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.

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

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

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

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

Bayliss returns to duty to discover the bosses have renovated the squad room in an attempt to make everyone forget the tragedy of last May. Gharty and Ballard have also returned and Ballard debates about whether she should ask Falsone to the Lodge party. New detective, Rene Sheppard, tells her just to go for it. Seizing the opportunity, Lewis goes for it and asks Sheppard to the party; it seems that he and Barbara have separated and are on their way to divorce. Meanwhile, Falsone speculates if he should ask Sheppard to the party. The first case Bayliss catches, now partnered with Munch, involves the dismembered body of Angelo Faltislo, a friend of Gee's cousin, Mario Giardello. Stivers and Falsone's case is similar: Leo Grimaldi, another friend of Mario, is also found dead. When Gee goes to question cousin Mario, he finds Mario's body in the same condition as that of his friends. Gee's estranged son, Mike Giardello, an FBI agent in Arizona, returns for the funeral. Mike asks Falsone (w

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

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

A body buried for 6 - 20 years is uncovered at a construction site. Munch and Lewis begin the process of trying to solve this old crime. Falsone and Ballard's relationship has heated up, and that fact becomes apparent to their fellow detectives. Sheppard returns to work, but is discouraged when Gee assigns her to desk duty. Gharty tells Billie Lou that he'll attend her bass-playing concert. Munch & Lewis with help from the ME and MGee, identify the body and then begin to piece together what happened to her. Gee lays down the law to Ballard & Falsone: they have to knock it off if they want to stay working on the same shift; they agree.

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

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

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.

Sheppard and Bayliss await the trial of Luke Ryland, the Internet killer. A number of delays keep the hearing from being held; the last time it is because Danvers can't make it due to being held up in another trial. Because of a technicality in the law, Ryland is set free. Bayliss is outraged and winds up pushing Danvers, who later threatens to put Bayliss up on charges. Gee's daughter Teresa arrives, to help with the celebration of her father's promotion. Gee asks Bayliss to apologize to Danvers and Bayliss declines. Lewis and Falsone look into the murder of a drug addict whose husband looks like the most probable suspect. The victim's mother-in-law isn't very cooperative and her sister is a nun who thinks her brother-in-law is an architect. Gee worries about whether or not he will be able to perform in his new role as Captain of the property crimes division, later he turns down the promotion. Bayliss and Lewis have words about the way each other handle their memories of the past.