The Susanoo Incident unfolded in the capital of Kyoto and ended with the death of the masked shogun, Mugensai. Having finished visiting the grave of his former master, Yoshida Shouin, Takasugi Shinsaku and his partner, Katsura Kogorou, return to Kyoto once again.
Suddenly, the earth trembles and the sky splits open, and the chronometer, which was supposed to have been destroyed, appears from a rift in space-time. Now with a will of its own, the chronometer starts going on an uncontrollable rampage!!