Detective Mike Mooney and Trout begin to investigate the murder of a young woman found in a Park Avenue penthouse, only to find their investigation overlapping with an undercover FBI operation at a Russian mob-controlled strip club. In order to keep their sting intact, Preecher and Flynn decide to ""deputize"" Mooney and Trout, thereby keeping them under their watch.
While Mooney and Trout continue to look into the murder of the penthouse stripper, they inadvertently get caught in the middle of an important FBI investigation. Preecher, to prevent NYPD interference in his investigation, orders the detectives to join the upcoming warehouse stake-out of Russian mobsters.
A Washington D.C Bureau administrator attempts to use Sarah Day as his information source within the New York office. Bob Cooper (guest star Dylan Baker, Thirteen Days), an FBI administrator, arrives in New York with questions about the manner in which Preecher is handling stripper Victoria Tomkin's murder investigation. In an effort to uncover the truth, he approaches Day to be his office spy.
Following the warehouse bust, Mooney, Trout and Flynn use one of the men arrested as well as a strip club informant to broaden their stripper murder investigation. Mooney comes to the realization that his sister who is fighting Lou Gehrig's Disease does not have much longer to live and with the help of fellow officers in the department he arranges to take her to see the Passport To The Universe show at the planetarium, something she has longed to see. In an emotional scene, Mooney tells Trout that whenever he hears him (Mooney) complaining about the job, to remember what his fellow officers went out of their way for him to help make his sister's last wish come true. Jimmy Flynn has ambivelent feelings about having removed the illegal surveillance from the back room of Terry Maddock's bar. Preecher compliments Day on her appearance the night before and lets her know that he knows that she left the fundraiser early the night before to help Flynn remove the illegal surveillance camera.
Mooney and Trout, furious that Preecher would rather pursue Stark's involvement in the stripper murder than investigate solid forensic evidence, leave the bureau to return to their precinct.
Mooney and Trout return to the bureau after Preecher reveals previously withheld key information about the Vicky Tompkin murder, and Flynn confronts Maddock with a dangerous ultimatum.