The year is 1931, the 64th year of the Meiji era. The 15th Shogun, Yoshinobu Tokugawa, continues to wield absolute power thanks to complete monopolization of a special natural resource known as "Ryumyaku." Supporting the Tokugawa regime from the shadows are the deadly agents of the covert organization known as Nue.

Sawa confronts Jin Kuzuhara about the truth behind what happened to her family and her village, but before she can get real answers a squadron of the shogun's troops arrives to try and capture her.

Asahi is alive, but Sawa has seen too much to ignore the crimes perpetrated by Jin Kuzuhara in the name of the Tokugawa regime. Hoping to secure a brighter future for the girl she has adopted as a sister, the assassin once known as Yukimura takes up her sword once again...