Samurai Takasugi Shinsaku and his partner, Katsura Kogorō, search for a legendary treasure called a chronometer that is said to possess the power to manipulate time.

Once inside the giant castle Takasugi is confronted by one of the 12 commanders of Susanoo who has transcended through time; people are being oppressed by the shadow of technology for the advancement of civilization.

Takasugi joins up with Katsura, Sakamoto and Izo after making it out of Susanoo Castle; Sakamoto looks for a young man named Seimei who has the ability to travel through time like the chronometer.

Katsura swears that he will get back the chronometer from Mugensai and free the townspeople from their fear; Katsura's skills during a swordsmanship test impress Kondo, Hijikata, Okita and the others.

Sakamoto and Izo square off against members of the Shinsengumi; as Takasugi tries to find Mugensai, he happens upon the captive emperor.

Yoshinobu and Susumu are hiding in the Kurama temple with special agent Kasumi when they receive a message indicating that they need to find Seimei and hide him in a safe place.