In New York City, a man named Brian Egan has been arrested for setting off a gas bomb in a subway that killed 20 people. He begs authorities to see to his family's protection in Baltimore, but will not reveal why he fears for their lives until he knows that his son is safe. This prompts the detectives to investigate further. Meanwhile, Egan's family is indeed attacked in Baltimore, leading to his wife's death and his son's attempt to flee the city before Detectives Frank Pembleton and Tim Bayliss chase him down.
NYPD Detectives Lennie Briscoe and Rey Curtis travel to Baltimore to aid in the investigation, and it becomes apparent that the two cases are linked to a gas attack in a Baltimore church five years earlier that killed six people. The investigation leads to the mastermind behind all of the attacks, an anarchist and Special Forces Vietnam War colonel named Alexander Rausch, who reveals that his bomb attacks on black communities were motivated by a desire to start a race war. Though Rausch is in the custody of the Baltimore police, NYC Assistant District Attorney Claire Kincaid demands extradition, creating tension between Pembleton/Bayliss and Briscoe/Curtis and starting a court battle between Kincaid and Baltimore District Attorney Ed Danvers. A Baltimore judge approves Kincaid's extradition order as all the detectives make their peace with each other.
As the detectives escort Rausch to the train station for his return trip to New York, he suffers a heart attack brought on by deliberately failing to take his medication. Pembleton, who had personalized the case, is heartbroken that Rausch has avoided the consequences of his actions.
In a comical subplot, Detective John Munch discovers that, after one of his ex-wives divorced him, she had a brief sexual relationship with Briscoe. Munch also learns that he is not as good a pool player as he thinks, losing $500 to Briscoe in short order.