There's a new boss who comes from IAD with a mandate to clean up the squad. Andy receives a dead rat in the mail. John is heading off the rails. A doctor is found dead, and linked to a man who had a sex change.
Detective John Clark Jr., Andy Sipowicz who just was promoted Sergeant and a military investigator examine the murder on military recruiter Sergeant Lester Bakewell, whose affair with a female colleague caused her divorce from a retired veteran Colonel; however the prime suspect is student Paul Corbelli, whose father was killed in service in Iraq. A woman reports her homeless Basque Uncle missing abnormally since four days; he's found dead and Detectives Baldwin Jones and Greg Medavoy investigate.