Simone visits his dentist who asks him for help with his daughter's drug problem. A rich man's son is found tortured and killed. The father blames his son's 'gay' lifestyle, and names a possible suspect, but Simone and Sipowicz uncover a different story. A young girl is reluctant to tell the truth, after an attempted rape. Russell and Kirkendall enlist the help of the girl's mother.
A shoot-out leaves 2 dead and a third injured when a drunk, off-duty cop witnesses an attempted mugging. The cop can't seem to get his story straight and angers ex-drunk Sipowicz. The cop's boss wants him to take the blame, but Sipowicz wants the truth. Russell has to take Simone to hospital when he becomes ill, during the investigation.
Simone's condition starts to worsen, requiring more tests. Sipowicz, Medavoy and Martinez investigate the death of a man found in the park, with his pants down. Sipowicz gets tetchy, over the lack of information from the hospital.
As Simone's condition worsens, Lt. Fancy makes a request to the Uniformed Officers to be aware of the need for a usable heart. Simone's colleagues have to occupy their minds with the case of an old lady found hacked to pieces in her apartment. Of her two sons, one doesn't seem to care about it and the other is too full of drugs to understand what has happened. Sipowicz's mood gets him into a fight.
Simone's recovery is hampered by a chest infection. The doctors differ in their opinions of which treatment to use. Sipowicz's ex-wife turns up at the station, drunk and asking for his help.
New squad member, Danny Sorenson, arrives and gets sent to a drive-by shooting, with Sipowicz. The rest of the squad, including Russell on her first day back at work, attend another shooting. The two incidents are related and cause friction between the two teams of investigators. ADA Costas asks Sipowicz to look into an old case she has reservations about.
Sipowicz and Sorenson are called to a robbery, where the aged shopkeepers have been beaten. The woman dies and Sorenson is affected. They hunt 2 black youths who were seen running away from the store. Russell and Kirkendall are sent to a 'Gentleman's Club' where a client has been killed. One of the girls implicates an ex staff member as the possible killer. Sgt. Dorning admits his doubts to Sipowicz, about an old case.
Confusion reigns as an off-duty cop shoots an undercover cop after taking a bullet in the shoulder. When the first shooter confesses to Sorenson, it triggers Sipowicz and Lt. Fancy to renew their own private little war. Russell and Kirkendall, meanwhile, are busy investigating another crime involving a member of the precinct staff. ADA Costas is still worrying over the death, in Ryker's Island, of a man she helped put inside.
Kirkendall's son witnesses a stabbing in a convenience store. Sorenson and Russell join forces to try and protect him from getting caught up in the 'system'. Medavoy and Martinez have to get their hands dirty to solve the killing of a vagrant with lots of enemies. Sgt. Dorning helps ADA Costas and Sipowicz with the Suarez case.
Russell is still struggling with the loss of Simone and enlists Kirkendall's help. ADA Costas looks for ways to get Freddie Asuncion and clear Luis Suarez's name. The whole squad is involved when a supermarket is robbed and an off-duty cop is killed. When the FBI and Internal Affairs become involved, it opens old wounds for Sipowicz and Sorenson.
A close friend of Sorenson's takes the law into his own hands when he confronts a groper on his bus route and puts his life in danger. A female tenant points the finger at a male tenant, when another female tenant is found strangled and beaten to death. Sorenson becomes her confidant in order to get to the truth.
When a man's body is found shot and dumped in an alley, Medavoy and Martinez have to calm the victim's angry brothers. Russell and Kirkendall get a confession to rape and murder while searching for a missing schoolgirl. The squad's PAA is missing and her friend believes he knows why.
When a dead hooker is found on a building site, her identification causes problems for Russell and Kirkendall. Sipowicz and Sorenson are called in to assist Lt. Fancy and Sgt. Dorning, who then find themselves in a dangerous situation. Russell gets a visit from an acquaintance of her late husband.
A 9 year-old girl is found dead inside a locked basement, the supervisor is the only key-holder, but he has an alibi. Sipowicz and Sorenson have to solve the whodunit. Medavoy and Martinez help an old man to trace the person who swindled him out of 8000 dollars. Sorenson's sister comes to visit him. Dolores father turns up at the squad room.
Sipowicz has a nightmare about his father and Officer Dorning. A Police Officer shoots a drug dealer but can't prove that the dealer was armed. Sorenson and Sipowicz use all their resources to help him. Russell and Kirkendall try to settle a dispute between a convicted mobster and his Polish neighbour.
Sorenson's private life affects the whole squad when his girlfriend turns up at the station. A body is found in a dumpster. The squad get a lead when the dead man's credit card is used.
Sipowicz and Sorenson have to find out who is responsible for a woman dying, after she was tied up during a robbery. The rest of the squad get involved in solving a truck hi-jacking. Information on the possible culprit comes from ex-detective Roberts, who also passes on a warning.
Ex-detective Mike Roberts is found dead, in an apparent suicide. John Irvine, the PAA, reveals his conversation with Roberts, to Sipowicz. The squad set up a sting to trap a suspect.
Officer Dornan disrupts an AA meeting, leaving Sipowicz no option but to involve Lt. Fancy. Dolores' father threatens to take action against Malcolm Cullinan and gets PAA Irvine into trouble. Sipowicz and Sorenson search for the pusher who supplied Mike Roberts. ADA Cohen continues to express his jealousy, over Kirkendall.
A man is shot dead in what his wife claims was a case of mistaken identity. Kenny Priest gives his evidence to ADA Costas, who has replaced ADA Cohen. Sinclair, Cullinan's lawyer, tries to goad Sipowicz.
Mike Shannon brings in a young boy who makes a confession to Sorenson. Sipowicz worries about his up-coming court appearance facing Sinclair. ADA Costas takes care of him. Dolores father attends the court hearing.
Sipowicz stays away from the squad and tries to come to terms with his loss. Evidence comes to light implicating Cullinan in more misdeeds and Sorenson turns to Sipowicz for advice. John Irvine is released from hospital, but is reluctant to return to the Precinct.