Inspector Lastarza from the Organized Crime Unit orders John to stop his "Dodge City campaign," but Lt. Fancy tells him, off the record, to keep the squeeze on Marino, especially after Sipowicz comes out of his coma with no memory of who shot him.
That night, John and Janice Licalsi have dinner, but the orders she's received from Marino to murder Kelly are weighing heavily on her mind. John senses something's wrong, but all Janice will tell him is that she thinks she's falling in love with him. She runs out of the restaurant, leaving John very confused, and goes to meet with Marino in his limo. Marino presses her to find out why Kelly isn't dead yet, and when he correctly guesses that she's fallen for him, a panicked Janice pulls out her off-duty gun and kills Marino and his limo driver, then quickly drives away in her car.
Meanwhile, John visits Andy in the hospital, and is relieved to hear that his partner is not only getting better, but that the week of forced sobriety (it's hard to drink while you're comatose) is helping him to dry out. John suggests that Andy "remember" what happened in Lois' apartment, but Andy figures Giardella's lawyer would tear him to pieces on the witness stand.
The next day, news of Marino's murder frustrates John on two levels. Not only did he lose his best shot at getting evidence against Giardella, but Lastarza takes over both cases, leaving John completely out of the loop. Janice, suddenly chipper, asks John for a second chance, and he warily agrees to meet her again that night. Their date eventually leads them to John's bed, where Janice tries to convince him not to get worked up over things out of his control, and they make love.
Andy comes back to work a few days later, needing a cane to walk and an inflatable seat cushion to sit, because one of Giardella's bullets hit him in the rear. Fancy informs him that the suspension he received right before getting shot has been rescinded, but for the time being, Andy will be on restricted duty in the squadroom. Adny tries to mend fences with Fancy and explain that he's sober, but the Loo says he needs time to reevaluate him.
After a few hours of "ass duty," Andy decides to stretch his legs, and spots a disguised Lois coming in downstairs to talk to Kelly. Realizing that once Lois gives up Giardella in the shooting he'll lose his chance at extracting personal revenge, Andy heads out to find his nemesis. Meanwhile, Lois gives a statement to Kelly and Fancy, explaining that she feared Giardella would kill her if she didn't help set Andy up, but that she still fears for her life. Once John finishes the interview, he decides to give Andy the good news, only to hear from Martinez that Sipowicz left the precinct shortly after Lois arrived.
John, realizing what Andy has in mind, finds his partner staring at a drink at one of Giardella's bars. Before he can talk Andy out of his suicide run, Giardella and three of his goons show up, ready to rumble. John manages to get Andy outside without a fight, and shoves him into his car, where he points out the detectives rapidly approaching the bar to arrest Alfonse and his bodyguards. Andy doesn't feel that arrest is good enough, and says that the only reason he managed to stay alive from the shooting was the hope of killing Giardella. John points out that Andy hasn't had a drink since getting out of the hospital. Andy, beginning to realize that he still has some self-worth, switches gears and gets out of the car to proudly tell Alphonse that he's suddenly remembered everything and is looking forward to seeing him and his wig in court.
Unfortunately, Giardella and his lawyer James Sinclaire quickly cut a deal with Lastarza: in exchange for no incarceration, he'll give up everyone else in the Marino family, including the cops Angelo had on his payroll. When Fancy finds out that Marino had a contract put out on Kelly, and that a cop was supposed to do it, he shows John the list of dirty cops, asking if he recognizes any of the names. John says no, but his eyes say yes.
He finds Janice having lunch at a local coffee shop, pulls her aside, and shows her the list, which has her father's name on it (Janice joined the force under her mother's maiden name, which is why Fancy didn't connect her to the list). He's put two and two together and figured that Marino approached Janice and threatened to give up her father, and wonders if the reason for her recent sunny demenaor isn't because she whacked Marino herself. The most Janice will say is that even if that's what happened, "the case never makes." She tries to tell him that they could have a life together, but John is too shocked to listen.
Back at the precinct, Andy gripes to John about Giardella's sweetheart deal, and mentions that Giardella had to confess to killing Marino in order to get things done. John laughs at the complete absence of justice in this case, but doesn't tell Andy about Janice.
The two partners head out for dinner, and a reflective Andy notes that while the system may not work sometimes, "On the bright side, I may be keeping company with a blue inner tube, but I wake up sober every morning and don't feel like I got hit by a Cessna, I'm in the running to get my job back, plus a buddy saw me through some tough times. So who's got it better than me?"
John pays a visit to the laundry room that night, where, sure enough, 4B is cleaning some clothes and lying in wait for his mugger to return. John tries to convince Josh to move on with his life, and says that this course of action won't help him ingratiate himself with Laura. "I caught crooks for 14 years, and it didn't turn her on." Goldstein doesn't want to listen and goes back to his wash.
A few nights later, John gets a call about a shooting at his old building, and arrives to find out that Josh was attacked by the same mugger, and shot him. On the way to the local police precinct to give his statement, a keyed- up 4B tells John that "I'm glad I shot him. I liked how it felt."
John spots Laura watching, and takes the opportunity to apologize for their recent fight. Laura returns the favor, and asks John about his relationship with Janice. John, thinking about Janice and Marino, says that he doesn't think it's going to work out between them. He tells Laura that he doesn't want to be alone tonight, and asks her if he can crash on her couch. Laura invites him up and wryly says, "We can negotiate where you'll sleep."
The ADA eventually works out a deal for 14 months, feeling lucky to get that without the gun, but when he and the counsel for the defense try to present it to the judge, Mr. Daniels pulls out a gun of his own and takes the judge hostage in an attempt to make his son's killer go on trial. After barricading himself and the judge in the judge's chambers, he tells the SWAT team that Kelly is the only cop he'll talk to. John, informed that the police shooters have a clean shot at Mr. Daniels and will take it if things get any tenser, tries to convince Daniels that this won't change what happened to Curtis. He promises that if he gives up now, he won't go to jail, and pleads, "Don't die in here. He's not worth it."
Daniels surrenders, but the humiliated judge tells John that no promise made to Daniels about immunity was binding. John asks the judge how it'll look to give Curtis' killer only 14 months and then send his father to jail, and scorns the judge's method of governing by law. "I work the streets and have to clean up the messes made by your way," he sneers. "Your way stinks."