Young assassins Azumi and Nagara continue their mission to prevent a civil war. In their hunt for Masayuki Sanada, who is protected by both an army and a dangerous clan, they meet Ginkaku, a person who shows a remarking resemblance with former friend Nachi.
Official Shogunate executioner Ogami Itto has been framed for disloyalty to the Shogunate by the Yagyu clan, against whom he now is waging a one-man war, along with his infant son, Daigoro.
The mother of a feudal lord's only heir is kidnapped by the lord. Her husband and his samurai father must decide whether to accept the unjust decision, or risk death to rescue her.
As police inspector Yamato Kansuke pursues a certain man in the snowy mountains of Nagano, a shadow suddenly appears in his field of vision. While he's distracted, a rifle bullet fired by someone grazes his left eye and causes an avalanche accompanied by a roar. Ten months later, Kansuke, having miraculously survived the avalanche, receives a report that a researcher at the Nobeyama National Astronomical Observatory has been attacked.
A sadistic Daimyo (feudal lord) rapes a woman and murders both her and her husband, but even when one of his own vassals commits suicide to bring attention to the crime, the matter is quickly hushed up. Not only will there be no punishment, but because the Daimyo is the Shogun's younger brother, he will soon be appointed to a high political position from which he could wreak even more havoc. Convinced that the fate of the Shogunate hangs in the balance, a plot is hatched to assassinate the Daimyo. The two most brilliant strategic minds of their generation find themselves pitted against each other; one is tasked to defend a man he despises, and has a small army at his disposal. The other is given a suicide mission, and has 12 brave men. They are the 13 Assassins.