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

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

While Pembleton is still interested in the housekeeper's ex-boyfriend, Ballard still thinks that the Wilson family needs to be looked at more closely. Also, a body is found at Camden Yards during a game between the Orioles and the A's. Falsone questions Stivers about the Mahoney shooting and that begins to make her nervous. Tensions mount because there appears to be a leak to the press within the unit about the Wilson case. Orioles' security wants the case quickly resolved. Munch and Kellerman have only 48,000 possible suspects. The victim is discovered to be a dead Yankees fan. Tim gets his old high school French teacher to help them check out the whereabouts of the housekeeper's ex-boyfriend. He is cleared because of his current incarceration in a Haitian prison, which leaves the Wilson men as more probable suspects. Are Gee and Pembleton protecting Felix Wilson because he is a prominent businessman in predominately black Baltimore, as outsider Ballard suggests? Munch and Kellerman g

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.

A young woman is viciously attacked. Falsone and Lewis are called to the scene because the victim wasn't expected to make it. Stivers is working in Sex Crimes and is second to the scene; however, because Homicide was first it is technically their case. The attack is the third in three months and the bosses decide they'll work the case together. Frank's wife is overdue on her delivery. Tim recommends a restaurant whose salad has been known to ""kick start"" delivery in pregnant women. Frank gives it a try. Georgia Rae Mahoney meets Kellerman and mentions to him that she has a surveillance tape from Luther's condo. She tells him she'll keep in touch. Kellerman tracks down the old surveillance equipment from Luther's condo. A possible suspect is found in the rape case that doesn't turn into anything. A recanvas of the bars brings a new suspect to light. The salad might have worked its magic, because Mary gives birth, although there are complications that cause Frank to think about the job's

Brittany's stalker in Baltimore is interviewed and says that he saw her being attacked by someone. When going to question the parents, the detectives discover that the Janaways have returned to Baltimore, so they make the trip to Charm City. They get the father in the box and he demands that they prove he did it. The attorneys fight over jurisdiction but the judge rules in favor of Baltimore and the two teams of prosecutors must work together.

This crossover starts on Law and Order S08E06 Baby, It's You (I).

Two Vietnamese teenagers witness the shooting of their parents and some friends. One of the friends was a cop and one of the shooters they say was another cop. That cop they discover failed her psyche evaluation but may have possibly gotten her job due to Affirmative Action; although strings pulled by her father proved to be her ticket into law enforcement. After they are able to implicate the cop in the shooting, as a bonus they discover the body of her string-pulling father. Ballard suffers from an allergic reaction to crabs. Falsone finds out that the case against Georgia Rae Mahoney is going to be dropped because of a lack of evidence. He suspects that the whole Mahoney thing is going to blow up in the department's face, because he knows the Mahoney shooting didn't go down the way Stivers, Kellerman and Lewis reported it. Kellerman debates with Cox about what he should do about the Mahoney situation.

A man falls between the cars of a subway train in front of horrified witnesses. Was he pushed? While the man is still alive, the prognosis is he will be dead the moment they extract from the position he currently occupies: pinned between the train and platform. Homicide is called in light of this condition and the fact he may have been pushed. Pembleton questions the victim, and Bayliss questions the witnesses, especially a strange one named Larry Biedron. The victim has no relatives in the Baltimore area. He does have a girlfriend who is supposed to be jogging in the area; Lewis and Falsone try to find her to bring her to the scene.

Ballard and Gharty investigate the death of a man at a laundromat. The Waterfront Bar gets ready for the Christmas holiday. Munch's ex-wife, Gwen, shows up; her mother (a literary critic and author) has died. Tim goes Christmas shopping and runs into Julianna; he invites her to come to the Waterfront's Christmas celebration. Ballard and Gharty interview the victim's girlfriend (as listed in his address book). Cox informs Ballard and Gharty that the victim was HIV positive and she also convinces Kellerman to tell Lewis and Stivers about the Mahoney videotape. Munch gets his brother to give Gwen a deal on her mother's funeral arrangements. The victim's mother knew about his HIV status and about a girlfriend he didn't use protection with, whose name didn't appear in the address book. Ballard and Gharty find this woman and find that she has full-blown, terminal AIDS, and they bring her in for questioning. Ballard feels the woman has suffered enough so she is reluctant to a get her confessi

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

A white man is found lynched in a historic black section of the city; Falsone and Lewis investigate. The day after Tim's dinner date with the male restaurant owner that Tim was positive about, Frank is perplexed by Tim's interest in Laura Ballard. The autopsy reveals that the hanged man was also whipped. Gharty worries about Ballard getting involved with ""switch-hitter"" Bayliss. Lewis is convinced the lynching is related back to the victim's Civil War ancestor, infamous runaway-slave catcher and free-blacks abductress. Tim and Laura attend an art show.

