The arrival of a new Chief Medical Examiner upsets Bayliss at first, but results in an old case's exhumation and correct determination as a homicide. The FBI investigation of Kellerman continues, increasing his frustration. The marriages of Pembleton and Lewis are tested, but with quite different results.
An article in The Baltimore Sun about an investigation of the arson unit upsets Kellerman. Munch catches the case of a woman whose husband discovered her dead in her bedroom and immediately suspects the husband. Brodie gets an offer to stay at Kay's place.
Survivors discuss, in a grief-support group, the circumstances of three murders one Saturday night in Baltimore: a girl strangled in an alley on her 16th birthday, a mother who dies as the victim of a carjacker who drives off with her 3-year-old daughter, and a man who was attacked in the Waterfront Bar in the presence of several uncooperative witnesses. One of the cases remains unsolved.
An outstanding computer genius at a prestigious prep school is found stabbed to death. The incident is believed to be racially motivated as he is one of only three black students. Bayliss and Lewis suspect a student whose protective mother is a powerful judge. Pembleton finally passes the firearms test.
On Pembleton's first case back, a divorced woman is found stabbed to death; her 10-year-old twin boys were shot in the head. He is convinced the boyfriend did it, but Bayliss believes it was the ex-husband. Kellerman is summoned to the Grand Jury. Once again a drug murder implicates Luther Mahoney, but the star witness is intimidated even while in police custody.
A robbery gone wrong kills Danver's bride-to-be while trying on a wedding dress. Once again Pembleton and Bayliss disagree on theories of the crime. Giardello tries to help Kellerman but runs into opposition; Kellerman is "comforted" by the new ME. Danvers confronts a jailed suspect with threats which has unexpected results.
A girl is found with a broken rib which punctured her lung and 26 belt buckle marks on her body. Pembleton and Bayliss question the mother and her live-in boyfriend after a social worker confirms abuse suspicions. Kellerman is exonerated by the Grand Jury but still feels tainted by suspicion. Bayliss reveals his own childhood abuse to Pembleton.
An Asian store owner, a war hero, tried to forbid dope dealers from operating outside his store. His killing leads detectives to Mahoney--again he is too "clean" to catch. Mahoney's parting shot to Kellerman throws the detective into a tailspin of depression. Lewis, his partner, follows up and tries to prevent another partner's suicide.
Pembleton and Lewis are assigned to the brutal murder of a wealthy woman. Each focuses on a different suspect: an angry talented art student from the projects and the woman's brother. A diamond ring with great sentimental value has disappeared from the victim's finger AFTER the body was found, which proves pivotal to the case.
When a police officer is found shot to death, Elizabeth Wu writes an article praising his dedication to the job. An informer calls her with a contradiction: the cop was shot when he demanded his money back in a dope deal. Her source later reveals that he was the shooter but claims self-defense. Meanwhile Kellerman's rogue brothers show up and he winds up in a jail cell with them. Lewis and Julianna to the rescue.
Two bombings near Valentine's Day result in two deaths with no apparent connections. Brodie finds a way to get a confession from a drug dealer who conned a victim into playing Russian Roulette with a fully loaded gun. The Pembletons' marriage seems to be disintegrating in spite of therapy. Lewis and Cox wait outside an office where a third bomb has been delivered.
Munch's high school love interest, Helen Rosenthal, is raped and murdered, leaving Munch and Kellerman trying to solve the case. Grief and 1960's nostalgia engulf Munch, and meanwhile he connects with Helen's mourning daughter.
Chris Thormann must confront the fact that the assailant who shot and blinded him is up for parole, and he might get it. Pembleton and Bayliss investigate the murder of a chef, and the family's background of abuse triggers bad memories for Bayliss.
Autopsy reveals that the death of a recent arrival from Europe was caused by a burst baggie he had swallowed, one of over 70 bags of heroin found in his stomach. Luther Mahoney MUST be involved somehow! Munch gets a tip from a con that a body is buried under the track at Pimlico, but eventually finds the "dead" man. The Mahoney problem is solved.
Just another midnight shift for the Homicide squad, with yet another shooting in West Baltimore. But this time there is a witness who is naming names. And at 4:00 a.m., why are Col. Barnfather and Capt. Gaffney taking such an active interest in the investigation?
Beau Felton's body is found. Was it suicide or murder? Was he part of a criminal operation or...? Megan Russert returns from France to help in the investigation. Pembleton discovers why Bayliss has been missing from the squad room so much.
Felton's murder investigation involves the whole squad plus Falsone from Auto and Gharty from IID (Felton had been undercover). Actually, Howard and Russert are shut out because of their personal involvement with Felton. Gharty and Falsone discover they have both had the same snitch and hone in on his possible role in the murder.