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

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

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.

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.

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.

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

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.

The Wilsons go on television to offer a reward. The newspapers are making the Homicide unit look bad and Barnfather wants quick resolution to the case. The man (and his wife) who gave up Junior Bunk are murdered; Falsone and Lewis investigate. The only survivor, their young son, is brought in to find out what he remembers. His memories-- and a recorded phone message-- lead Stivers to believe a former member of the Narcotics unit is involved. The officer cops to a deal that implicates Georgia Rae Mahoney, though Giardella doesn't want to pursue that yet. Falsone's questioning of the Mahoney shooting leads Cox to doubt her actions at the time of the investigation. Incriminating evidence leads the detectives to Hal Wilson being their prime suspect. Frank goes to interview Felix and Hal Wilson; son and father confront some long-standing issues. Hal's confession is inadmissible in court, the Wilsons leave the Baltimore area, and the case remains officially open.

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

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.

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.

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 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.

The semi-nude body of a man is found in a dumpster outside of a restaurant. Bayliss returns Cox a pair of her earrings that she'd left at his place the night before. Disturbed by him doing that in public and while at a crime scene, she suggests they take some time off, instead they decide to break it off. The owners of the restaurant thinks that this murder might be tied to another murder (one that Munch is working). Lewis confronts Kellerman about the Mahoney videotape and the need to let Stivers know that she is also ""in the soup."" Lewis tells Stivers about the videotape, so she demands a meeting with Kellerman. Falsone confronts his ex-wife about getting to see his son more often; however, they argue and he plans to pursue getting joint custody. Kellerman decides that he will try to force Georgia Rae's hand, since he doesn't plan on doing anything corrupt for her anyway. Kellerman tells Georgia Rae that she can do whatever she wants with the videotape, he doesn't care. Bayliss decid

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.

Ballard and Bayliss are called to the scene of the mysterious death of a woman, whose body is found at the bottom of a forty-foot cliff. This victim was to be married the following morning. The two detectives work to determine whether the death was accidental or intentional (via murder or suicide). Meanwhile Sheppard and MGee begin investigating the death of a movie patron, whose body was discovered after the show ended and the theater cleared out. MGee mentions to Sheppard that his sister is about to have a baby, which means Gee is about to become a grandfather. Their investigation reveals that the movie patron was regularly loud and obnoxious and thus bad for business. When an overdose of a sedative is found in his bloodstream, the detectives question the theater owner, who was currently in litigation with the victim. Unfortunately for Ballard and Bayliss, their case remains unsolved.

A woman brings to the homicide unit her mystery-writer husband's videotaped declaration that his literary agent is responsible for his murder. Ballard and Gharty catch the case -- only there is no body or crime scene. Meanwhile, Munch and Bayliss investigate the death of an elderly woman that occurred during a break-in -- was it a homicide? Munch would rather leave for his weekend rendezvous with Billie Lou. Ballard and Gharty's investigation becomes a red-ball as they find evidence in the writer's office that a crime was committed. A break leads to the arrest of the literary agent and his accomplice, although Danvers can't guarantee a conviction. Falsone asks Ballard if she would like to go out Saturday night; just then the jury comes back. And a sharp-eyed juror insures that justice is done.

Bounty hunters shoot, killing the wrong man, as they enter a building where their fugitive---a man named Joe Errico---has shot at them (and subsequently gotten away). Gharty has vague memories of a drinking binge from the night before. Falsone and Stivers catch the bounty-hunter case. Sheppard, during her days with the fugitive squad, had dealings with the head bounty hunter. Gaffney stops Gee and MGee on their way in, Baltimore magazine wants to do a father and son piece, using the wine case as a focal point. Gee is not interested, especially about the use of the wine case. Gharty struggles as he tries to reconstruct the events of the night before. Munch is bothered by Gharty's stories of Vietnam and each grows to dislike the other - perhaps some competitiveness over Billie Lou is beginning to brew here. Bounty hunter P.J. Johnson, who was identified as the triggerman, is charged and placed in one of the holding cells, near some of his previously captured quarry. Within an hour his ba

Lewis is transported to the hospital, as is the passenger of the car that MGee hit. Gharty is worked up about women and finances, because he and Flora and their lawyers are going to be working out the financial details of their divorce. Gee & MGee are not interested in cooperating with the bounty hunters; however, Knoll is the only one who can get any information on the whereabouts of Errico from Errico's mother. She has promised to page Knoll when her son calls. (Joe Errico has gone south to Miami.) Knoll offers to pay the expenses of having homicide detectives go to Miami and work with him, but Gee declines that generous offer and sends his detectives separately. In Miami, Bayliss and MGee work with Knoll to capture Errico. Knoll offers to split the huge bounty with the homicide detectives, which they of course refuse. MGee decides that the best use for the bounty might be for the man whose wife had died from the injuries she sustained in the car accident.

When the men are nowhere to be found, Sheppard and Ballard team up to investigate the death of young girl, who's a teenage gang member. With the wedding one week away, Billie Lou asks for Munch's help with her neighbor's abusive boyfriend. After Munch approaches him strongly, the boyfriend retaliates by coming to the Waterfront and slamming Billie Lou's head on the bar. Munch claims he came on strong with the guy, because his ""testosterone riddled behavior"" was due to the celibacy Billie Lou imposed on him, to make their wedding night more special. Billie Lou wants to delay the wedding until the welt on her forehead goes away in about 3 weeks. After Sheppard and Ballard solve their case, Sheppard reminds Lewis that his problem with her is not going to keep her from doing her job.

