Kotaro is a young orphan, seen in the opening scene being told by Father Shouan to run far away from the monastery. He finds himself being pursued by assassins sent by the Ming dynasty as well as the soldiers of Akaike. With no idea why he is being pursued, when he encounters Nanashi he seeks protection from him. His sole traveling companion until meeting Nanashi is his dog, Tobimaru.
His mother died at his birth and his father joined her not too long after her death.