Note: Garcelle Beauvais-Nilon, Jessalyn Gilsig, and John F. O'Donohue did not return for the twelfth season. With the exception of Eddie Gibson being replaced as squad commander, their absences are not explained to the audience.
Detective Laura Murphy joins the squad and has an uneasy start to her partnership with Ortiz. A new Lieutenant, Thomas Bale, formerly of Internal Affairs, takes command from Sergeant Gibson. Someone sends Sipowicz a dead rat and keys "PAB" ("Payback's A Bitch") into his car. Ortiz and Murphy investigate the murder of a homeless man while the rest of the squad work the murder of a doctor who is in town to research a book. Clark obviously still has not gotten over Devlin's suicide.
Notes
Bonnie Somerville makes her first appearance as a Detective Laura Murphy
Currie Graham makes his first appearance as Lieutenant Thomas Bale. Graham had appeared in a different role in Season 4's "Emission Impossible".
The doctor's murder storyline is based loosely on the life of David Reimer and Dr. John Money.
243
2
"Fish Out of Water"
Jesse Bochco
Story by : Bill Clark & Nicholas Wootton Teleplay by : Nicholas Wootton
Bale announces his mandate from the department to make the "rogue" 15th squad reflect "today's policing" and insists on micromanaging the details of every case, which causes friction with the detectives. Cases include a dead 8-months pregnant woman in a dumpster and a push-in robbery. Investigation of the pregnant woman's death exposes an adoption scam. Andy and John Clark's relationship continues to deteriorate as John struggles to cope with Devlin's death and his father's suicide and takes out his anger on Andy. Andy's stalker poisons the fish in Andy's squad room tank.
Theo is briefly kidnapped, but returned unharmed. Sipowicz secretly tries to find out who is responsible while the rest of the squad works the case of a murdered rapist who had been harassed by one of his victims. Bale's latest irritating move is to mount the squad movement log next to the squad room door and put John Irvin in charge of ensuring detectives sign in and out whenever they arrive and depart. Sipowicz is barely speaking to Clark.
245
4
"Divorce Detective Style"
Mark Tinker
Story by : Bill Clark & Keith Eisner Teleplay by : Keith Eisner
Cases involving a young woman found in a closet who has been bludgeoned to death and a man's kidnapped son dovetail into one larger situation, and Bale's stupidity during the case leads Andy to blow up at him. During the trial of Steve McClintock, who is accused of murdering a pregnant woman ("Fish Out of Water") Clark's testimony is impeached when he admits to having sex with Carly, McClintock's girlfriend and co-defendant. Andy's stalker orders child sex abuse material with Andy's credit card, which brings a visit from the FBI. A police mechanic finds a bug in Andy's police car. John Irvin traces the manufacturer, enabling Andy to hunt for his stalker, which Bale tacitly allows. Following a lead developed by Medavoy, detectives find that the kidnapping was staged by the victim, and his conspirators killed his girlfriend, who was the young woman in the closet. When Clark has a flippant attitude about ruining the murder case, Andy informs Clark he is going to request a new partner.
Andy attempts to pull a drunken John Clark from a bar and is shot by an unseen assailant. When he returns to the squad the next day, three AA "friends" confront him based on an anonymous tip they received and Andy has difficulty making them believe he had not been drinking. The bar's bouncer provides Ortiz and Murphy information about John's behavior at the bar, which does not concur with John's version. Medavoy finds out Hatcher's detective agency did a credit check on Andy. Andy confronts Stan and threatens to kill him if he does not stop stalking Andy. Hatcher recorded the conversation and reports the threats to the police department. Bale reluctantly brokers a deal with Hatcher's uncle, the deputy chief for personnel, who agrees that Andy will not be charged with any crimes in exchange for Hatcher's banishment to a private security job in Miami. Clark receives a verbal reprimand from Bale. Bale also tears into Andy because of the influence Bale had to expend to save Andy's career. Clark quietly asks Andy if they can stay partners and Andy agrees.
Notes
Jonah Hill guest stars as a store clerk, in his television debut
After being brought up short by both Bale and Baldwin, Clark reassesses his recent behavior and makes a tentative move to mend fences with Sipowicz. A man is stabbed while riding the bus with his family. A video store clerk is stabbed by a robber. A wealthy antiques dealer reports a suspicious burglary. Medavoy takes a part-time job as bouncer at a bar. Andy has a surprise visitor who helps him gain perspective.
Notes
Jimmy Smits makes an uncredited appearance as the spirit of Bobby Simone
John and Andy begin to put their relationship back together. A material witness in a murder case is beaten in an alley. John Clark volunteers to protect the witness, enabling him to begin repairing his relationship with Munson. Clark and Andy continue to deal with Bale's interference and micromanagement. Greg is caught moonlighting as a bouncer, placing his job at risk. Baldwin Jones wants custody of Michael — but so does Michael's criminal father.
Lucy, the murder case witness Clark is voluntarily protecting, is fired at from a passing car. The shooting persuades Bale to authorize overtime so Ortiz and Murphy can take over the detail. Lucy reveals a name that enables detectives to identify other witnesses and solve the alley murder ("My Dinner With Andy"). Jones appears at a family court hearing, but Michael is missing and his father accuses Baldwin of hiding him. Greg pleads with Bale to informally handle the discipline for Greg's violation of department rules by working as a bar bouncer, but Bale insists he face a formal internal affairs hearing. Greg consults a department lawyer, who barely listens to him and says Greg's best move would be to have an unnecessary heart procedure so he can retire with 75 percent benefits. Andy prepares for the sergeant's exam and Bale volunteers to loan his study aids to Andy, who begrudgingly accepts.
