Many millennia in the past, a meteor hurtling from space threatened to annihilate the world, but Arceus intervened and halted it. During that act of protection, Arceus sustained severe injuries, and Damos (ダモス) nursed it back to health. In gratitude, Arceus vowed to make the barren land of Michīna fertile and prosperous, and thus presented Damos with the Jewel of Life (命の宝玉).
Arceus allowed Damos to borrow 16 portions of its own body in order to create the Jewel of Life, with the condition that they be returned on a designated day. But the parts were never given back, and Arceus, feeling betrayed, swore that it would judge humanity when it awakened.
Many millennia later, Satoshi, Hikari, and Takeshi arrive at the riverside town of Michīna (ミチーナ), a place enveloped in natural splendor. They head for the ruins of Michīna, which stand atop a huge rock, with a wide, beautiful lake spread out at its base. Satoshi and his friends are entranced by the lake, yet suddenly waves rise upon its surface and a watery tornado starts wreaking havoc.
A girl named Sheena, a descendant of Damos, rushes out from the Michīna ruins. Perceiving the danger, she summons Dialga and cries out, "Dialga, please!" and Dialga manages to quell the tornado.
At last, Satoshi and his friends are able to enter the ruins, where Kevin and Sheena relate the ancient legend of Michīna. Just after they finish recounting it, the battle among Dialga, Palkia, and Giratina grows violent, and the Michīna ruins are shattered. Then Arceus awakens...