Lewis and Crosetti uncover a woman who's been killing her husbands for insurance money. Howard tries to keep her cases-solved record perfect, but she is reassigned with Felton as her partner. Bolander convinces Munch to help him finish up an unsolved case. A new guy, Tim Bayliss, from the mayor's office gets his first case in homicide, the murder of an 11-year-old girl. His partner Pembleton, we find out, is less than enthusiastic to work with him or anyone else in the unit.

Bayliss and Pembleton continue to struggle with the Watson case. Bolander and Munch discuss ""iguana style"" and are called to check out the homicide of a victim that isn't dead, at least the first time they're called. While checking out some leads for the Watson case, Crosetti gives his theory on the conspiracy to kill Abraham Lincoln. Lewis wants to flood Memorial Stadium. Bolander expresses an interest in Dr. Blythe; Munch advises and sends flower's in Stan's name. Danvers needs a stronger case; however, Howard is frustrated with a dead end. Then the ghost of the victim leads her to the undiscovered proof. Tim attends Adena's funeral.

Crosetti and Lewis investigate the shooting of a fellow police officer whom Crosetti regards as a son, Howard suspects a rabid Spiro Agnew fan of murder but ends up solving the Calpurnia Church case meanwhile Bolander makes a friend whose death interrupts his date with Dr. Blythe.

Crosetti focuses his investigation into the shooting of Officer Thormann on one suspect, while Lewis continues to investigate. Meanwhile, Pembleton and Bayliss pursue different leads in the murder case of eleven-year-old Adena Watson.

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

While Giardello is busy sending off an old friend to retirement Pembleton and Bayliss investigate the murder of a dog, Howard and Felton argue over whether Felton finds Howard attractive while dealing with a drug-related homicide and Bolander and Munch take Dr. Blythe's son on a ride along. Meanwhile, Crosetti takes care of the bed-ridden and blind Thormann.

Howard and Felton are in court over the Pony Johnson case, Crosetti and Lewis go head to head with the Secret Service and Bolander and Munch argue over drug legalization. Meanwhile, Pembleton gets an unexpected job offer.

Quitting smoking dominates the conversation ad behavior of the homicide detectives even as they solve what may be a gang-related killing of a 14-year-old boy. Lt. Giardello discovers a secret asbestos removal project on the third floor and confronts his superiors on behalf of his squad.

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.

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.

Gee informs the detectives that they must meet with a sensitivity consultant. Felton protects a friend who's going to help his terminally ill father commit suicide. Pembleton investigates a routine murder that escalates into a case of possible police brutality. Bolander has no intention of meeting with the consultant to the point where he takes a suspension without pay. Lewis investigates the death of the father of Felton's friend and discovers the truth and confronts Beau.

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 asks Kay if she would double date with him and Linda, to try to take the pressure off his first real date. A slain phone-sex operator is found clutching a note naming her boss as the perpetrator, Bayliss and Pembleton investigate. Munch has trouble dealing with Bolander's happiness, so he crashes the double date and makes everyone miserable. A man is shot to death over a pen at the library, Lewis and Crosetti investigate and find a man with a pen fetish. As Bayliss looks into the murder he begins to get involved.

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.

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.

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.

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.

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.

After uncovering the fact that an elderly woman's tongue was cut out, Kay decides it is time to take a vacation. She returns home and while she is there she looks into the murder of an environmentalist. The suspects include her brother, an ex-beau and their co-worker. Pembleton reluctantly becomes Felton's partner and they finish investigating the murder of the elderly woman. Munch is against having a television put in their bar.

Munch spreads his usual Christmas cheer. Russert, who misses detective work, joins Meldrick on an investigation into the murder of a material witness, when she discovers she knows something about the victim's case. Munch and Bolander investigate the death of a man in a Santa Claus suit and Munch spends the evening with whom they believe is the victim's son. Beau buys Christmas presents for the kids, although he still doesn't know where Beth and the kids are. Bayliss searches the station in search of a game of hearts.

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.

The deputy commissioner invites Pembleton to lunch and gets him to investigate a case involving a congressman. Beau hires a private detective to find Beth and the kids when his clue that they are in Wilmington falls through. Howard and Felton investigate a case of a dead homeless man. Their job is made more difficult when they can't find the body. Lewis and Munch investigate the death of a motorcycle gang member. Pembleton finds out the truth, participates in the cover-up and then resigns when the media gets hold of the real story and the deputy commissioner doesn't back him up.

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.

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.

Pembleton receives an extradited prisoner from New York City Detective Logan. Bayliss is put in charge of investigating the death of Gordon Pratt, but gets no cooperation from anyone on the force. Beau wants to return to active duty. A woman recognizes Munch from an old picture that is hanging in an art gallery across from the precinct. To Munch's embarassment he discovers that an old girlfriend, who's a photographer, is displaying an old picture of him in the buff at her gallery showing. Pembleton and Meldrick investigate a random shooting of a woman, and they clash over where the weapon may have been fired. They also find a woman who's shot her boyfriend and stuffed him in the freezer. Beau accompanies Gee on an investigation and must come to grips with his inability to look at a dead body the same way.

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.

