Thousands of years ago, a meteor from space threatened to annihilate the world until Arceus intervened to save it. During this battle, Arceus sustained severe injuries, and a human named Damos (ダモス) tended to its wounds. In gratitude, Arceus promised to transform the barren land of Michīna into a prosperous region, gifting Damos the Jewel of Life (命の宝玉). To create this artifact, Arceus allowed Damos to borrow sixteen fragments of its body with the agreement that they would be returned on a specific date. However, the fragments were never given back, leading Arceus to vow judgment upon humanity upon its awakening.
Millennia later, Satoshi, Hikari, and Takeshi arrive at the riverside town of Michīna (ミチーナ), a place surrounded by natural beauty. They decide to visit the ruins located at the summit of a large rock formation. A magnificent lake lies at its shores, captivating Satoshi and his friends, but suddenly, waves churn in the water and a destructive water tornado begins to form. Sheena, a descendant of Damos, rushes out from the Michīna ruins. Witnessing the chaos, she summons Dialga, pleading, "Dialga, please!" Dialga responds and manages to halt the tornado.
Satoshi and his companions finally reach the ruins, where Kevin and Sheena recount the ancient legend of Michīna. Shortly after the story is told, the battle between Dialga, Palkia, and Giratina intensifies, causing the ruins of Michīna to be destroyed. Arceus awakens...