Julianna wins the recognition of her peers. At dinner, Julianna and her colleagues swap stories about how they've cracked cases. Julianna relates a story that happened a few weeks earlier, a suicide might actually be turn out to be murder, when it is determined that the victim was shot in mid-jump. A bickering elderly couple proves to be the key to the crime. Meanwhile, Falsone investigates the legal possibilities of obtaining custody of his son. Ballard and Gharty investigate the death of a drug dealer, which takes them up into the hills of western Maryland in search of their suspects. Georgia Rae Mahoney sues Stivers, Lewis, Kellerman, Giardello, Cox, the department and the city for the wrongful death of her brother, to the tune of $60 million. Lewis confronts Georgia Rae and winds up with a suspension for his trouble.

Kellerman is trying to find Lewis, who's disappeared since his suspension. Bayliss is on vacation. Stivers rotates into homicide and Kellerman isn't happy to see her. A priest is found murdered. Falsone attends a custody deposition hearing. A tape is delivered to Channel 11 that contains some startling information from a Swami about the priest's activities involving young boys. Munch and Kellerman seek out the two boys who were at the scene of the crime; meanwhile the other detectives seek out the Swami. Both are located, though the boys do not provide anything conclusive; they are held in protective custody. Kellerman searches for Lewis. Meanwhile, church members protest in front of the station house. Falsone gets his son for a weekend. Ballard and Gharty detain a corner kid who might be identifiable as one of three who had frightened a priest. Unfortunately, that priest (a monsignor) can't make a positive ID. Because of public pressure, the boys are released from custody to stay with

With the addition of the latest murder, the ""red ball"" investigation continues full force. The detectives and the returning Bayliss pose as priests in an attempt to flush out any leads. Munch's cover attracts two young thugs, but they prove to be nothing. Gee is called upstairs, where his performance doesn't sit well with Barnfather. Lewis turns up and seeks some help from Falsone. Pembleton receives a call that the two missing boys have been found. Pembleton and Stivers travel to collect them. Meanwhile, Gharty and Ballard find the pawnbroker who had accepted a stolen chalice. Cox and Bayliss prevent a drunken Kellerman from driving home. Ballard and Gharty use the pawn-receipt false address to track down the corner kid with whom they'd previously had a run-in. They bring him into the box and Gharty loses his cool. The kid is tough to crack, but Pembleton has an idea involving the morgue and a trip to the shore. While stumbling home, a drunken Kellerman decides he doesn't like the loo

A slightly intoxicated man (driving with his wife) aggressively whips his car around a state-owned truck; the offended truck driver rams their car; their aggression results in a collision where both drivers die. The man's wife is in serious condition. Kellerman and Munch investigate this case. Falsone gets prepared for the final hearing in his bid for custody of his son. Meanwhile, the other detectives investigate the death of a man who made a mobile phone call from the coffin in which he had been buried alive. The coffin was buried in the parade ground of an old spy school. The victim might have remained alive if the lid hadn't been sabotaged to collapse. In the car / truck collision case, Cox's boss wants her to ""verify"" the results of the car driver's blood alcohol level to help protect the state from serious litigation. An old Russian friend of Gee's furnishes them with information that leads the detectives to the discovery of a group of men who couldn't make it as spies. (They cal

Pembleton and Falsone look into the death of an elderly man who might have been killed by the pit bulls owned by his grandson. The other detectives hang out at the Waterfront and tell stories about stupid criminals they have met. The judge in the wrongful death suit of Luther Mahoney decides there is enough evidence to turn the suit into a jury trial. Kellerman suspects there might be something up, so he tries to go and see the judge.

