The church asks that the public know the details of the murders. Pembleton has an interesting time in the box with a witness who has multiple personalities and is shown to be the killer, but before he can get a confession, her lawyer arrives and later she confesses on television. Pembleton begins to question his faith. Bayliss becomes a not-so-silent partner. Beau spends some time with his family and decides to end his relationship with Megan.

Crosetti's body is found and Bolander is the primary and he thinks the evidence points to suicide. If it is a suicide, there will be no honor guard for the funeral. Refusing to accept the death as a suicide, Meldrick launches his own investigation and tries to thwart Bolander's investigation. Bayliss and Pembleton make arrangements for the funeral reception. Pembleton has reservations about going into the church for the services. Munch works with his brother, an undertaker, to arrange for a coffin. The preliminary ME report shows Crosetti had a blood alcohol level of .25 and wide variety of anti-depressants, The verdict: suicide.

Russert's old partner joins the homicide unit, but she suspects that he is taking his work frustrations out on his wife. Pembleton struggles with his pride and domestic life as Gee and Bayliss try to convince him to return. Bayliss is partnered with Lewis and on the way to the crime scene gets the ride of his life. Bayliss tangles with a reporter. Beau is in Philadelphia with his kids. The bar has its grand opening.

Bolander, Munch, Howard and Felton all meet to serve a warrant, but Bolander, Howard and Felton are shot in an ambush. Pembleton becomes the primary in the investigation and is partnered with a detective who specializes in the psychology of their prime suspect: a pedophile. Stan's ex-partner Mitch Drummond offers his help. Kay's father and Beau's wife and the kids come to the hospital. A clerical error is discovered to be the cause of why the detectives went to the door marked 201, instead of 210.

The detectives continue chasing their only lead, the child molester. Munch is teamed with Stan's old partner. Beau has no feeling in his foot, but feels guilt about Kay's condition. Stan's ex-wife arrives in town, but has a hard time going to see him at the hospital. Barnfather and Granger want Russert to review Gee and see if he was negligent in his duties regarding the paperwork that led to the shooting. The pedophile is located and it is discovered he was responsible for the strangulation of a young boy, but not the shooting of the three detectives.

Tim's cousin shoots a Turkish exchange student and his partnership with Pembleton may be in jeopardy when they both stand on opposite sides of the case. Lewis hires his grandmother to cook at the bar.

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.

Jay Leno stops by the Waterfront Bar while in town visiting his cousin Mary; Munch and Bayliss don't want to bother him. A new year starts out with a clean board and Brodie begins his work taping with the detectives. A sniper takes the city hostage, threatening to and executing people every 8 hours. The sniper uses Hangman as a way to leave clues for the detectives. Bayliss is the primary and his back is giving him trouble as he worries about surgery his doctor wants him to have. To combat the pain, he keeps taking muscle relaxants. A suspect is found and cornered and he shoots himself before they can take him into custody. Russert gets demoted when Barnfather doesn't like the way she handled the investigation.

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.

A trash-talking radio talk-show host makes a proposal to his listening audience. Lewis announces to Kellerman that he is getting married today, then he throws up. He motivates the rest of the squad to help him with the final details as he is getting married ""tonight after the shift ends."" Kay brings her sister with her to the station. Since the whole squad is busy with Lewis' wedding, Gee takes Howard out to work the homicide of the radio talk-show host. One of his listeners took him up on his proposal. Munch is skeptical about the Lewis wedding; he thinks it's an elaborate practical joke. Bayliss and Kellerman vie for the attention of Kay's sister. Gee shoots and kills a potential suspect, but the suspect was in jail at the time of the talk show host's murder. The guy who fingered him admits that he did it as a joke. The wedding is no hoax. During the festivities Pembleton's wife goes into labor.

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.

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.

Pembleton and Bayliss have only twelve hours to grill their prime suspect in the Adena Watson case before they must let him go.

The search for Georgia Rae and the war against her organization begin. Stivers, uncomfortable with the whole situation tells Gee about the Luther Mahoney shooting. Ballard and Gharty begin to deal with their recovery. A lead on Georgia Rae's whereabouts is uncovered. During the assault on the building, Georgia Rae's body is found and Bayliss takes a bullet that would have hit Pembleton. Gee asks Pembleton to get to heart of the Luther Mahoney shooting that started it all. Pembleton and Falsone start with Lewis and then they move onto Kellerman. The truth about the shooting comes out and Kellerman claims sole responsibility, Pembleton asks him for his badge. To protect Stivers and Lewis from prosecution, Kellerman resigns. Feeling remorse for the hesitation that caused Bayliss to take a bullet for him and with Gee's plans to cover-up the truth about the Luther Mahoney shooting, Pembleton decides it is time to resign.

