Dr. Yukio Daitokuji (Masahiro Motoki) runs a popular medical practice in Tokyo in the late Meiji Era (circa 1910). He lives with his doctor father Shigefumi (Yasutaka Tsutsui), his sickly mother Mitsue (Shiho Fujimura), and his new wife Rin (Ryo), a beautiful woman with a mysterious past.

Rin's amnesia is the cause of some friction in the family, but Yukio is a decorated war hero and the practice is popular and things can only get better.

The house and surgery are near a slum, however, and Yukio is occasionally required to treat victims of the vicious slum children. The family is also disturbed by the uneasy feeling that someone is watching them, or in fact, living among them. At times, a noxious stench bothers them too. Shigefumi becomes obsessed with finding the source of the smell.

Rin starts to feel the presence of an intruder too, and goes to investigate one night. Drawn by the stench, she makes her way to Shigefumi's room but finds it empty. As she turns to leave, she comes face to face with Shigefumi's corpse. It stands behind the door, the face a rictus of terror, the mouth stuffed with mud.

After the funeral, Rin and Yukio sleep in Mitsue's room to comfort her. She talks of unfinished business, and remarks again on Rin's mysterious past. Later that night, Mitsue gets up and wanders off in a trance-like state. Rin and Yukio follow her, but Mitsue convinces them she's only going to the bathroom.

In the corridor, Mitsue sees a shadow. She watches in terror as a man, dressed in rags but with a face identical to Yukio, comes cartwheeling toward her. The man shows her a birthmark on his leg, then disappears. Mitsue dies from shock.

Soon after the strange deaths of both his parents, Yukio is disturbed one evening by the arrival of a slum woman and her child. Yukio hesitates to treat them, knowing that the child is infected with the plague. At the same time, the mayor is brought with a nasty wound. Yukio chooses to treat the mayor first, and urges the nurses to see to the plague victim. Rin upbraids Yukio for ignoring the woman and child but he gruffly dismisses her. The relationship sours.

One morning, Yukio goes for a walk in the garden where he's attacked from behind. Yukio gets a look at his assailant--and finds himself staring at his own face. The man half-throttles him and throws him down a disused well.

The assailant is Yukio's identical twin, Sutekichi (Masahiro Motoki). He calmly takes over every aspect of Yukio's life. By imitating Yukio exactly, Sutekichi succeeds in passing himself off without any suspicion. (He also closes the surgery for a while.)

Each day, Sutekichi comes to the well to throw scraps to Yukio and taunt him. Sutekichi sleeps with Rin, and baits Yukio about it. As Sutekichi taunts Yukio, flashbacks fill in the details of their tortured past. As a baby, Sutekichi had been cast down the river in a bundle. He was saved and brought up in the slums by a troupe of entertainers led by Kakubee (Akaji Maro).

There Sutekichi had lived a life of crime, stealing and killing with his lover--Rin.

After the particularly cruel murder of a young man (Tadanobu Asano), Kakubee banishes Sutekichi and bans him from ever seeing Rin again. Sutekichi vows to come back for Rin.

Abandoned, Rin turns to housebreaking, but she's caught in the act by a householder (Naoto Takenaka), and in making her escape, burns the house to the ground. Rin goes to the river to cleanse herself after the fire, and it's there that she first sees Yukio. He falls in love with her immediately, while she is confused by the transformation that she thinks has come over Sutekichi.

Back at the Daitokuji house, Sutekichi continues his impersonation of Yukio. Rin's memory returns slowly, and she starts to suspect that 'Yukio' is in fact Sutekichi. She tries to check the birthmark on his thigh--but Sutekichi evades her.

At the bottom of the well, Yukio gives up thoughts of escape and begs Sutekichi for death. Sutekichi throws Yukio a knife and invites him to commit suicide.

That night, Sutekichi paints over his birthmark with makeup and shows it to Rin. She is now convinced that Sutekichi's spirit has returned to her by taking possession of Yukio's body. The imposture has succeeded.

Next day, Sutekichi goes to the well to confirm that Yukio is dead. He sees a corpse-like mound of rags at the bottom, but then notices the knife--by the side of the well. Suddenly, he's attacked from behind. With the strength of a madman, Yukio strangles Sutekichi to death. Sutekichi's dying word is simply, "Brother."

Rin, still confused and distraught by Yukio's cruel behavior, goes back to the river where she first met him and contemplates suicide. She wades into the water, and then turns round to see at the edge of the woods, Yukio, his clothes in rags, his face covered in filth, the very image of Sutekichi in the slums.

Later, back at the house, Rin cuddles a baby boy, the image of graceful, maternal bliss. Yukio prepares for his rounds. Outside the house, he's insulted by a beggar monk (Renji Ishibashi) but silences him with a look. Yukio walks out of the surgery, and followed by a ragged child, heads toward the entrance to the slums...