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There is no Next Episode of NYPD Blue planned.
Lazy cops in a neighboring precinct think they have stuck the 15th's detectives with an impossible case, but some details lead to a suspect, who fires some shots at Andy. Andy is unhurt but freezes, and worries about his approach on the job; later, Andy confronts the suspect and proves the guy is a killer and a coward. Andy was preoccupied over Theo's health and his own weight gain. The former issue is resolved when the doctors say Theo is a healthy baby and the latter when Andy and an also-portly Greg decide to have a weight-loss competition. Greg also befiends an attractive officer named Abby while trying to work out on some confiscated stair climbers. New PAAs arrive for the squad, with one being very young and attractive and other being overweight. Bobby is surprised when an inheritance lands him an apartment building, and the creep who was counting on receiving it comes to the 15th and snarls at him. Det. Simone's news gets worse after that: he asks Diane to marry him and she says she is not ready for that.
Bobby's frustrations over Diane's non-yes to his proposal and the apartment building continue. And the job gives him no comfort when he and Andy lend help to an exhausted, not-too-bright night shift cop investigating the kidnapping of an infant. While Vince Gotelli and James Martinez compete in the Union Delegate election, Vince beats a suspect in an attempt to elicit a confession for the kidnapping of the missing baby. The case goes through several twists and turns before revealing that the father of the infant killed the child after becoming jealous of the attention she was receiving from her mother. Diane suggests she and Bobby takes things slow, and he shoots back that maybe one of them should move out of town. Later, he gets a page informing him that a woman's been shot to death in the apartment building he inherited—and she lives in the apartment that Henry Coffield (creep from last week) used to reside in. Andy and Greg have their first weigh-in.
An ex-con whom Bobby put away years ago comes to him and says another man is in jail for a crime he did not do. Andy remembers the case, a robbery where the getaway car hit and killed a female pedestrian, mostly because he was a new detective then and the senior guy did a crappy job investigating. Some witnesses admit the truth and the case is reclosed with the guy in jail free to resume a life of drug-dealing. James wins the Delegate election by three votes and Vince becomes hung-over and sorrowful. Diane calls Bobby selfish for wanting more than she can give. Bobby takes out his frustrations on Henry Coffield when he cannot get any solid information about who might have tried to kill him and murdered an innocent woman instead. Andy cannot stand President Clinton, and Geri the PAA has a thing for rubber undergarments.
A painful part of Andy's less-pleasant past emerges when activist Kwasi Olashula is found shot to death in his car along with a drug dealer. Lt. Fancy orders Andy to not talk bad about Kwasi until they know the whole story, which ends up with Kwasi dying a hero over a drug dealer's confiscated items. Kwasi's family angrily confronts Andy about his racism, and Bobby later listens in discomfort as Andy explains the origin of his problems with African Americans going back to his childhood and early days on the force. Elsewhere, James and Greg investigate a murder at a bodega, but are unable to close the case because everyone involved is lying.
The American-born wife of a European prince is severely beaten during a robbery attempt, and the prince quickly angers the cops by being too insistent that his wife would want to be taken off life-support. With some help from disgraced ex-Det. Mike Roberts, they learn about a plan to steal paintings and then claim the insurance payoff. James gets a sticky case as Delegate when he has to deal with a detective who seems to have two wives. He does well enough to ask Gina the PAA out to dinner and she says yes. Diane gets an offer to return to OCCB work and reconnect with an arms dealer named Jimmy Liery who might have gone active again.
Detective Jill Kirkendall joins the 15th and immediately picks up a case where a guy is being threatened unless he marries an overweight young woman her brother claims he impregnated. The cops move in before anyone gets hurt and arrest the brother for murder. Andy tells Fancy that Geri's behavior is bothering him, and Fancy has Geri and Gina switch working locations at the 15th. A limo driver's murder is connected to a closeted businessman and his bad taste in male prostitutes. Diane remains in her undercover role. Bobby slaps Henry Coffield in the face a few times and the little weasel finally reveals he was the target of murder because he had promised money to some dealers and that failed when he did not inherit the building.
A developmentally disabled young girl is sexually assaulted by a group of rich students. The girl's angry mom and the meddling Councilman father (from Season 2's "Innuendo") of one of the kids roil Andy and Bobby, but everyone shares heartbreak when the young girl kills herself. Bobby advises her mom to sue the kids, and Sylvia Costas rocks the students by pointing out they will never face any punishment and can look forward to a life of being disgusting and contemptible. Diane is out on UC with Liery when a rollerblader bumps into her and Liery beats the guy, leaving her unable to forcefully protect the guy, though she does keep Liery from killing him. Diane later tells her OCCB boss that the work is getting to her, and has an ugly argument with Bobby. A mentally disturbed young man named Fred comes to the house babbling about his mother, and Andy finds out she died of a heart attack and Fred tried to bury her in a Dumpster. Sylvia talks about how she does not want to leave her job because no one would have tried to get through to the students who did something terrible otherwise.