Judge Gibbons has been stabbed. On their way to the crime scene, Bayliss and Pembleton talk about a book that Bayliss is reading, then Pembleton wonders if anyone would ever write a book about their Homicide unit. A probation officer is murdered in a drive-by shooting. The FBI gets involved with investigation of the Gibbons death. Agent Bauer mentions to Bayliss that Kellerman's confrontation with Gibbons probably got the judge killed. He wants Kellerman clear of the case. A fingerprint lifted from the Gibbons' crime scene points to Georgia Rae's son, Junior Bunk. Falsone and Stivers get a lead on their probation officer shooting case. As Junior Bunk is brought in for questioning, he eyeballs a handgun being put in a drawer. Pembleton and Bayliss get Junior in the box and he is no longer able to be intimidated. While waiting to be transferred to central booking, Kellerman, Lewis & Gharty harass Junior. Slightly freed up to make a phone call, Junior gets the gun out of the desk and begi

Things begin to heat up between Pembleton and Gee over the alleged police brutality case and one of the suspects is an ex-lover of Kay's. Bolander meets a waitress who encourages him to resume his cello playing. Munch's girlfriend is less than enthusiastic when he surprises her with a new fish for her tank. Frank, in the box, gets the confession that Gee is looking for. Unfortunately, the suspect is anything but guilty of that crime.

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.

Gaffney allows a possible murder site to be washed down which causes Pembleton to go off on him. Russert takes Gaffney off the case and Pembleton is made the primary. Things get more complicated as a second victim is found. Beau tries to decide between his family and his relationship with Megan and he confides in Kay; his wife tries to reconcile with him. Russert wrestles with the media demands about the case. Something from Bayliss' past comes out when they try to get the liquor license for their bar. Bayliss goes to the liquor commissioner to work things out. A collector of the macabre comes in search of the victim's white gloves. A third victim is discovered.

A young man comes into the squad room and after getting their attention, tells the detectives that his brother has been shot. Pembleton is sued by the multiple personality serial killer, who states he violated her civil rights during interrogation; he is discouraged when the city agrees to settle out of court. Munch must attend an alcohol awareness seminar to meet a requirement for the bar. Lewis has ""love at first sight"" with a woman who makes models of crime scenes, but she has ""love at first sight"" when she sees Bayliss and he sees her. Later, they attend an art exhibition and have an unusual sexual encounter in her ""bed."" All is not well at the Felton household, when he returns home to a cleaned out house.

Pembleton and Bayliss investigate the shooting of a young boy. During the investigation, the mother of the victim meets the mother of the shooter in the aquarium. The shooter shows no remorse for the killing, although he shot the wrong kid. Munch, Bayliss and Lewis can't remodel the bar when they discover it's been classified a historical landmark. Then when they find out back taxes are due on the building, which shuts them down before they open. Beau finds out his kids are in Upper Darby, Pennsylvania, so he goes to find them.

Bolander has a relapse. The detectives sound off to the local news about the shooting. Apartment 201 is opened up and the occupant, Gordon Pratt, is a gun freak who once tried to be a cop. Russert and Howard declare a truce. They find the shooter, but lack of a weapon gets him released; later he is found with a bullet in his head.

Beau meets Megan's cousin, NBC's Tim Russert. Kay and Stan return to duty, after Stan undergoes a final test, and Kay finds her desk has been moved. They, like Beau, must both get used to the job again. Tim and Beau investigate the discovery of a skeleton found buried in a backyard. Bolander and Munch discover an unlikely suspect in the murder of a quiet elderly couple: their grandson. Gee exposes Granger, who used his relatives in some department plumbing contracts; the information is leaked to the papers, Granger is forced to retire. Barnfather is made colonel and a new captain is named, Megan Russert. The higher ranks of the Baltimore police department are now more politically correct, but Gee doesn't like it.

A 16-year-old murder case must be reopened when the daughter of the convicted killer holds Col. Barnfather hostage. Pembleton and Bayliss investigate an elderly man whose wife died of drowning in the bathtub. Gee and the newly appointed Capt. Russert clash over the handling of the hostage situation. Bolander, Munch, Howard and Felton must go to the archives to find the records of the case. Lewis meets a strange homeless man who's witnessed the suicide of a man who committed the original murder and the detectives race to overturn the previous conviction. A new ""old"" bartender tries to convince Munch to go with the latest rage, microbreweries. Bolander and Lewis try to connect the suicide victim to the man on death row.

Bolander and Felton are suspended for 22 weeks without pay for incidents related to activities at a police convention in Washington, DC. Howard plans to take the sergeant's exam. Pembleton and Bayliss are assigned to investigate the death of a body found at an arson. At the scene they meet an arson detective that clashes with Frank's working style. Frank hesitates chasing a suspect, and later we learn that his wife is pregnant. Munch also decides to take the exam, and when the wagering begins on who is going to pass, everyone favors Howard. While the detectives are debating whether the fire was set to cover the murder, another fire is started.