Ballard is annoyed when she finds out that the fact that she had a date with Falsone is around the squad room. Munch has a doctor's appointment and he's not talking about it. Dr. Griscom calls on the homicide unit when he sees a number of deaths that are related by a poison named phosphozine. The FBI steps in on the poisonings and they put MGee in charge of a task force; they consider it an act of domestic terrorism. One of the victims was a priest; two others were his parishioners. Gharty suspects the communion wine. Following this idea, wine bottles are collected from churches around the city. A needle hole is found through one of the corks. A citywide canvassing of all places where wine can be purchased is launched. Gee disagrees with the bureau's policy of keep information from the public. One possible suspect is captured; however, strange as he is, he's not the one. Through an internal leak, the media is alerted and warns the public, sparking chaos. MGee suspects the source of the

Sheppard and Lewis investigate the death of a man who has a twin brother. Gharty talks about wanting to live his life; he and Ballard go to the hospital to investigate the death of a teenager. Bayliss has interest in Sheppard; later he seeks advice from Stivers, who tells him to get in line behind Lewis and Falsone. Lewis and Sheppard interview the remaining twin and his mother; she confirms his story and they try to point to the dead twin's girlfriend. Meanwhile the friend of the teenage victim in Ballard and Gharty's case confesses that his friend wasn't shot in Baltimore, but rather D.C.; he drove his friend back to Baltimore so their parent's wouldn't ""kill them"" for buying drugs in D.C. Gee hopes to get the case moved to D.C. Mike Giardello puts in for his FBI transfer, but the only openings they have in the area are for liaisons to local police departments. He interviews with Gaffney, who is so open to the idea, he can't wait to tell Gee. That's something Mike was going to wait f

Mike Kellerman's new vocation is private investigation, where the majority of the work involves catching cheating spouses. Falsone and Stivers catch a case where a newborn baby's body is found buried behind a motel. A young couple had checked into the room where the baby was delivered. The room was paid for using the girl's credit card. When they locate the girl (Debbie at home with her parents), she collapses and is brought to the hospital. The boy, Craig, is also located. Both say that the baby was stillborn; however, the autopsy reveals that the baby took a breath after it was born, so the death is ruled a homicide. Falsone notes that of the two, only the boy Craig seems to show any compassion for the baby. Kellerman meets Sheppard for a beer and tries to ask her about Falsone's baby case, later he asks around the squad room. Kellerman is hired to conduct his own investigation by the girl's defense team. Gee demands that Falsone and Stivers find convicting evidence before Kellerman

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

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.

In Stivers and Falsone's case, a man is found shot dead in his bed, with no signs of a struggle. Gee lobbies Barnfather to find a way to get them the ability to have some control over their FBI liaison, so they don't experience the same problems they had with the Janine McBride case. Barnfather lets Gee know that there is Captain's position opening up and he should be inline for it with no catches. Lewis lets Ballard accompany him on a bar stabbing, when she accuses him of being afraid to work with a female, since the incident with Sheppard. While she does get to help him with the initial investigation, Lewis manages to work the rest of the case on his own, leaving her to handle the details. Meanwhile, Ballard's usual partner Gharty spends a ""mental health day"" at the Waterfront Bar, drinking and proposing to Billie Lou. Stivers and Falsone discover their victim had a bad breakup with his ex-wife Eleanor Burke, and she admits to committing the crime; however, as an assistant US attorne

Falsone and Lewis investigate the murder of a man in his own backyard. The victim's nose was removed from his body. Ballard and Gharty investigate the murder of a bartender at a strip club. Canvassing the neighbors, Falsone feels that one of the neighbors isn't what she appears to be. Later when they interview her husband, he gets the same feeling. The MEs complete a record setting day of completing autopsies, but find themselves with one unidentified extra body. Munch and Bayliss get the call, but insist that until they can get a crime scene to go to, the problem isn't theirs. Griscom finds the crime scene in the morgue freezer. Ballard mentions to Gharty that he might want to consider stopping his drinking. Falsone's theory about the victim's neighbors proves true when MGee checks into the Witness Protection program. MGee's phone call puts the wheels in motion to get the family moved. Falsone and Lewis arrive just in time to take their suspect into custody and away from the Feds. The

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

Gharty has a Vietnam flashback. Sheppard is placed back into rotation. Lewis asks Falsone to switch cases, as Lewis is still unsure about Sheppard's ability to be back on the street in the part of town where their call lies. Munch and MGee work a case where the victim was hit and run. One of the victim's possessions is a knife that has some meaning for Gharty, who later is able to recognize the tattoo found on the victim. Sheppard confronts Lewis about the case switch. She and Stivers talk more... after Stivers, working with Falsone, sees him ""go off"" on a potential witness... Munch and MGee find their hit and run vehicle, a rental SUV, whose renter claims to know nothing of the incident and says he had filed a stolen-vehicle report. Munch pulls the victim's DOD file and---for good measure---Gharty's! Munch, begins to spread doubts with the other detectives about Gharty's Vietnam experience, because the file tells him that Gharty had a less than honorable discharge. A kid, who had stol

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.

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.