When the winner of the city's Good Samaritan Award is murdered, Gee and his staff are called to help the new female night shift commander. Pembleton is at odds with the detective he shares a desk with. Beau and his wife separate and Kay gets caught in the middle. Meldrick and Munch have plans to buy a bar and try to persuade Bolander to also become a partner. Bayliss agrees to become a ""silent"" partner. In passing, Crosetti is said to be in Atlantic City on a ""shots, slots and sluts"" dream vacation.

Bayliss continues his relationship with the artist, but she's told her boyfriend. When she tells Bayliss that her boyfriend hit her upon hearing the news, it makes Bayliss so mad he confronts him. Pembleton and Bayliss investigate the death of a woman who's received a delivery of fresh flowers, although she's been dead over two weeks. Bolander and Munch investigate the shooting of Thorne's source, who's linked to a cocaine cartel, then Thorne is shot. Gee tries to get the department to get him a replacement for Crosetti. Thorne's daughter decides to keep his newspaper going. Beau tries to find out where his wife has moved the family. With Meldrick and Bayliss' disagreement over the artist, Munch is left without partners for the bar. Bayliss goes over the edge when the artist dumps him, so he holds up a liquor store for 11 cents; Pembleton gets him out of it.

After uncovering the fact that an elderly woman's tongue was cut out, Kay decides it is time to take a vacation. She returns home and while she is there she looks into the murder of an environmentalist. The suspects include her brother, an ex-beau and their co-worker. Pembleton reluctantly becomes Felton's partner and they finish investigating the murder of the elderly woman. Munch is against having a television put in their bar.

The deputy commissioner invites Pembleton to lunch and gets him to investigate a case involving a congressman. Beau hires a private detective to find Beth and the kids when his clue that they are in Wilmington falls through. Howard and Felton investigate a case of a dead homeless man. Their job is made more difficult when they can't find the body. Lewis and Munch investigate the death of a motorcycle gang member. Pembleton finds out the truth, participates in the cover-up and then resigns when the media gets hold of the real story and the deputy commissioner doesn't back him up.

Pembleton receives an extradited prisoner from New York City Detective Logan. Bayliss is put in charge of investigating the death of Gordon Pratt, but gets no cooperation from anyone on the force. Beau wants to return to active duty. A woman recognizes Munch from an old picture that is hanging in an art gallery across from the precinct. To Munch's embarassment he discovers that an old girlfriend, who's a photographer, is displaying an old picture of him in the buff at her gallery showing. Pembleton and Meldrick investigate a random shooting of a woman, and they clash over where the weapon may have been fired. They also find a woman who's shot her boyfriend and stuffed him in the freezer. Beau accompanies Gee on an investigation and must come to grips with his inability to look at a dead body the same way.

The fire investigation continues. Bayliss' back is acting up and Kellerman is paired with Pembleton. Kellerman shows Gee something, so he is offered a transfer into the department that he first rejects. Kay takes the sergeant's exam, Munch misses it due a ""comedy of errors.""

Lewis and Kellerman interview a suspect and uncover a 10-year-old crime, which is assigned to Howard and Munch. Tim lets Frank's secret about Mary's pregnancy slip out. Howard and Munch find the body from the 10-year-old murder bricked up in a wall. John has a date with Alyssa, the ME, but finds himself in bed with her new roommate before their date, so he begins avoiding her. Howard and Munch's murder suspect has a fascination for former Baltimore resident Edgar Allan Poe. Munch plays up that angle while trying to break their suspect.

Russert and Munch are assigned to work a case together; they find a retired cop who was murdered near his wife's tombstone. The dead cop's son asks Lewis, whom he went to the academy with, to get involved with case. He also makes his own inquiries, which get him into a bit of trouble. A suspect is arrested; however, despite the overwhelming evidence against the accused, the jury acquits him. The son contemplates delivering his own justice.

Mary gave birth to a girl named Olivia; Tim is more excited about it than Frank. Their latest case involves a multiple shooting a restaurant. Lewis is back from his honeymoon, but while working a case with Kellerman, he confesses that they have yet to consummate their marriage. Later he tells him that they've separated. Tim stops by to see Frank and Mary's baby. They get a suspect for their case in the box. Frank collapses in the box while interrogating a suspect. Frank is put under the knife to release the pressure built up in his head from the stroke he had. After the surgery the doctor tells them that he doesn't know if Frank will recover.

