite Sheena's best intentions, remains unappeased. Satoshi must now prevent the destruction of the entire human race, as Arceus' wrath causes tears in the fabric of space-time, provoking the Legendary trio—Dialga, Palkia, and Giratina—and disrupting the world's balance.