Diane goes over to Bobby's and they sleep together, but Bobby is not impressed with her idea of a casual relationship and asks her to leave. She throws herself into her undercover work with Jimmy Liery and gets a strong idea of how he is moving stolen guns, but Jimmy has a nasty plan of his own in mind for her. Bobby and Andy catch a murder case where the prime suspect is Arthur Cartwell, a smart but obnoxious guy who was involved with the brutal murders in "Heavin' Can Wait". Neither cop wants to cut Arthur any slack, until a new witness puts the case in a different light. Lt. Fancy is rocked when his former foster son, Maceo, is arrested for running drugs. Fancy has to deal with Maceo's rude and sullen behavior, the evil actions of Maceo's biological mom, and worthless cop Ray Kahlins (from "Hollie and the Blowfish") to save Maceo from a long prison sentence. Greg asks Abby out on a date and she tells him she is a lesbian.
Diane wakes up in Jimmy Liery's apartment and has no idea what happened the night before. Jimmy denies he did anything, but he does not clarify what "anything" means until Diane fires one round about a foot to his left. Fancy is upset when the brass tells him Bobby is in line to get a promotion to Detective First Grade, but Andy will not, while his wife feels Andy is getting what he deserves. Fancy has to choose whether to green-light Bobby's good fortune. The two top cops, meanwhile, are tied in knots when an overbearing woman was strangled and her browbeaten employee and the employee's boyfriend both claim guilt. And the rest of the cops are not getting any information in a tight-knit neighborhood when a repairman is shot to death.
Bobby finds out about Diane shooting at Liery when his neighbor makes a complaint, so Bobby visits Jimmy, beats him, and illegally seizes an AK-47 from the place. Diane is livid that Bobby interfered with her work, and Bobby is mad that Diane is acting like she has lost her mind. He asks for a day to deal with the case, and he and Andy proceed to tell one of Jimmy's contacts he is cooperating with the cops. At Bobby's promotion ceremony, Diane confronts Bobby with the news that Jimmy is dead. Bobby not only is not sorry about that, he tells Diane that if she wants to cry over Liery, then she should not even stay for the ceremony. Bobby tries to make Andy's case for advancement to the NYPD Commissioner, who is not receptive to the idea, but Andy ends up attending the ceremony anyway to support his partner. Andy and Bobby earlier try to help out a witness to a Mob killing who has had his prized paintings stolen, and have to save his life before they convince one of the killers to flip on his partners. James is reminded of his brother's problems when a young runaway witnesses a murder and he has to deal with the kid's abusive father.
Gina the PAA is slashed and nearly raped by a vagrant, and James is ready to burn down the precinct to catch the guy. Greg and Diane convince him to be by Gina's side as she is treated for her injuries, and they later bring the creep in. When Greg's low-key approach does not work, Fancy sends in Andy, subtly suggesting he beat a confession out of the creep (who is guilty). Greg and Andy then have a conversation about the use of violence on the job, which does not make Andy feel all that good about himself. Diane remains on a knife's edge in the aftermath of Jimmy Liery's death and her growing estrangement from Bobby, not least after Bobby has a friendly dinner date with Jill Kirkendall. Diane later calls Andy from a diner because she is on the verge of relapsing into alcohol. The main case involves a diamond dealer's sister, who went missing with a large quantity of stones alongside her no-good boyfriend. And Sylvia decides to take an indefinite leave from work to care for baby Theo, leading Andy to say he will do moonlighting to earn extra money.
A popular uniform cop who was bodyguarding a local Italian crooner says the crooner was shot to death by two men, but Andy and Bobby find themselves in serious conflict with the 15th's uniformed officer as this story produces more and more questions, egged on by a bully of a sergeant. Elsewhere, a teenaged girl's murder is connected to a grotesque fetish video and drugs, and Diane breaks down in Bobby's arms as she finally relates how her father sexually abused her for years.
A construction site that is a battleground between shady outfits led by African Americans and Puerto Ricans becomes a murder scene when the number-two man from the latter coalition is shot to death. Andy and Bobby find out he was a good man who was targeted by a wide-ranging group of scummers, and they are not able to arrest anyone but a perfect patsy. Andy is disgusted when PAA Geri wants to talk to him, but she has news about a man's death. Diane and Jill are assigned to the case and learn the victim was close to Geri and into domination and S&M, but it falls to Andy to see through Geri's facade and help her avoid jail time. Elsewhere, Diane and Bobby's relationship finds a new solid ground on which to continue, and James and Gina have their first sleepover.
A junkyard car's trunk yields the body of a tortured female bartender. Andy and Bobby find a suspect in a nerdy guy with a porn fetish, and cook up a plan to insult him into confessing. Greg and James get a very odd death when a guy had his head crushed by a flying typewriter. Diane tells Bobby she is having therapy sessions, while Bobby gets sucked back into Henry Coffield's orbit when a crotchety old woman with a rent-controlled place in the building demands Henry do all of her household chores.
