A young girl is abducted in broad daylight, and the only link to the girl is an ex-convict who wants a deal before he's willing to talk.

The deaths of three women with the same name lead Fontana and Green to the nine-year-old conviction of Leland Barnes, who had shot and killed his wife in an office full of people. With two of the three witnesses against him dead and Jack McCoy on the hit list, the detectives struggle to determine how Barnes, who has been in prison the entire time, got someone on the outside to kill the only people who could keep him in jail. The investigation leads them to Leland's two sons, with surprising results.

After the body of a teenage boy is found dead in a warehouse, detectives use DNA to connect the boy to a convicted rapist and serial killer, then to the boy's mother, Allison Ashburn, the convict's ex-wife. While trying to solve Danny's murder, Fontana and Green learn that he recently got his girlfriend Tina pregnant, and his mother had seen him recently when she had given him money despite having claimed she hadn't seen him for months. Allison finally admits that she murdered her son after the police arrest her new husband John, but claims she did it to save the world from her son, whom she was convinced would become a monster just like her father. Borgia and McCoy face an uphill battle trying to convict the perfect soccer mom.

The shooting of a local businessman is linked to a killing in Iraq, and McCoy and Rubirosa refuse to allow the killer to plead out.

A has-been actor wearing blood-stained clothing arrested for drunken driving reveals religious prejudices during his rantings.

After Michael Jones dies in his mother's hospital room with no immediate explanation, his mother Ashley accuses her former husband's adult children, Miles and Hillary Foster, who are fighting her for control of their father's substantial fortune. The autopsy rules out the Fosters, and points Green and Cassady in the direction of illegally harvested donor bones, which Jones had received in a transplant eighteen months prior. McCoy and Rubirosa struggle to prosecute the case after it becomes clear the only way they will get the evidence they need is to test another young man who received bone grafts from the same woman who had given Michael Jones his legs.

After publisher Serena Darby is found murdered in her apartment, suspicion turns to J.P. Lange, a former professional baseball player acquitted of his wife's murder who had written a book hypothesising how he would have committed the murder. Green and Cassady follow the trail of evidence from Lange to Gerald Stockwell, a former ghostwriter on the book, but Stockwell tries to clear himself by offering McCoy and Rubirosa proof that one of the jurors in Lange's trial was paid off to force an acquittal.

The explosion of a package including scientific research injures a pregnant security guard, leading to the investigation of the scientist's experiments.

A terrorist organization seems to be tied in with the violent death of an art dealer, until the victim's troubled son with ties to a fanatic religious group is investigated.

Internal affairs takes a special interest in Detective Green after a gambler is found dead by his bullet, and the investigation turns up a part of his past he's taken pains to conceal.