During the Bakumatsu period, the young men of Japan were anxious about their country's future. Takasugi Shinsaku, a mercenary from the Choshu clan, and his companion Katsura Kogoro, board a government vessel to seek out a mysterious "timepiece" that has the power to manipulate time. Takasugi believes that the government wants to keep it for themselves and plans to destroy it to prevent it from falling into the wrong hands. However, their mission is complicated when the artifact is stolen, and they must pursue the thief to Kyoto, the capital. When they arrive, they find that the government has been overthrown, and the deity Susanoo now rules the city. The streets are unrecognizable, but their mission remains the same. They must reset time to save their nation from sinister forces threatening to take control.