The detectives are called to investigate when a girl's body is found in a duffel bag outside of a church. The victim, Marnie Foster, was reported missing the previous day. Evidence suggests that Marnie was sexually assaulted, but since no DNA was found, the penetration was done by a smooth object.
Dr. Huang is away in Washington, so the team enlists the services of Dr. Cap Jackson, who notes that the killer still had some empathy for the victim, as they made sure Marnie was comfortable. A doll was placed with her in the bag. The autopsy reveals that Marnie was given sleeping pills so she didn't suffer pain during the assault. The killer didn't wish to murder Marnie; they might have taken the girl's life because they didn't want to get caught.
According to Marnie's mother, the doll is not Marnie's. In fact the doll hasn't been made since 1989. As Benson and Fin head back to Marnie's home, they spot the girl's mother (Susan) arguing with a man. The man, Chet Hadler, had an affair with Susan. Chet actually has a police record, getting arrested for forcing himself on his previous girlfriend's daughter, and for suggesting that they have a threesome together. Chet has an alibi. Susan was with him at a hotel the night Marnie was killed.
Cap wonders whether the killer is a woman, but Benson and Stabler dismiss the suggestion. Female rapists are extremely rare and female rapists who kill their victims are even rarer.
Benson and Cap have a conversation over coffee, with Benson giving her condolences for the death of Cap's daughter. Benson also asks whether Cap plans to reopen his clinic, but Cap explains that he lost credibility with his colleagues for cooperating with police and breaking doctor/patient confidentiality.
Cap thinks that the tenderness that the killer gave to the victim suggests that the perp is a woman, and probably was abused as a child herself. Maybe the doll is a totem for the killer's lost innocence.
The detectives start to focus on the other adults in Marnie's life, which leads to her piano teacher, June Frye. June and Marnie seemed particularly close, and June is devastated with news of her young student's death. June explains that both her parents died a long time ago.
Evidence suggests that June may be connected somehow with the murder. Cap speaks with June, who finally agrees to allow him and the detectives to take a look around her brownstone. Cap discovers some doll's hair on a pile of sheet music, and Benson finds pillows which match the pillow found in the duffel bag with Marnie's body. Luggage which matches the style of the duffel bag is found in the garbage outside of June's house. None of this is hard proof, however.
Cap interviews June, who says that her mother was the one who first taught her piano, saying that it was where she could find perfection in her life. When June asks for a lawyer, the detectives have to make Cap stop questioning June, otherwise everything else she says can't be admissible in court.
Cap goes back to June, explaining that he can't talk to her anymore with a lawyer present because she asked for one. However, June doesn't want to stop talking, waiving her right to a lawyer. As the detectives explained, it's legal if she changes her mind afterwards. June continues to talk about her past, with her father being the one who gave her the doll. Her father sexually abused her when she was 7. June confesses to giving Marnie the milk and the sleeping pills, and then sexually abusing the girl and placing her body outside the church.
The detectives focus on the rest of June's students, most of whom have only good things to say about their piano teacher. One student says that she saw June arguing with an older lady outside and was acting strangely. The student tried to speak with June, but she was ignored. The older woman is June's mother, Elaine. Cap explains that June lied about her mother being dead because she wishes for her to be dead. Her mother covered up the sexual abuse June suffered from her father and didn't do anything to help. Elaine appears to be the killer.
Benson and Stabler talk to Elaine, and Elaine is surprised to hear that June claimed that she was dead. Elaine remarried after leaving June's father, but says that her second husband was as useless as her first. The detectives then say that Elaine killed Marnie, then enlisted June's help with the body.
Suddenly a young woman enters, Elaine's daughter by her second husband, Katie. Katie is Elaine's alibi, saying that she dropped her mother off at a bridge tournament during the time of Marnie's disappearance. When Katie denies having done anything wrong, Elaine verbally abuses her, which causes Katie to run off and hide in a closet.
Stabler and Cap go back to June, and they tell her that they know she didn't kill Marnie. Katie comes in, demanding to know why June betrayed them by telling everything to the police, but June didn't say a thing. June is sorry that she left Katie alone with her mother.
Katie recounts the day Marnie was taken and killed. Katie wanted to go over to June's house, and so June cancelled her piano lessons for that day, but Marnie, who didn't get the message about the cancellation, was there waiting for June. Katie took Marnie, drugged her and molested her. June then came home and helped to get rid of the body.
Benson explains to June that Katie will most likely go to a psychiatric facility, but that their mother will have to go to court to address the crimes she committed against her two daughters. June feels like she can't forgive herself for what happened to Marnie, but Cap thinks that he can help her.