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Howard and Bolander return to work. Proving to herself that she can handle the job, Kay solves one of Pembleton’s cases without leaving her desk. Giardello convinces Colonel Granger that the building's plumbing must be fixed. Granger sends in Cooder Plumbing to do the work. Shortly thereafter, the fixtures break and flood the bathroom. Giardello discovers that the Cooders are Granger's in-laws, and that they have been double billing the City. After confronting Granger, he leaks the information to the newspapers. Because of the nepotism scandal, Granger is forced into early retirement and Barnfather is promoted to Colonel. Giardello expects the empty captain position to be given to him, but Russert is named to the position. Giardello is angry because he believed in the system.
Pembleton meets Mike Logan, NYPD, at Penn Station to take custody of prisoner R. Vincent Smith. Bayliss is forced to investigate the murder of Gordon Pratt. The cop shooter was killed with a standard police issue Glock. Bayliss suspects his fellow officers but he's alone on an investigation that no one wants to see solved. Pembleton and Lewis clash while they probe the shooting of a white woman near a black neighborhood. Felton gets a rude welcome upon returning to work.
Barnfather gives the unit 48 hours to find the shooter. Lewis runs names of the apartment tenants through the computer and finds that Gordon Pratt, who has a record of weapons violations, lives in Apartment 201, the residence the detectives mistakenly tried to enter. Drummond, Walker, Pembleton and Bayliss search Pratt's apartment. They find teflon bullets and heavy-weather gear. Pembleton, Walker, Lewis, Munch, Bayliss and Drummond take turns interrogating Pratt. To get a confession, Pembleton gets the suspect, a racist, to lose his cool over questions of intelligence. But Pratt calms down long enough to ask for a lawyer. He is released on bond for the assault charge. Later, Bayliss responds to a call at Pratt's apartment building. He finds Pratt dead; no other police officer responded to the call.
Captain George Barnfather has Russert review Giardello's actions in the wake of the shootings. She finds that he initialed the warrant with the wrong apartment number, but she covers for him. Meanwhile, Felton decides not to try and work things out with Beth. He blames himself for Howard's being shot, since he let her though the door first. Finally, he overcomes his guilt and visits her bedside.