The detectives try to link the suicide of an Argentine immigrant to her husband who has a history of violence. While the subsequent investigation is not successful, they discover his hatred might be linked to a string of unsolved murders with the same MO.

The daughter of narcissistic psychotherapists takes desperate measures to exact her revenge for years of their abuse and neglect, leading to tragedy for a young man caught in the web of her parents' promiscuity, mind games and competitiveness.

When Goren and Eames search for a jewel thief who murdered her accomplice, they discover that the clever larcenies are the brainchild of her lover, Nicole Wallace, Goren's long-standing nemesis. As the detectives delve into the personal and working relationships between the two women, they uncover a plot to cause the death of Wallace's ex-husband, the only person who can lead them to evidence of the very first murder Wallace committed.

Goren and Eames are frustrated when the law has no provision for the arrest of a man whose abusive control of his family and neglect of his severely depressed wife led her to several murder-suicide attempts which he did nothing to prevent, and eventually resulted in the deaths of three of his sons.

When a young woman is shot at an appointment she never should have been at, Goren and Eames investigate her death and learn she had received a kidney transplant a few years earlier. Initially they believe that Vanessa Nikos may have been killed so that her organs could be harvested, but soon learn that her death was more closely connected with the organ she initially received from living donor Boyce Wainwright. When her shooter, also awaiting an organ transplant, is also found dead, the police realise they're on to something.

It's open season in New York when not one but two powerful judges are executed. At first they seem to have no connection; one was a family court judge whose entire family was attacked, the other is an appellate court judge. After investigating the judges more thoroughly, Goren and Eames realise that their first set of suspects was simply a smokescreen, and there is a far more insidious threat. Their investigation leads them to a non-custodial father who has a beef with the court system.

After Aidan Grant, an employee for a local computer company, is found dead, Goren and Eames investigate, initially believing that Grant was murdered because of a business deal gone wrong involving biometrics, lip-reading, the company Ubicool and the military, but their investigations lead them to a young man named Robbie who worked in the office opposite Ubicool. Goren soon realises that Robbie isn't fully in control of his actions and suspects his therapist, Dr. Pynchon, of wrong-doing, but Carver wants them to get the answers from Robbie no matter what they need to do.

Logan and Barek investigate after secret service agent Paula Kendall is found dead in her home. Suspicion initially turns to the husband after detectives realize that it took him eleven minutes after a first failed attempt to get in touch with 911, and their investigation leads them to her husband's role in a proposed Indian casino. Logan and Barek are especially interested when it turns out that the 'witness' Paula was supposed to be meeting that night had ties to a local politician, Peter Bellingham, who also had ties to Kendall's husband.

Goren and Eames investigate a fire at St. Gerald's which led to the death of a Church employee and soon realize that an arsonist around town is targeting churches. Throughout their investigation, they realize that St. Gerald's was the arsonist's primary target, and clues lead them to Justin Reid, who had donated $100,000 to rebuild the Church, his step-mother Regina, whom they soon learn had seduced Justin when he was only a teen, and his half-brother Glynn, who works for a clean-up crew that had worked at all the churches that were burned down shortly after they were renovated. Deakins comes under fire when an e-mail surfaces that insinuates he got Martinez (from To the Bone) to lie about the Logan shooting by getting him a promotion. The e-mail is soon traced back to former cop Frank Adair (from Season 4, Ep. 22 - My Good Name), who is doing time for murder.

Det. Megan Wheeler teams up with Logan on an investigation involving the murder of a womanizer.

Captain Ross, Goren and Eames have their Thanksgiving plans interrupted when the deputy commissioner's daughter, a US soldier home from Iraq, goes missing. At the same time, Goren has difficulty coping with the failing health of his needy mother.

Terrorism is initially suspected after the body of a young Arabic diver washes up on the shore, but Goren and Eames soon learn that the victim was part of a trio of con artists that were working as salvagers for a wealthy local man.

Goren investigates when his nephew, a prisoner who's bipolar, claims that inmates are being abused to the point of murder.

Captain Ross loses his objectivity, and jeopardizes the case, when an old flame becomes a suspect in the disappearance of her husband and his lover.