The hummer bust doesn't hold up in court, despite Andy's fanciful theories on how Giardella could've picked up the nails at a construction site. ADA Sylvia Costas, stuck with Sipowicz's garbage case, chastizes him for wasting her time. Sipowicz's boss, Lt. Arthur Fancy of the 15th Detective's Squad, is equally nonplussed, and tries to convince Sipowicz's younger partner, Det. John Kelly, to abandon Andy to salvage his own career. Kelly backs his partner in front of the Loo, but when he approaches Andy -- getting loaded at a nearby bar while still on duty -- he's much harsher, and decides to call it quits with him after Andy brushes him off.
Feeling abandoned by his partner, Sipowicz decides he has nothing left to lose. He confronts Giardella at the mobster's favorite restaurant, pulls a gun on him, and forces him to chew on his wig. Kelly, who knew what Andy was planning, arrives in time to stop things before they get lethal, but Giardella is completely humiliated and vows revenge.
Internal Affairs catches wind of Andy's stunt and places him on "modified assignment" -- with no gun and no shield. Seeking solace, Andy leaves the precinct and heads towards his regularly scheduled appointment with a hooker named Lois. But their latest tryste doesn't get past the undressing stage, as Giardella -- who'd been tipped off by Lois -- bursts into Lois' apartment, empties his gun into Sipowicz, and walks out.
The bullets don't kill Andy, but he gets rushed to the hospital in critical condition. John doesn't feel the need to do much investigating -- he knows Giardella did it. He heads to a mob social club to confront Giardella's boss, Angelo Marino, and demand that he give up Alfonse. Marino refuses. In the middle of shoving some mob goons off his back, Kelly unwittingly knocks out a surveillance microphone planted in the club by the police's Organized Crime Unit, which doesn't endear him to OCU Inspector Lastarza.
After Lt. Fancy tries to take him off the case, Kelly grabs his temporary partner, young James Martinez from the Anti-Crime unit, and proceeds to roust several Marino businesses with the same message each time: this will continue until Marino gives up Giardella.
Giardella and his attorney, James Sinclaire, show up at the precinct the next morning to make a statement -- that Giardella was on his way down to Atlantic City at the time of the shooting, and has a number of corroborating witnesses. For the time being, he's let go, and Sinclaire extends Kelly an invitation to meet Marino for dinner that night. Marino asks Kelly to leave him alone and let him handle the matter (Giardella acted without checking with him first) internally. Kelly refuses and storms out of the restaurant.
After nearly two days of avoiding it -- mainly because Andy is in the same hospital where John's own father died after being wounded in the line of duty -- he finally screws up the nerve to see Andy. He speaks to his comatose partner as if he were awake, and, when he takes Andy's hand to say goodbye, is surprised when Andy's hand closes around his.
At the precinct, John approaches uniformed officer Janice Licalsi, who used to work in Queens, and asks her if she can help in getting a sector car to regularly drive past his old building. She's more than happy to help, and surprised to find out that Kelly and his wife are getting a divorce.
Kelly gets a visit from Josh Goldstein, a neighbor from apartment 4B in John's old bulding. "4B" is a lawyer and has volunteered to act as a go- between between Laura and John. John spots a gun in Goldstein's briefcase; the young man says he bought it because of the recent crime in the area, and promises to get a permit.
John misses an appointment with Laura and Goldstein because of Andy's shooting. Laura attempts to chastize him for it until she finds out the reason why. Janice offers John a sympathetic ear should he want to get a beer and talk about Andy, and he takes her up on the offer. They hit it off, are soon having dinner, and, eventually, making love back at John's apartment. Unfortunately, Laura picks that moment to stop by to find out how John's coping; when she finds out that her bathrobe-clad ex has "company," she angrily accuses him of not caring about her or Andy.
The next night, John gets a call to go to his old building, where Goldstein has just gotten mugged while doing his laundry. Laura apologizes for being harsh towards him the night before, and John forgives her.
While John is at the hospital with Andy, Marino meets Janice in an underground parking garage and asks her whether she thinks Kelly will back off. She expresses doubt, and he tells her to kill Kelly. When she asks how, he replies, "You're a cop. Figure it out."