The Intelligence Unit finds a man's body in an alley with his penis severed. They identify the victim as a known sex offender and find a witness who saw a woman fleeing from a local park. The woman is Emily Vega and her fingerprints are found on a bloody knife there; she says the victim attempted to rape her.
The picture gets cloudier when the medical examiner tells Atwater and Rixton that the victim didn't die from the missing anatomy but from being strangled. Emily admits that she told her friends about the attempted rape, and Halstead and Rixton are directed to "special police" who admit they had run-ins with the victim.
Digging further the team starts to realize that their victim may be just one of several that the "special police" have killed. Voight confronts the leader, Sergeant Lowdell, but Lowdell refuses to cooperate.
Another witness identifies one of Lowdell's cops, James Mooney, as the last person to have put hands on the victim and Mooney tries to hang himself when left alone in the interview room. Lowdell comes forward and says that Mooney was following his orders.
Meanwhile, after Jimmy has an awkward encounter with Voight at the station, Halstead tells Lindsay he's going to run Jimmy's DNA even though she said not to. The test comes back negative causing Lindsay to confront Bunny, who claims she had no idea. Jimmy accuses Lindsay and her mother of being scam artists and leaves angrily.
Bunny accuses Voight of running the DNA test but also suggests that he have his DNA tested too, reminding him of a night that they spent together, but no definitive answer is given.