Homicide is called in when a woman is distressed at the fact the Dr. Turner helped her brother stop suffering from his colon cancer by injecting him with a lethal dose of morphine. Other members of her family were comfortable with the way he died. Pembleton and Bayliss investigate the issue of murder or mercy. Ballard and Gharty spot their city goats at a shopping mall, where Gharty was using Ballard as a consultant in his purchase of a gift. Stivers and Falsone catch a case where a schoolgirl and the owner of a pizza parlor are murdered during the holdup of the pizza parlor. Kellerman confronts Judge Gibbons and tapes their conversation about his ruling in making the wrongful death suit a jury case. Ballard and Gharty round up their city goats after they confront their mother. Gee warns the rookie homicide detectives, Stivers and Falsone about the baggage that comes with working their first case involving the death of a child. Pembleton and Bayliss' investigation of Dr. Turner's pract

A four-year-old boy is abducted while riding a merry-go-round in the park under the supervision of his mother. The Homicide unit, which helps in the investigation of all child abductions, is called in and Falsone is the primary. When the boy's father has an alibi that checks out, the detectives beginning to check on known pedophiles and later they receive a call from the possible kidnapper. When that doesn't pan out, they start over. The host of a nationwide television program, This Weeks Wanted, suggests that they hypnotize the little girl who was riding on the horse next to the boy. Hypnosis reveals a partial plate number and that leads to a lucky break. Ballard and Stivers discuss motherhood and Falsone checks on his son.

Munch and Gharty probe the death of a high-school athlete who appeared to have everything going for him. Pembleton and Bayliss have only one lead to a potential suspect, a pager number; however, Bayliss has a plan that should lead to the apprehension of their suspect. Kellerman and Ballard get a case with a drug dealer that Kellerman is less than enthusiastic to work. The victim is one of Georgia Rae Mahoney's lieutenants and there are four other unsolved murders in the last two weeks where the victims were members of the Mahoney organization. Pembleton and Bayliss apprehend the wrong suspect, but the fact the suspect was trafficking 200 Kg of narcotics gets them a commendation. Meanwhile, using the information provided to him by Falsone, Lewis has had members of the Mahoney organization under surveillance. Is Lewis involved in these murders? Kellerman receives some good news for a change; passing a tape of his conversation with Judge Gibbons onto the FBI won't be necessary. The FBI is

Ballard and Gharty investigate the deaths of two single women who were bought drinks by a married couple. The victims were stunned and then strangled. The other detectives receive detailed information that helps them close the open Mahoney drug shootings. Their helpful informant turns out to be Lewis, who has a hearing coming up Ballard and Gharty get their suspect in the box and he claims to be the one to stun the victims, but his wife actually did the strangulation. Ballard is skeptical about the woman's involvement, but the evidence points to the couple.

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.

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.

Judge Gibbons has been stabbed. On their way to the crime scene, Bayliss and Pembleton talk about a book that Bayliss is reading, then Pembleton wonders if anyone would ever write a book about their Homicide unit. A probation officer is murdered in a drive-by shooting. The FBI gets involved with investigation of the Gibbons death. Agent Bauer mentions to Bayliss that Kellerman's confrontation with Gibbons probably got the judge killed. He wants Kellerman clear of the case. A fingerprint lifted from the Gibbons' crime scene points to Georgia Rae's son, Junior Bunk. Falsone and Stivers get a lead on their probation officer shooting case. As Junior Bunk is brought in for questioning, he eyeballs a handgun being put in a drawer. Pembleton and Bayliss get Junior in the box and he is no longer able to be intimidated. While waiting to be transferred to central booking, Kellerman, Lewis & Gharty harass Junior. Slightly freed up to make a phone call, Junior gets the gun out of the desk and begi

The search for Georgia Rae and the war against her organization begin. Stivers, uncomfortable with the whole situation tells Gee about the Luther Mahoney shooting. Ballard and Gharty begin to deal with their recovery. A lead on Georgia Rae's whereabouts is uncovered. During the assault on the building, Georgia Rae's body is found and Bayliss takes a bullet that would have hit Pembleton. Gee asks Pembleton to get to heart of the Luther Mahoney shooting that started it all. Pembleton and Falsone start with Lewis and then they move onto Kellerman. The truth about the shooting comes out and Kellerman claims sole responsibility, Pembleton asks him for his badge. To protect Stivers and Lewis from prosecution, Kellerman resigns. Feeling remorse for the hesitation that caused Bayliss to take a bullet for him and with Gee's plans to cover-up the truth about the Luther Mahoney shooting, Pembleton decides it is time to resign.