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.

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

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.

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.

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.

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.

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.

Technically it's not a homicide; however, Pembleton and Bayliss investigate the ""murder"" of a small boy who's the victim of a stray bullet, which makes him brain dead. The parents must choose what to do with their son. The Pope is in town.

All the detectives scramble to solve the case, when the mother, in a family on vacation, is murdered during a holdup. The husband has a hard time dealing with the reality of him not doing anything during the situation and Felton's indifference. When the suspects are found Howard is convinced that the youth who confesses to the murder didn't do it.

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.

A man transporting 72 condoms filled with heroin bound for Luther Mahoney is found dead in hotel. The department takes this opportunity to set up ""Operation Get Luther."" The operation almost goes off as planned, except Luther Mahoney gets Lewis' gun and is holding it on him as Kellerman and Stivers enter. Frank and Tim agree to become partners again. Tim stops by to see his uncle. Munch takes a call from a convict who was looking to talk to Bolander. He has information on an old murder case that should be a done deal. That involves the digging up of section C of the parking lot at a racetrack. Munch discovers that the supposed victim is alive; however, he isn't that way for long.

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.

Bayliss suffers from a recurring dream about the Adena Watson, his first homicide case and one that remains unsolved. An elderly man comes to the Homicide unit to confess to Bayliss that his father had committed a murder 66 years ago. Falsone is assigned to the case, only the case file is missing and found to be in the possession of retired homicide detective, Thomas Finnegan. Gee allows Finnegan's request to participate in the reopened investigation. Questioning the elderly man leads to the recovery of the gun that might close the case. Falsone, Finnegan, Lewis and Kellerman celebrate their potential victory as Bayliss recontemplates the Watson case.

Sheppard and Bayliss await the trial of Luke Ryland, the Internet killer. A number of delays keep the hearing from being held; the last time it is because Danvers can't make it due to being held up in another trial. Because of a technicality in the law, Ryland is set free. Bayliss is outraged and winds up pushing Danvers, who later threatens to put Bayliss up on charges. Gee's daughter Teresa arrives, to help with the celebration of her father's promotion. Gee asks Bayliss to apologize to Danvers and Bayliss declines. Lewis and Falsone look into the murder of a drug addict whose husband looks like the most probable suspect. The victim's mother-in-law isn't very cooperative and her sister is a nun who thinks her brother-in-law is an architect. Gee worries about whether or not he will be able to perform in his new role as Captain of the property crimes division, later he turns down the promotion. Bayliss and Lewis have words about the way each other handle their memories of the past.

Emmet Carey is holding his two children hostage in the apartment of his wife's sister. He sees MGee on television and decides that he will talk only to him and occasionally Gharty who is also on the scene. The wife also shows up on the scene and gets past the security. Her screaming sets of Emmet, who fires two shots out that window that strike his wife dead. MGee has to keep the information from him as they continue to negotiate. The crisis ends when Emmet releases his stepdaughter, but makes a deadly choice for himself and his son.

A convict is released from prison and begins to get his revenge on Frank by frustrating the investigation he is currently working on and also by terrorizing his wife.

The entire squad is put on 24-hour surveillance when a mass murderer has been identified, isn't at home and doesn't know that they know. Gee debates leaving the squad in the midst of the stakeout, so he can attend his daughter's wedding in California. As the detectives rotate through shifts on the stakeout, the main topics of discussion are the homeowners and Bayliss' plans to leave the unit.

Lewis and Kellerman investigate a series of homicides that put them into the middle of a drug war. Kellerman suspects that Lewis is seeing someone, but he doesn't ""kiss and tell."" As the red piles up on the board Gee gets edgy. Kellerman seeks comfort from the godmother of the daughter of the victim's family. Kellerman and ""Drak"" have a confrontation. At a ""Peace on our Street"" demonstration, the current drug war is ended.

The homicide team pulls the graveyard shift on the hottest night of the year. Bayliss is consumed by the Adena Watson case, driving a bigger wedge between him and partner Pembleton. Giardello finds a baby in a cage. A renegade Santa Claus runs loose in the building and the whole squad tries to figure out who's responsible for a candle that keeps getting lit.

The squad returns to the station. The FBI joins with the detectives to stop a ""thrill killer"" who's working his way north on I-95. Gee tries to reconcile with his daughter. The killer smells a rat at a roadblock so he bails out of his pickup. Everyone mobilizes to find him and when they do, the suspect in custody, while identical to the killer, claims he is innocent.

Their rotation in robbery is up, Frank and Tim return to the homicide unit. They find that citations are being handed out to the unit and a delighted Gee, whose clearance rate is the highest it has been in five years. Kellerman and Lewis are also scheduled to return. Howard is still on assignment with the fugitive squad. Additions to the unit through rotated assignment include Det. Ballard who actually comes from a Seattle homicide unit, Det. Falsone and Det. Gharty. Falsone and Gharty worked with the unit on the Felton case last spring; however, nothing is mentioned about the status of that case. (Sharp-eyed viewers note that Felton's name is still in red under Pembleton's name on the board.) Meanwhile, Gee attends a black tie function honoring Felix Wilson, a respected member of the community. Because he grew up with them, Gee sits at a table with Felix, his wife and their family. Everyone attending the function at the hotel is kept late because the body of a woman is found dead in t

Debbie Straub signs the plea agreement, pointing to Craig as the killer of the baby. Falsone wants more time to work on the case. Danvers reminds Kellerman there was a time when the truth mattered more than his paycheck. Gharty goes off when Sheppard and MGee ask to many questions about Kellerman's leaving of the homicide unit. Kellerman appears to begin doing the right thing, but doesn't pass anything on to anyone who might be able to do anything with it. Craig believes that Debbie isn't going to let him down and he has no plans to testify on his own behalf. Ballard searches for a dinner date when Falsone leaves a message he won't be joining her. When she sees him in the Waterfront later, she lets him know how she feels about his method of communication. The case goes to trial, Debbie testifies that Craig killed the baby; with no evidence to the contrary, the jury finds Craig guilty. Falsone talks with Craig about what really happened; however, it is all to no avail as the following m

A riot breaks out at the prison, where two inmates are killed. The squad goes to the scene, but Frank must still stay behind. Bayliss, Lewis, Kellerman and Howard interview the inmates; many of them have familiar faces. Frank works on his target practice. Bayliss thinks that one inmate really wanted to tell him something, so he puts together a deal to get the information. The inmate confesses to the murder and Bayliss doesn't believe him. Another riot breaks out and the truth is finally discovered.