It is 1604, four years after the Battle of Sekigahara, perhaps Japan's greatest civil war. The people try to recover from its aftermath and enjoy the newly attained peace. Amid such times Yuya Shiina, a roughneck girl who earns money by capturing outlaws, mistakes a roaming and peace-loving medicine seller Mibu Kyoshiro for the legendary wanted man "Onime-no-Kyo." But she soon realizes that she is wrong when she sees that Kyoshiro is just a weakling. Nevertheless, she ends up capturing Kyoshiro anyway -- he is wanted for running off without paying for a meal. As they travel together Kyoshiro tries to help Yuya catch another wanted criminal. In the process Kyoshiro is cornered. Then he mumbles, "Here he comes," and the color of his eyes turn a deep red. He pulls out his sword which he had never touched before and suddenly, Onime-no-Kyo, the legendary assassin said to have killed one thousand men with this sword, is standing there.

Kyoshiro and Kyo: Two spirits in one body. Yuya is looking for a "man with a wound on his back" who killed her older brother. The two head to Edo together. One after another, samurai come after Onime-no-Kyo. Why do Kyoshiro and Kyo share the same body? Historical figures, such as Tokugawa Ieyasu and Oda Nobunaga, emerge in the story and the mystery of the two souls is gradually resolved.