Kellerman and Lewis (with Brodie) investigate a shooting at the New Moon motel, where everyone there has a motive for the crime. They split up and canvass the denizens of the motel; Lewis also searches for the victim's missing boot. The murder is just one of the many crimes that has occurred or is occurring at this establishment.

Bayliss has disappeared again as Pembleton and Brodie make their way to the scene of a shotgun suicide. The victim appears to be Beau Felton. Gee's letter, including information gained in the ""Burundi"" case, begins to make an impact at the highest levels of the department. Frank returns to the department with the news about his case. Lewis goes off, wondering who is going to be next. Det. Falsone comes to the squad with news about why he thinks Beau Felton killed himself. Lewis and Stivers discuss the Mahoney shooting. Cox finds something interesting about the Felton case; she digs in deeper and the results change the case to a murder. Bayliss turns up the next day and disappears again to his Uncle George's place. Pembleton and Howard try to work with Falsone to find Beau's killer. Gee finds out that Beau had been working undercover for the past six months on the Cantwell auto-theft ring. Megan Russert returns from France.

The semi-nude body of a man is found in a dumpster outside of a restaurant. Bayliss returns Cox a pair of her earrings that she'd left at his place the night before. Disturbed by him doing that in public and while at a crime scene, she suggests they take some time off, instead they decide to break it off. The owners of the restaurant thinks that this murder might be tied to another murder (one that Munch is working). Lewis confronts Kellerman about the Mahoney videotape and the need to let Stivers know that she is also ""in the soup."" Lewis tells Stivers about the videotape, so she demands a meeting with Kellerman. Falsone confronts his ex-wife about getting to see his son more often; however, they argue and he plans to pursue getting joint custody. Kellerman decides that he will try to force Georgia Rae's hand, since he doesn't plan on doing anything corrupt for her anyway. Kellerman tells Georgia Rae that she can do whatever she wants with the videotape, he doesn't care. Bayliss decid

MGee (Mike Giardello) and Ballard investigate a double shooting at the home of a prominent sports doctor and his wife, a dermatologist. The doctor (who was wounded) did not realize the deceased (thought to be a prowler) was his sister-in-law. Munch contends with the IRS; his Waterfront partners want him to make sure that his cousin, their accountant, has been paying their taxes. The Waterfront needs a loan to pay for some improvements. Gharty has taken the day off, to take care of personal matters, like his recent separation from Flora. Munch has his hearing with the IRS; he owes $30,000 in back taxes. Bayliss and Sheppard discuss his sexuality and the possibility of a date. Falsone takes MGee and Ballard to meet an old fight man who knew their doctor. Ballard becomes excited while watching Falsone spar in the ring. MGee and Ballard's investigation lead them right back to the doctor's house, where his wife may be guilty of conspiracy to commit homicide. Gharty stops by the Waterfront t