Even though he saw all that happened, John feels like he has no choice but to arrest Nathan for manslaughter and hope things can sort themselves out later. Nathan, who has led a clean life ever since a short jail stint for posession when he was 18, can't believe that his friend would put him back into a jail cell, even for a little while.
Unfortunately, Nathan's angst gets him into trouble when he punches out a prison guard and tries to escape, which only adds an assault charge to his list of problems. John visits Nathan, now manacled because of his earlier outburst, in lock-up, and tries to make peace with him, even offering to ask the guard to drop the charge. Nathan realizes John is on his side, and asks for help in getting back to his family.
During his testimony to the grand jury, John tries his best to paint Nathan's side of things in a positive light, but the district attorney insists on asking if it seemed like Nathan struck in self-defense, which, John has to admit, he didn't. But after the coroner testifies that Larry had a dissecting aneurysm, and would likely have died even if Nathan hadn't hit him, the grand jury declines to indict.
But even though the initial charge was dropped, Nathan still has to stand trial for felony assault on the guard, Corrections Officer Hardwick. Kelly tries to convince Hardwick to cut Nathan a break, but the prison vet refuses to drop the charges. At the arraignment, Nathan is assigned a bail much higher than he can afford, and makes an impassioned plea to the judge, stating how sorry he was to have struck Hardwick, and asking, "Can I have my family back? Can I have my life back?" Hardwick, moved by Nathan's words, agrees to reduce the charge to misdemeanor assault with probation, and Nathan and his wife embrace.
At the next scheduled game, Nathan is late, and John and the other three buddies start wondering whether they should prepare to play 2-on-2, when Nathan finally arrives. Needing a sixth player, they ask a random gym-goer if he can play. He confesses that he's not very good, "but that never stopped you guys." Figuring that this kibbitzer will fit right in, the others invite him to play, and the game resumes.
Lt. Fancy manages to get approval for Kelly, Sipowicz, and James Martinez to canvas motorists at the off-ramp nearest to the shooting. One particularly impatient driver keeps leaning on his horn during the delay, and roars away without bothering to answer any questions, flipping Sipowicz the bird in the process. Andy doesn't take the affront lightly, and hops into a squad car to chase after the jerk, and, after cutting him off, decides to make the interview process move as slowly as possible.
Returning to the precincthouse after a fruitless morning, John and Andy find an angry Mr. Zimmer waiting for them and demanding to know why they're calling all his friends and relatives to find out whether he might have wanted to kill his wife. The detectives try to explain that all investigations start by ruling out every possibility to see what's left, but Zimmer doesn't buy that and stalks off. Andy figures they should probably attribute Zimmer's outburst to his grief, but even though the physical evidence says that the shooter had to have been in another car, he can't help but wonder why Zimmer makes him suspicious.
Fancy, deciding to gauge how much young Martinez has learned from spending time with the detectives, asks him what he thinks they should do with the investigation at that point. James suggests distributing information flyers to motorists, but other than that, figures they're at a dead end. Fancy agrees, and tells John and Andy to put themselves back into the rotation. Andy decides that before he starts on a new case, he'd like to "agitate" Mr. Zimmer a little to see what happens. He calls Zimmer to ask about his life insurance policy, and gets an earful of profanity for his trouble.
The next day, Zimmer comes to the precinct armed with the results of a lie detector test he just took with a reputable polygraph expert. Andy studies the results, and, sure enough, Zimmer didn't kill his wife or take part in a plot to do it, but he suggests that Zimmer take a second test and say whether or not he knows more than he's told the cops. After a little more prodding from Andy to unburden his soul, Zimmer finally breaks down and says that he did kill his wife. After declining a lawyer, he explains that while he was driving on the FDR, he got cut off by another car, lost his temper, and started a game of high-speed chicken with the other driver to keep the man from passing him. As Zimmer's wife screamed at him to stop, the other driver pulled up next to them and fired a shot, killing her. Zimmer admits that he got a good look at the man and the license plate number, but was too ashamed to give it to the police.
Andy tracks down the plate number from the DMV, and sure enough, the car's owner is in posession of the murder weapon. Zimmer identifies his wife's killer in a line-up, then tries to attack him as he's being escorted to holding. Andy and James break it up, and as Zimmer and the murderer continue to yell at each other about who should have pulled over, Andy angrily suggests that the two go another round in some bumper cars if they're going to act like children over a matter like this.
During the raid, the cops seem to have all the dealers subdued when a skell bursts out of a closet and aims his gun at John. Janice, the only one to spot him, screams a warning to John, who swings around and empties his weapon in his assailant's direction, and though he misses with every shot, the perp is scared enough to drop his gun and surrender.
At a bar afterwards, Kelly, Sipowicz, Licalsi, and Lucas have a few drinks (Andy sticks with club sodas) and crack jokes about Kelly's unorthodox method of subduing the perp. After Lucas heads home to his wife and Andy goes to get another round, John and Janice find themselves alone for the first time in a while. Both admit that they've been thinking about each other. John says that, the murder of Marino and his driver aside, he's having trouble getting over the fact that Janice only approached him at Marino's orders. Janice assures him that while that's true, she went to bed with him because she wanted to, and killed Marino because she didn't think she had any other choice. John asks for some more time to think.
The next day, John decides to go to confessional to sort out his feelings about Janice, but can't get very far because he refuses to tell his priest exactly what Janice did. Eventually, the clergyman gets frustrated and tells John, "Why don't you come back here when you're ready to stop acting like a tubesteak?" John exits the confessional booth, and is quickly followed by his priest -- who, as it turns out, is Jerry Downey, one of John's basketball buddies. Jerry apologizes for losing his temper while acting in his official capacity.
That night, John goes to Janice's apartment. She opens the door, sees him, and beams as she invites him in.