This episode opens with Pembleton explaining to Bayliss about a horrific crime that took place five years ago, where six African American's were killed in a Church fire. The detectives head to the Egan house where they question Stephanie Egan, whose husband Brian is doing time for a brutal subway attack that killed 20. The detectives ask about the Church fire, but Stephanie says her husband didn't have anything to do with it. When Kendall gets tired of the questions, the detectives leave, with the idea that the mother and son are in fear for their lives.
Not 2 hours after interviewing Mrs. Egan Pembleton and Bayliss arrive back at the house where she is found dead, the ME thinks she could have poisoned herself. Egan's teenage son, Kendall cannot be found; a flower delivery man said he saw a kid matching Kendall's description leave the area, the detectives set out to find him. Bayliss gets information from a girl who she saw Kendall with a bloody hand earlier, and said he was trying to catch a bus.
Homicide detectives Lennie Briscoe and Rey Curtis are talking to Brian Egan in his New York jail cell. Egan tells the detectives that "he" (someone) killed his wife to prevent him from talking. Egan begins screaming and pleading with the detectives to get his son Kendall out of Baltimore before "he" kills him. The New York detectives head to Baltimore to find out who this "he" is.
The New York detectives tell Pembleton and Bayliss that Brian Egan will give them the name of his conspirator (also the guy who killed his wife) when he knows his son is safe. Briscoe heads to the detectives bar with Munch and hustles him for $300 in a game of pool. Munch also finds out that Briscoe had slept with his ex wife. Munch also remembers Egan in a picture with Col. Alexander Nathaniel Rausch beside some sort of flying boat. This information cracks the case and the detectives track Col. Rausch down.
Pembleton and Bayliss grill Rausch in the "box" about the church fire, the evil Rausch, referring to blacks says "I want the mongrels to stop feeding on the hard work and good faith of the rest of us".
Danver's and ADA Claire Kincaid from New York go before a judge to see where Rausch will be tried. Kincaid wins and Pembleton and Bayliss along with Curtis and Briscoe escort the racist Rausch to a train station. Just as they are about to board the train to New York Rausch keels over and dies, after apparently poisoning himself. Pembleton is furious and says "they'll never know" referring to the people hearing about Rausch's horrific hate killings.