Tomasu was raised by his mother in a Hidden (a religious sect that worships a single god that forbids killing, and judges each man equally, regardless of rank) mountain village called Mino. Iida, a powerful warlord, has been finding such villages and destroying them. After returning from a trip out in the woods across the mountain one day, Tomasu finds his village on fire. He surprises the Tohan (Iida's men), and is able to avoid Iida's blade and even dismount him. He flees into the woods, hoping others have also fled. Two Tohan men follow him, but he is stopped by a stranger in the woods who kills one of the men, and cuts an arm off the other.

Tomasu's savior is Shigeru Otori, a beloved Lord of the Otori lands. During their journey back to Hagi, Shigeru's home, Tomasu (now known as Takeo) stops talking. He begins to develop super human hearing; he witnesses the affair between Shigeru and Lady Maruyama (the woman Iida wants to marry so he can get her lands).

Thanks to his super hearing, Takeo hears an assassin scaling the wall of Shigeru's home. He wakes Shigeru, and they are able to repel the assassin. He kills himself with a poison pill to prevent being captured. Shigeru has decided to adopt Takeo as his son. Soon after, a visitor arrives; he has the ability to be in two places at once, and can make himself look young or old. Takeo is not fooled by these tricks, but Shigeru's guards are. He is a friend, however, and a member of the Tribe (a secret society of people with supernatural skills); he has come to train Takeo (who is of the Kikuta branch of the Tribe).

Shigeru installs a nightingale floor (it is built so that it makes noise like a bird call whenever someone steps on it). It is revealed that Iida has one in his palace. Without stating it explicitly, we discover Shigeru wants Takeo to learn to navigate the floor silently so he can assassinate Iida.

Meanwhile, the story follows a girl named Kaede, who has been sent as a political hostage to a realm of the Tohan. She is extremely beautiful. One day, she is assaulted by a guard and she stabs him. Another guard sees what happened and he kills the man to protect Kaede's offense. It is decided she must marry. The first man chosen for her dies, however, so people begin saying that anyone who desires her dies. Iida decides to have her married to Shigeru to both take over the Otori lands as well as to have an excuse to bring him to Inuyama and have him killed.

Shigeru agrees to the marriage on the condition that Takeo is adopted into the Otori clan. Takeo, Shigeru, and Kenji journey to meet up with Kaede. Kaede gets to the meeting spot first and she is trained in sword fighting by her maid (a Tribe member). Upon arriving, she and Takeo see each other and fall in love. They arrive in Inuyama knowing that Arai (an ally of the Otori) has reclaimed some Tohan land and is marching that way. On the night he is meant to assassinate Iida, he is taken by the Tribe (they feared he would die in the attempt). Shigeru is then accused of being a member of the Hidden, and strung up to die outside the palace.

Takeo promises the Tribe he will join them if they let him go take Shigeru's body down. He, Kenji, and Kenji's daughter head to the palace. They claim Shigeru, but he is near death and he has Takeo cut his head off to return to the grave of his brother. He asks Takeo to bring Iida's head there as well. Takeo and Kenji return to the palace where Iida is about to rape Kaede. As he approaches, though, she stabs him in the eye with a needle, and then uses a dagger hidden under her mattress to kill him. Takeo crosses the nightingale floor to find Kaede standing over Iida's dead body. They have sex. He leaves to tell Kenji they must free Kaede. A battle breaks out, and Kaede helps Takeo fight his way out of the Palace. They return the head to Shigeru's grave.

Takeo stays at the shrine (gravesite) for some time, and when Kaede arrives he explains why he cannot marry her. The Tribe comes for him that night, and he leaves with them without incident.