JC and Nina are called into the office of the chief of detectives after 6 months of being off to deal with the deaths of Macnamara and Torres. They are assigned to the Special Investigation Division. Along with new detectives Alec Stone, Nell Delaney, and Lt. Malcolm Barker they go after armored car robbers. During the investigation JC and Nina find out they have been recruited to go after Nadine Jordan, the women who killed Macnamara and Torres.
After a model's drug overdose, Williams and Barker pose as publishers of a new magazine.
The unit goes after a Ukrainian kingpin who is using this "pipeline" to distribute cocaine, and causing massive deaths. But when the unit bust him, they find out that he is under diplomatic immunity and can't be prosecuted by the laws of the US. Under direct orders they are told that the case in closed. In secrecy under the order of the Chief of Detectives the unit goes undercover to shut down the "pipeline" once and for all. During the investigation, Nina considers giving up her badge if that means she can be with her daughter.
Missing teens prompt a probe of a private hospital's organ-donor program.
The detectives go undercover on Wall Street to foil a stock-manipulation scheme.
Delaney is torn between family ties and duty when her brother becomes the suspect in an arson case.
The detectives discover that the CIA is involved in a money-laundering scheme involving the killer of Moreno's husband at a bank in a Cuban neighborhood.
In order to uncover the detectives responsible for a series of killings, Williams and Delaney pose as uniformed cops.
Following the shooting of a nanny and a baby, Stone, Delaney, Williams and Barker go undercover to try to capture the weapons-suppliers.
The Special Investigations Division tries to track a serious serial killer who targets young men on the rave scene by giving them a tainted drug. During this G catches Nina and his dad together in bed.
Lt. Barker and the unit go after a leader of a criminal empire that is extorting money from several businesses in Manhattan. This case turns personal for Barker when he is reunited with an old flame and is treated like family by the target. Meanwhile JC and Nina try to find where their relationship is at after sleeping together.
Delaney poses as a bartender, in order to learn why three Irish terrorists were killed and why they were in America.
Nadine Jordan, the accused killer of Torres and McNamara has been convicted of their murders. She receives a life sentence with no parole which upsets Moreno. Meanwhile The District Attorney who prosecutes a radical terrorist by the name of Eve Flemming finds that his daughter is kidnapped and held for ransom until Flemming is released from prison. He receives a videotape of her tied up and crying for help. Barker devises a plan where they are going to play along to see where Flemming's people lead them to. One part of the plan includes Moreno going undercover as a fugitive to get close to Flemming. While undercover in the prison, Moreno finally gets the chance to settle the score with her husband and partner killer.