250
9
"The 3-H Club"
Mark Tinker
Story by : Bill Clark, Greg Ball & Steve Blackman Teleplay by : Greg Ball & Steve Blackman
Michael's father Craig is shot and killed. Both Michael and Baldwin's off-duty gun are missing. Sipowicz and Clark investigate Baldwin and Michael as suspects. Greg's hearing officer orders him to forfeit five days' pay, but subjects him to no other discipline. Greg upbraids Bale for not handling his violation of the rules informally, and carries himself with more confidence afterwards. A boy is molested by someone driving a church van and Ortiz and Murphy have to deal with a cop whose personal experiences impact his behavior on the case. Michael and Baldwin's gun are found. Craig's murderer confesses.
The brother of a mentally disabled man is found dead. A conman rents the same apartment to multiple parties. Greg makes a connection with one of the conman's victims, realtor Bridgid Scofield. Andy and John Clark clash with Bale when Bale decides to conduct a sting on an upset father who offers a bribe to drop drug charges against his son, rather than simply warning the father not to follow through. Sipowicz takes the sergeant's exam. Bale is enraged when the father who offered the bribe returns and tells Bale he has no idea what Bale is talking about. Bale blames Andy, but Andy's response makes Bale into a joke to the squad and he backs off. Rita later reveals to Andy that she warned the father, and does not regret it.
Notes
Mary Page Keller guest stars in a recurring role as Realtor Brigid Scofield
While investigating closeted gay men who have been beaten and robbed, Andy finds Bale's credit card in the suspect's home. Andy returns the card to Bale and says he has no intention of looking into the matter any further, prompting a change in Bale's demeanor toward the detectives. A respected attorney is shot to death in his car. Ortiz and Murphy investigate a drive-by shooting at a basketball court. Clark accompanies A.D.A. Munson to a party honoring a lecherous judge. Greg and Bridgid have a lunch date.
A young pregnant woman is murdered, and the detectives find that the father is a bigamist whose two families hold the key to solving the case. Attractive young women who had just begun attending Alcoholics Anonymous meetings are being killed. Andy leads the squad in an undercover investigation to find the killer. Greg helps Bridgid close a sale.
Ortiz and Murphy go undercover to catch the AA killer. Steve McClintock is found stabbed to death in his apartment, which is full of steroids. The investigation leads Clark to Steve's girlfriend Carly, the witness with whom Clark previously had sex. Steve's killer claims Carly set up Steve to be robbed, but that Steve was not supposed to be home. Clark believes Carly arranged things so that Steve would be killed, but is unable to prove it, though Carly confesses to setting up the robbery and will face major prison time anyway. ADA Munson is initially angry at Clark over Carly's return but apologizes when she notices the change in his demeanor. Bale informs Andy unofficially that he has passed the sergeant's exam.
Andy and John Clark investigate the murder of a successful immigrant restaurateur with a taste for young girls. Ortiz learns the Joint Narcotics Task Force is after the boyfriend of Rita's cousin Paula, and that Paula may be involved. Greg and Baldwin probe the murder of a public relations consultant whose clients included a famous, paralyzed former cop. Ortiz and Murphy arrange to arrest Paula with a small amount of drugs, preserving the federal investigation into Paula's boyfriend while removing Paula from involvement.
Sipowicz and Clark investigate when a wealthy businessman is killed in a car explosion. They pursue the victim's business dealings in Colombia and an Israeli ex-security guard, but find that the victim's cold-hearted daughter holds the key to solving the case. Ortiz and Murphy investigate the death of a teenager who was beaten to death in an alley.
Sipowicz and Clark investigate when an elderly millionaire whose wife is more than 50 years younger is found smothered to death. Medavoy and Jones look into the murder of a State Supreme Court judge's elderly mother at a retirement home. Munson introduces Clark to her arrogant and powerful father. Sipowicz is promoted to sergeant.
A U.S. Army recruiter is shot to death and Clark suspects the brother of a soldier killed in Iraq. Medavoy and Jones investigate the death of a homeless man whose body was found dead in a dumpster and find a connection to Murphy's first case after being assigned to the 15th precinct. Bridgid makes Greg an offer he cannot refuse and Greg tells Baldwin he intends to retire from the police force to join Bridgid's real estate business.
Sipowicz, Murphy and Ortiz investigate the shooting of a fellow police officer. Clark and Jones become partners and investigate the beating death of a woman whose newly religious husband owns a jewelry store. Bale is shot during the course of a murder investigation. Medavoy makes his retirement official.
Bale is hospitalized and his temporary replacement is more interested in playing golf than running the detective squad. When a young Muslim bride is found stabbed to death, Ortiz and Murphy suspect her husband. Sipowicz, Clark, and Jones arrest the man who shot Bale. Bale reveals he is permanently disabled and recommends to the chief of detectives that Sipowicz take over as the commander of the detective squad. At the celebration that includes Medavoy's retirement, the chief of detectives gives Andy the chance to make the case for why he should be the new squad commander and agrees to give him the job.
Ray Quinn and Joe Slovak join the detective squad. Andy questions his decision to take over as detective squad commander after top brass try to stop the investigation of a rich and powerful murder suspect. Medavoy stops by while on a sales call and realizes that organizations continue to function even after one person leaves. Bale commends Andy for continuing to search for the truth and defending the detectives from the bosses, even though the chief of detectives had ordered him not to pursue the case.
