When the dead body of Karen Hall, an investigator with the State Attorney General's Office Criminal Division, is found in a Manhattan river, Detectives Briscoe and Green find that her boss, Frank Conroy, had written off her disappearance as a random kidnapping from an Albany train station. But as more is learned about Conroy's controlling relationships -- with the dead woman, with his wife and with a long-term girlfriend -- he quickly becomes a suspect.

The fatal stabbing of a man leads to the discovery of his status as a Vietnam war veteran and the truths uncovered about an incident that occured with him and three former soliders in his division.

A tenement building explodes and the lone victim is Joseph Haden. The building was rent controlled and there had been a tenant strike, so the police initially suspect arson. But the landlord doesn't have insurance, ruling out their arson theory, and the medical examiner discovers that Haden's neck was broken and he was tied up before the explosion happened. Trying to figure out Haden is even more difficult. He didn't appear to have a family or a girlfriend and never got any substantial mail. He worked at the Jiffy Job service station making minimum wage, yet had $90,000 in the bank. Briscoe and Green do some more digging and find out that Haden was using an alias, and his real name was Yusuf Haddad.

The discovery of a body in Hells Kitchen who had been wearing a $40,000 diamond ring leads the detectives back to the World Trade Center attacks as the victim had been reported to have died when Tower One collapsed. The ensuing investigation leads to a fiancee and a lover and the determination that the events of 9/11 may have been good timing to hide the fact that she was murdered the night before.

The death of a stockbroker leads the detectives to his girlfriend whose mother is a cosmetics mogul who has a long standing friendship with Branch, and will stop at nothing to protect her corporate image by using hormone replacement therapy withdrawal as the basis for her defense.

Briscoe and Green catch four murders and a kidnapping on the same day, and get handed confessions in each case.

When a con man passing himself off as a grief counselor is poisoned by a respected doctor he victimized, McCoy must determine whether revenge or insanity prompted the crime.

The investigation into a bar room brawl fatality reveals a detective's decades-old vendetta against a petty criminal turned murderer who was falsely accused of one murder after evading conviction on another.

The investigation into the death of a governor's wife uncovers a web of infidelity, greed, and corruption which forces McCoy to counter a defense based on a ground-breaking interpretation of spousal privilege.

Police and prosecutors go after a fanatical cult leader who encourages sex with children among her followers.

After Jeffrey Pope, a private military contractor, is found dead, suspicion eventually leads Green and Fontana to Robbie Howell, the younger brother of a man who died because of Pope's incompetance, and Kevin Boatman, Nick Howell's former co-worker who had witnessed the tragic events in Iraq.

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.