Crosetti's caseload is distributed among the detectives and Howard's 100% clearance rate may be in jeopardy when she gets his most difficult unsolved case; this is further complicated when Beau misplaces some new evidence. Gee meets one of Megan's friends at lunch and is convinced she isn't interested in him because he is too black. The guys close on the bar but wind up penniless when they must pay extra fees that they weren't aware of. Beau looks to Megan for comfort when he can't recover the evidence and it looks as though Beth and kids are never coming back.

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.

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.

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.

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.""

A gas leak causes the detectives to evacuate the building, so they relocate to an old bank building. Lewis is paired up with Kellerman on the murder of a woman. Sergeant Howard tries to carve out a place for herself with the other detectives, but her efforts prove unpopular. Pembleton has trouble adjusting to the new surroundings and his wife's pregnancy. A cameraman who was at the scene of the murder has who he thinks is the perpetrator on tape; however, when he brings the tape to Gee, he is thrown out before he can say why he's there. The cameraman eventually strikes a deal with Lewis and Kellerman.

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.

Pembleton and Bayliss investigate a murder that was committed in a gay neighborhood by skinheads and the victim's sexual preference is questioned. Brodie is hired by the department to videotape the detectives' crime scenes. A voice stress analyzer is brought in for a demonstration. Meldrick gets a lead and closes an old Crosetti case that even Howard couldn't crack; it causes a little tension between them.

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.

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.

The sniper continues the shootings and everyone returns to duty lacking sleep. The media starts to make their presence felt. Munch begins to worry about Howard's safety, fearing she'll be wounded again. Frank makes his wife wear a bulletproof vest. Gee asks for Russert's help even though Barnfather had ordered her to stand down during the rest of this investigation. A man at the scene of both of the day's shootings is put into the box for questioning. Russert has a talk with the suspect with the subject being keeping people's attention and respect.

Gee is sent upstairs to see Barnfather and everyone speculates about the vacant Captain's position. Lewis and Kellerman are sent to Pennsylvania to extradite a woman back to Baltimore where she is a suspect in the murder of her husband. Munch tries to find a videotape in Brodie's pile. Later after reviewing the tape, they discover a key piece of evidence isn't contained on the tape. Munch wants the tape erased, but Brodie delivers the tape to court and that results in the outcome Munch feared. On the trip back from Harrisburg, Kellerman convinces Lewis that they have time to stop at Neptune's Castle and they lose the suspect, for a moment. Later they lose her again but find her at the house of her dead husband's mistress, delivering a hat. Much to everyone's surprise but not the viewers Gaffney is promoted to Captain over Gee. Captain Gaffney lays down the law.

Lewis and Kellerman try to subdue a large man who's gone on a rampage. The large man is finally subdued and they find him digging up his mother. This case brings out some information about Meldrick's family, and he tries to see his brother, who doesn't want to see him. Kay tries to keep the identity of her new boyfriend a secret, mainly from John, which drives him crazy. Pembleton and Bayliss investigate the death of a man whose body is found in a car. Scheiner says he died from internal bleeding, not the gunshot wound to the groin he was treated for at an emergency room earlier that day. They discover that the doctor may have had a motive for doing a less than adequate job treating her patient.

Continuing the investigation in New York City, Egan's wife is questioned by Frank and Tim. Just a few hours later, Egan's wife is killed and Egan's son is seen running. Kendall is taken into protective custody until he gives up the suspect's name. Lennie Briscoe and Rey Curtis come to Baltimore. The suspect tried to escape in a seaplane but is caught. This crossover started on Law and Order S06E13 Charm City (I).

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.

Jake Rodzinski has trouble dealing with the verdict of the trial and takes justice into his own hands. Kellerman is back from a family wedding in Wisconsin picks up the case of the murder of Kenny Damon. Lewis is not allowed to know all the details of Kellerman's investigation, because of his past relationship with Rodzinski, their chief suspect. Bayliss is at odds with Pembleton over the disposition of a grilled cheese sandwich.

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.

A young girl is murdered, in a style similar to Adena Watson's murder. Frank demands to work the case alone as Bayliss begins to think that the two crimes might be related. Bayliss' obsession with trying to get this case solved and linked to Adena's murder causes the two of them to clash. Howard learns that Brodie has a crush on her and tells him she doesn't like the joke that's being pulled-- only problem there is that it's the truth.

Kellerman and Lewis (with Brodie) investigate a shooting at the New Moon motel, where everyone there has a motive for the crime. They split up and canvass the denizens of the motel; Lewis also searches for the victim's missing boot. The murder is just one of the many crimes that has occurred or is occurring at this establishment.

Lewis and Kellerman's investigation of a murder in a housing project puts them at odds with a civilian-patrol group, run by the Black Muslims. Munch is excited because Stan is scheduled to come back June 1st. Russert and Munch catch a case where both the victim and shooter are dead. She with Howard must decide whether to circumvent the so-called ""blue wall of silence"" among police officers when it is discovered that the officer on the scene didn't react in time. Barnfather stops Lewis and Kellerman's charging of a Muslim, until something is leaked to the newspapers. The ""big man"" is scheduled to come to the bar, but changes his mind, twice.

A prominent attorney is murdered and the murderer presents himself to Pembleton and Bayliss with a videotape that implicates him. Brodie works on increasing his self-image. Kellerman is determined to find out who's the ""lunch bandit."" The NSA steps in on Pembleton's murder investigation and provides him with a guilty party, even though they know he didn't do it. Bayliss' disgust with the interference doesn't sit well with Gaffney who wants to charge him with insubordination.

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.

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.

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