More drug-related homicides are occurring. Pembleton is still relegated to desk duty and now so is Kellerman. A federal grand jury investigation is being conducted that goes back to the time when Mike was in the arson unit. Frank is still not taking his medicine and getting ready for the range test. Brodie moves out of Munch's place and into Bayliss'. Lewis finds out that the witness to his drug homicide has been brought downtown. He goes after him and meets Stivers, a female detective in narcotics. Lewis's witness points toward Luther Mahoney as the initiator of the contract. They go to find the executor, who's been executed. Stivers pages Mahoney and he comes in for questioning, but they can't make a case that Danvers thinks will stick. Frank misses a passing grade on his test by four points.

On New Year's Eve, the detectives sit back in the quiet of the evening and watch a documentary that Brodie has made about them and their work. In this documentary, entitled ""BACK PAGE NEWS: Life and Homicide On The Mean Streets Of Baltimore"", one of Frank and Tim's cases is covered where some ""lies and hidden truths"" are revealed. During a sequence about one of Mike and Meldrick's cases, they chase a suspect right into the filming of something called ""Homicide"" by director Barry Levinson and his crew. Mike and Julianna agree to try a date. Also, the identity of the ""lunch bandit"" is revealed to be Gaffney. Brodie reveals that the documentary has been sent to PBS and gives his reasons why. As the new year rolls in, things return to normal as the phones start ringing.

A woman that Munch had a crush on in high school is found murdered. He struggles with his faith as he works with Kellerman on the case. Meanwhile, Frank also struggles with his faith and the fact that Mary has left him.

A man falls between the cars of a subway train in front of horrified witnesses. Was he pushed? While the man is still alive, the prognosis is he will be dead the moment they extract from the position he currently occupies: pinned between the train and platform. Homicide is called in light of this condition and the fact he may have been pushed. Pembleton questions the victim, and Bayliss questions the witnesses, especially a strange one named Larry Biedron. The victim has no relatives in the Baltimore area. He does have a girlfriend who is supposed to be jogging in the area; Lewis and Falsone try to find her to bring her to the scene.

A slightly intoxicated man (driving with his wife) aggressively whips his car around a state-owned truck; the offended truck driver rams their car; their aggression results in a collision where both drivers die. The man's wife is in serious condition. Kellerman and Munch investigate this case. Falsone gets prepared for the final hearing in his bid for custody of his son. Meanwhile, the other detectives investigate the death of a man who made a mobile phone call from the coffin in which he had been buried alive. The coffin was buried in the parade ground of an old spy school. The victim might have remained alive if the lid hadn't been sabotaged to collapse. In the car / truck collision case, Cox's boss wants her to ""verify"" the results of the car driver's blood alcohol level to help protect the state from serious litigation. An old Russian friend of Gee's furnishes them with information that leads the detectives to the discovery of a group of men who couldn't make it as spies. (They cal

Ballard and Munch catch a case involving the death of a prominent businesswoman. Pembleton and Bayliss catch a similar case. Both deaths might be the suicides they appear to be, but as the detectives begin their investigations the facts reveal otherwise. Lewis attends his disciplinary hearing and receives his punishment and is allowed to return to duty in the Homicide unit. Falsone and Lewis investigate another Mahoney related death. The situation within the Mahoney organization may be getting out of control as jury selection begins in the civil suit. The judge dismisses the civil suit, just as he told Kellerman tbat he would. Kellerman confronts him after the trial about the FBI's investigation in front of several witnesses. Bayliss joins Ballard for dinner and he reveals some of his secrets.

MGee (Mike Giardello) and Ballard investigate a double shooting at the home of a prominent sports doctor and his wife, a dermatologist. The doctor (who was wounded) did not realize the deceased (thought to be a prowler) was his sister-in-law. Munch contends with the IRS; his Waterfront partners want him to make sure that his cousin, their accountant, has been paying their taxes. The Waterfront needs a loan to pay for some improvements. Gharty has taken the day off, to take care of personal matters, like his recent separation from Flora. Munch has his hearing with the IRS; he owes $30,000 in back taxes. Bayliss and Sheppard discuss his sexuality and the possibility of a date. Falsone takes MGee and Ballard to meet an old fight man who knew their doctor. Ballard becomes excited while watching Falsone spar in the ring. MGee and Ballard's investigation lead them right back to the doctor's house, where his wife may be guilty of conspiracy to commit homicide. Gharty stops by the Waterfront t