Lewis and Munch investigate the death of Andrew "Monk" Whetherly, a member of the Deacons Motorcycle Club. Whetherly's wife, Bree, leads them to Preacher, the gang's warlord, who says Monk was killed "because he loved his little girl." The case is further complicated when Lewis is approached by an FBI Agent who is also investigating the Deacons. Deputy Commissioner James Harris enlists Pembleton to look into a delicate matter involving a congressman - with disastrous results.
Detective Douglas Jones, Russert's former partner, joins Homicide from Narcotics. Later, when Jones' wife Natalie is admitted to the hospital with suspicious injuries, Russert confronts Jones about possible spousal abuse. Pembleton prepares to testify against James Harris and the department, with his future and friendships hanging in the balance. Bayliss, Lewis and Munch finally open The Waterfront Bar.
Detectives Howard, Bolander and Felton are shot during an ambush and left in critical condition. Pembleton feels obligated to get justice, Munch becomes traumatized and shocked, and Giardello faces an investigation of his work.
The Homicide Unit captures Glenn Holton only to learn that he wasn't the one who shot Felton, Bolander and Howard. Meanwhile Russert is forced to investigate Giardello's work to find out if he should be at fault for the ordeal.
The scene of the crime, Apartment 201, is searched and reveals that the occupant, Gordon Pratt, is a gun freak who once tried to be a cop. A possible suspect is apprehended, but lack of a weapon gets him released. Later, Bayliss returns to the apartment building and is shocked to find that another shooting has claimed another victim. Russert and Howard declare a truce. Still recovering in the hospital, Bolander suffers another relapse.
Pembleton and Lewis investigate the random shooting of a woman, meanwhile Bayliss suspects Munch of going vigilante and murdering Gordon Pratt. Felton tries to get used to being back at work but finds getting around to be difficult.
Both Detectives Bolander and Howard return to work on the same day. Kay Howard obsesses over the relocation of her desk while she was out and refuses to assist Pembleton until it has been moved back, but changes her mind after the murderer unexpectedly walks in and confesses. Meanwhile, Bolander and Munch use the "good cop/bad cop" routine to solve the brutal murder of two elderly wealthy people. Bayliss & Felton tackle the case of a skeleton found by a dog digging in a neighbor's backyard, and Lt. Gee hopes for a promotion after leaking to the press the corruption of...
On the eve of his execution, the accused's daughter takes Col. Barnfather hostage, demanding a reinvestigation of the case to save her father. Bolanger, who had originally investigated the murder, discovers links to a recent suicide. BPD races the clock to get a stay of execution. Meanwhile an elderly woman's death in a bathtub leads to a poignant conclusion on a dance floor.
When Crosetti's caseload is to be distributed among the detectives, Howard's 100% clearance rate leads Giardello to assign her his most difficult unsolved case. Her partner Felton's obsession with finding his children causes him to lose key evidence; he turns to Russert for comfort. Bayliss, Munch and Lewis close the deal on the bar only to find that their troubles are just beginning. Giardello exhibits real emotions following a rejection by a friend of Russert's.
When Bayliss' cousin shoots a "crazed" Turkish young man at his door, Pembleton and Bayliss differ on motive. A Grand Jury is called to determine whether it is manslaughter or rightful protection of the home. Was it racially motivated--that is the question. Meanwhile, attempting to increase their bar business, Munch fires the French chef and Lewis hires his grandmother as cook.
Pembleton is oblivious to being relentlessly stalked by "The Gas Man," a man he sent to jail for negligence in a gas explosion that killed a whole family. The stalker steals evidence from a gruesome crime scene--the severed head of a Gypsy fortuneteller and a bloody knife. His plan is to force Pembleton to meet him alone and exact revenge.
The arson-murder scenes now include two teenagers, a boy and a girl, one of whom was killed before the fire. Barnfather agrees to another detective for the Homicide Squad IF they solve the arsons, and Giardello can choose his own candidate. Kellerman turns out to be an excellent interrogator and is offered the job.
Since Lewis has unsuccessfully been partnered with every member of the squad, the newbie (Kellerman) is assigned to him. Their first case involves the shooting death of an elderly lady waiting at a bus stop. A young man has captured the shooter stashing his gun, but he has trouble getting the cops to watch the tape. Howard has made sergeant and is trying to establish her authority in the squad, but irritates her colleagues. The climax is an arrest of the groom during a wedding ceremony.
John Munch and Kay Howard try to frighten a drug dealer into confessing to murder, by using his love of Edgar Allan Poe's works to their advantage. Meanwhile Munch's date with a beautiful colleague backfires when he meets her roommate.