Theo and Nicole's evening out ends with an unexpected tragedy when Nicole is shot and rushed to hospital. With no reason for her to be the target of a contract-style shooting, the investigation is slow to develop. It is the discovery of a dead body at the bottom of a cliff that provides the crucial lead. The dead man, Lance Stiffner, was shot by the same type of gun that shot Nicole. It quickly becomes clear that Nicole was the victim of mistaken identity. The intended target was Nina Napolitano, who was having an affair with Stiffner. Her imprisoned husband found out and put out a hit on both her and Stiffner. The identity of the shooter is provided by a reluctant accomplice, and Joe and Theo are soon involved in a high-speed chase with their suspect. The chase ends when Joe draws his gun and shoots the suspect, believing to be in danger of being shot himself. However, upon searching the car, no gun is found. Was Joe mistaken or was it a case of cold-blooded revenge?

The police's Critical Response Team is brought in to investigate Lloyd Zuker's death. Theo lies about seeing Zuker with a gun to help Joe but his story doesn't hold up under scrutiny and lead investigator Frank Conti tries to get him to turn on Joe, threatening to charge Joe with murder and Theo with the attempt to pervert the course of justice. Despite the findings of Conti's report, Joe does have the Commissioner's support, but he's haunted by the shooting and is determined to find Zuker's missing gun and clear his name. Meanwhile, the detectives investigate the murder of a man whose body is pulled from a lake. Nicole comes out of surgery.