Fancy and his wife are pulled over in Bayside, Queens, by two uniformed officers on the basis of driving in an all-white neighborhood. Fancy angrily plans to transfer the senior officer Szymanski to a precinct in the all-white Bedford-Stuyvesant, Brooklyn, as punishment before some criticism from Captain Bass leads to Officer Szymanski's arrival at the 15th. Andy begins having dreams where he see his dead son, Andy Jr., but he is confused and angry about the uneven and pointed nature of their conversations. The dreams play into Andy's psyche when he and Bobby investigate a real life string of bar robberies. They have to deal with a stolen .45 automatic, the involvement in one robbery of Vince Gotelli, and a too-eager cop who is trying to solve the case on his own before they get a break and make arrests. Diane and James come up with a plan to bust scam artists who are ripping off disabled women. Andy learns he will need to find a different outlet to see his dead son in the future.
A Russian mail-order bride is strangled to death. Andy's xenophobia gets a workout, while another serial killer and a Russian cab driver are considered and discarded as suspects, before Andy puts a misplaced purse and the dead woman's husband together and solves the case. Greg is on edge because of a mysterious dinner coming up with Abby, and he binges on peanut butter and becomes violent and aggressive on a case where gangbangers fired shots from a city bus. One of his fury storms provides a key break, but another leaves them without a confession. Greg later calms down and the dinner with Abby turns out to be low-key; she wants him to come over and meet her partner over another meal. Andy moonlights as a night watcher of drug couriers at JFK Airport, and finds his world view challenged by one detainee before an emergency involving another one.
A young Latino man is shot to death and no one, including his pregnant girlfriend, wants to talk about it. Bobby works with a gang member's childhood friend, now a straight-arrow former MP who is on the background check list to join the NYPD, and they put the case together. A high-profile case involving the murder of an auto-repair shop owner who was a huge booster for the police has unlikely lead detectives in Greg and James. However, Greg finds an offbeat way to solve the killing. Diane and Jill catch a shaken-baby case that turns into a homicide; they find the baby's parents disgusting and sympathize with her caregiver as the sad story is revealed. Greg drinks too much wine and tells some stupid jokes, but otherwise enjoys his dinner with Abby and her partner, and Diane is inspired by Jerry Maguire into having a new answer to Bobby's marriage proposal.
A drag queen's boyfriend wants her to have a sex change operation or else. There is no good end to the case. Jill's old friend is spiraling into drug use and Jill tries to help her while the friend's mother is deep in denial. There is no good end to this case, either. Fancy's wife has him sell products for her Amway-type business and the detectives buy them up happily, but Fancy feels very guilty about being a salesman to the people he leads, so the end is kind of muted. Bobby and Diane celebrate their engagement at a restaurant where Bobby is approached by a guy with whom he went to school, who is now a very dangerous criminal.
Andy and Bobby investigate the shooting of a rap star who does not want to cooperate and is much more hostile to the cops than to whomever shot him. It takes some stakeout time and a guilt trip, but the truth comes out in time. Fancy is upset when Officer Szymanski whose actions in "Taillight's Last Gleaming" refuses to save himself when he is falsely accused of stealing drug money. Greg asks Abby exactly what she wants from him, and she says she wants him to be a sperm donor so she can have a baby. Bobby gets an unwanted visit from an FBI agent who wants him to do some undercover work regarding his old "friend" Joey Salvo, and Bobby later tells Diane a story that illustrates just what a bad guy Salvo is.
A jumpy waiter leads Simone and Sipowicz to the killers of five Ecuadorians at a social club; a nervous Medavoy awaits Abby's ovulation and hampers Russell's interview strategy with a child molester; and Simone must withhold information from Sipowicz, who disapproves of his partner's undercover wardrobe.
Bobby gets in trouble over the license plate he ran for Joey Salvo the previous week at the FBI's request when they will not stand up for him after IAB finds out about it, and he learns that the FBI suspects IAB of having someone on Salvo's payroll. Bobby's relationship with Andy gets worse as the secrecy about the case continues (though Andy learns Bobby has talked to Diane about it) and affects their investigation of a rape-assault. Andy tries to protect scared witness Steve Cameron, but indifference from ADA Leo Cohen and Bobby's focus being elsewhere leads to a horrible ending. The cops find out that Vince Gotelli hijacked a city bus while drunk and Fancy works to save Vince from jail time.
Bobby gets suspended by IAB and told to follow the FBI's playbook, but Bobby breaks bounds to tell Andy the whole sad story. Andy and Diane have serious conflict over Bobby's situation, only putting them aside to investigate the murder of a young woman who was seeing a psychiatrist after being raped. A reporter who has little admiration for the NYPD's tactics is the victim of crime himself, and Greg and James deal with his attitude while doing their investigation. Bobby tells Joey Salvo he is out of a job, and Joey says he wants Bobby to come work for him, but then Joey is shot three times and killed.