Gaffney and Barnfather give Gee a hassle about the return of Frank to duty and the sudden departure of Russert to Europe. Bayliss and Munch are called to the scene of a homicide, where the victim, Mrs. Uba, was cooking breakfast and the only witness may be a male pig named Angie. Frank returns to work and Gee tells him what his limited duties are going to be and that he's called in all his favors and both their asses are on the line. The squad is called out for a hostage situation at a middle school.

Night has fallen and the crisis is no closer to being resolved. Gee demands that Barnfather make a decision. Frank continues to trying to adjust. Frank insists on going to the hostage scene. The identity of the hostage-taker is made when he demands that his pig be brought to the school. When the pig doesn't arrive in time, he sets a fire and seriously wounds a hostage (who later dies) and then becomes badly burned. Brodie takes issue with Munch's treatment of Pembleton. The paperwork gets completed and the hostage-taker is formally charged. Frank makes a decision regarding his recovery.

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.

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 new Chief Medical Examiner (CME), Julianna Cox, speeds into town. An FBI agent, Pandolfi, conducts interviews with the squad about Kellerman. Frank looks for way to celebrate his anniversary with his wife. The new CME arrives on the scene of a homicide that Lewis and Bayliss are working on, they lay down their respective ground rules. Bayliss' murderer confesses to committing another crime. Kellerman is worried by the ongoing investigation and takes it out on another arson officer. Brodie offers to make chili for the Lewis family but the dinner turns into a fight for Meldrick and his wife. From a suggestion by Frank, Bayliss and Lewis get the other body exhumed and checked out. Frank and Mary celebrate their anniversary. Bayliss gains some insight into the new CME.

An article appears in The Baltimore Sun about Kellerman and the other members of the arson unit who are under investigation. Munch investigates the death of women whose husband returned home to find her dead, cause unknown. He suspects the husband but Cox thinks differently. Pembleton tries to help Bayliss close the Lambert case. The article puts Kellerman on edge and he goes to Roland's office where he discovers Roland is a federal witness. This incident gets him suspended until he takes a polygraph test. Brodie gets an offer to stay at Kay's place. Munch presses his witness and breaks him but Cox's evidence still says otherwise. Kellerman takes the test and while waiting for the result tells Lewis the truth. Cox visits Munch's suspect in his cell. Frank reflects on his past and the future. Kellerman passes the polygraph, but so did the federal witness; one of them beat the test.

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.

Lewis and Bayliss investigate a homicide at a boarding school. Gee goes to Frank's house to pick him up for a trip to the gun range. Kellerman wants the investigation into corruption in his old arson unit to move along, but he finds out that all the real guilty parties have made plea bargains. Frank's firearm test looked promising. The tiny little voice in Bayliss' head tells him that McPhee Broadman might be their suspect despite the fact that his mother is a powerful judge in Baltimore. A student comes forward and confesses to the student's killing; however, the detectives aren't convinced he alone was responsible. Frank passes the exam and can return to active duty, but as far as he is concerned the real test is in the box.

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.

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.

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.

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

Kellerman is disappointed with his treatment in the press (or rather the lack of it). Back on the job, Mike gets his first case. There was a shopkeeper who was killed for chasing the drug dealers out of his corner. The prime suspect is Luther Mahoney. Frank tries to reconnect with Tim who is still resolved to no longer be Frank's partner. Mike is visibly on the edge, with all the pressures of the past months and his reputation tarnished, and agitated by the fact that Luther Mahoney may get away with another murder. Meldrick tries to talk him down, not anxious to lose another partner.

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.

A new Baltimore Sun reporter gets into the middle of Frank's investigation of the death of a county cop who was shot because of drugs. Gee likes her style. Mike's brothers, Drew and Greg, come to town, who want to take him and his boat to Miami to set up a charter service. Mike learns that they are on the run from a bookie that Drew owes $18,000. To pay that debt, they've stolen Babe Ruth's Baltimore uniform from another bookie with the intent of selling it. Lewis and Cox go in search of the Kellerman boys. They find them in jail where they spent the night after trying to return the uniform.

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.

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 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.

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.

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.

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.

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