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Kamui Shirou returns to Tokyo after six years, obeying his mother's final request while refusing to explain himself to childhood friends Fuuma and Kotori Monou. Dreamseer Hinoto identifies him as the person whose choice will decide whether humanity survives or the wounded Earth is freed from civilization.

The Dragons of Heaven gather to protect the barriers sustaining human society, while the Dragons of Earth prepare to destroy them. When Kamui finally chooses his friends over the planet, destiny awakens an opposing Kamui in the person closest to him and turns the coming apocalypse into a battle against the life he wanted to preserve.