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.
The detectives tie the death of a pregnant woman to an adoption scam; Medavoy and Jones interview a woman who claims a masked assailant stole her valuable ring; and someone poisons Sipowicz's beloved fish.
A man who cared for his brain-damaged brother is found dead; Medavoy falls for a wealthy woman while investigating an apartment rental scam; Bale tries to nail a man who offered the detectives a bribe.
A call-girl's death is linked to other murders involving women who'd gone through rehab; Ortiz and Murphy investigate the death of an artist who'd been carrying on an affair with a wealthy man married to two other women.
Sipowicz and Clark investigate the stabbing death of a coffee-shop owner who was attracted to young girls; Ortiz tries to keep her cousin out of trouble; and Medavoy and Jones link a murder to a paralyzed police officer and his family.
Detective John Clark Jr., Andy Sipowicz (who just was promoted Sergeant) and a military investigator examine the murder of 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 brother 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.