Pembleton waits with anticipation for the phone to ring. It does and with Bayliss as the primary, they proceed to investigate the triple murder of a divorced woman and her children. Kellerman asks Brodie not to return to the boat. Lewis and Munch get a homicide that they can track back to Luther Mahoney. Bayliss and Pembleton disagree on who the primary suspect is in the murder. Mahoney's nephew wants to remain ""monogamous"" in implicating his uncle. Kellerman gets his summons to appear before the grand jury. Frank and Tim must work out the finer points of working in the box together again. Mahoney's hand reaches out from jail and silences his nephew; the case is a bust. Lewis lays down the law to Luther Mahoney in the Waterfront Bar. Cox finds Kellerman and his predicament intriguing and offers him some company, the night of his summons.

The episode was rated 8.04 from 27 votes.

Family members of murder victims (Widmer, Rath and Silvio) are in a support group where they discuss their feelings about the loss they have each suffered. Short-handed, Gee investigates the Widmer homicide at the Waterfront Bar. Bayliss' homicide is unidentified for 48 hours before she is identified as being Rath. Lewis and Munch investigate a car jacking at Federal Hill, where the mother is the victim and the 3-year-old daughter in the car at the time is missing. Meanwhile, Howard, Kellerman and Pembleton stay behind. Frank interviews the two witnesses that Tim had in for questioning and gets a lead on a suspect. Cox joins the support group meeting late; she is still coping with the death of her father.

The episode was rated 8.04 from 24 votes.

A girl complains to the desk sergeant about her father's abuse of her mother. Meldrick spends the night remembering Crosetti with the Chris and Eva Thormann. Chris reflects on his own memories of the shooting incident that blinded him, the shooter is now up for parole. Bayliss with Pembleton investigate the homicide of a man shot to death in his own house. The shooter, the murdered man's wife will testify, is their daughter. The case triggers a painful memory for Tim who goes to visit his Uncle George.

The episode was rated 8.05 from 21 votes.

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.

The episode was rated 8.10 from 21 votes.

Kellerman assures Lewis that he is seeking some professional advice; he also takes some time off. Lewis is assigned to work with Pembleton and neither is happy with the situation. Together they investigate the murder of a wealthy woman. They suspect the brother may have had a touch of sibling rivalry. Meanwhile, the brother insists that the police have stolen his sister's diamond ring. Mary tells Frank that she thinks they need to talk to a marriage counselor. Cox investigates whether the missing diamond ring might have been taken by one of her staff. She gets Brodie to help her add some video surveillance to the morgue. Mary asks Tim to be Frank's partner again.

The episode was rated 8.13 from 24 votes.

Brodie suggests that a classmate of his named Schack should be a suspect in the death of the student that Munch believes committed suicide. Frank and Mary meet with their marriage counselor and they begin to air some issues. Bayliss and Kellerman try to link together two deadly bombings. Schack attacks Brodie, but he can't prove it. He does offer a way to get Schack to admit to the murder. Frank tells Mary that he will agree to getting Olivia baptized. Mike connects the two bombings; the victims were both connected through the death of the Korean grocer who was murdered by a man who worked for Luther Mahoney. They suspect that there may be more bombs, including one at the courthouse where Meldrick and Julianna are waiting to meet with Judge Aandahl and Danvers, both of who were associated with the Korean grocer case. Frank arrives late to the baptism; Mary takes this as a sign and tells him she is leaving him for a while.

The episode was rated 8.17 from 24 votes.

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.

The episode was rated 8.23 from 26 votes.

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.

The episode was rated 8.24 from 25 votes.

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 episode was rated 8.30 from 23 votes.

There is a major police chase after an armed suspect, as he holes himself up in a row house that is the headquarters of ARM (African Revival Movement). The head of that house, a former cop, calls in a favor, high in the police department. Munch and Pembleton try to work the case as Bayliss seems to be missing. Their investigation seems to be thwarted every step of the way. Stivers' has second thoughts about what she saw at the Mahoney shooting. An attempt to serve ""Burundi"" Robinson an arrest warrant breaks out into a war between the police and ARM. Gee goes into the house to confront Robinson and finds out who and what he knows.

The episode was rated 8.33 from 24 votes.

Frank and Tim investigate the death of a young girl whose abused body was found by the side of the interstate. Brodie goes to an interview with a new potential roommate. Kellerman finally gets his day in court, where he is supposed to take the 5th amendment. Frank and Tim disagree with their pursuit of the investigation. Frank tries a different approach with the mother and she tells him the story-- only they won't be able to get a murder one conviction. Julianna comes down to the courthouse to offer Mike some moral support. He sees Connelly come out of the courtroom and thinks things are going bad, so he prepares to give it all up. However, his appearance before the grand jury doesn't go quite as he expected. Brodie walks out of the building with his new roommate. The detectives try to celebrate Kellerman's freedom, though he has different thoughts about the situation. Tim tries to come to grips with the child abuse he experienced in his past and also tells Frank he doesn't want to be

The episode was rated 8.38 from 26 votes.

Frank gets his first case as a primary-- unfortunately it is a case that involves the shooting of Danver's fiancée. Danvers is concerned about Frank being the primary and keeps throwing his opinions into the investigation. Danvers changes his perspective on the death penalty and also reflects on his past performance in many of the cases he's tried. Brodie continues to look for housing; the latest place he tried staying was the morgue. Kellerman is discouraged when it appears as though Cox may have only been looking for a one-night stand and nothing more-- so he takes a sick day. Gee takes some time out of his day to have a talk with Kellerman's former partners to see where they stand with him in regard to their testimonies to the grand jury. He also sees the Deputy Commissioner to see what can be done for Kellerman; what he learns instead are some truths about the Gaffney promotion.

The episode was rated 8.39 from 28 votes.

Mike and Julianna wake up the morning after a night of drinking and passion. The investigation into Beau's death continues; Howard wants to be the primary while Frank tries to maintain control. Gee asks her to step aside and let him do the job with a more unbiased approach. The investigation creates some unlikely pairings: Pembleton with Gharty and Bayliss with Falsone and Munch on his own. Meanwhile, Howard and Russert make arrangements for Beau's funeral. Lewis and Kellerman's investigation into a homicide is stalled; when Kellerman's hangover laden police work is shoddy. When it appears as thought the investigation is going nowhere; Kay demands to be put on the case. Gee refuses. Because of his bad day and finding Julianna drinking with someone at the Waterfront Bar, Kellerman suggests that they should stop drinking. Frank tries to call Mary; eventually they connect and reconcile; with Frank saying that he is willing to give it all up. They find out who killed Beau, but when they go

The episode was rated 8.52 from 23 votes.

Bayliss has disappeared again as Pembleton and Brodie make their way to the scene of a shotgun suicide. The victim appears to be Beau Felton. Gee's letter, including information gained in the ""Burundi"" case, begins to make an impact at the highest levels of the department. Frank returns to the department with the news about his case. Lewis goes off, wondering who is going to be next. Det. Falsone comes to the squad with news about why he thinks Beau Felton killed himself. Lewis and Stivers discuss the Mahoney shooting. Cox finds something interesting about the Felton case; she digs in deeper and the results change the case to a murder. Bayliss turns up the next day and disappears again to his Uncle George's place. Pembleton and Howard try to work with Falsone to find Beau's killer. Gee finds out that Beau had been working undercover for the past six months on the Cantwell auto-theft ring. Megan Russert returns from France.

The episode was rated 8.58 from 26 votes.

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. During the filming, Brodie also happens to capture the lunchtime bandit red-handed.

The episode was rated 8.63 from 24 votes.