A truck with three handcuffed federal prisoners arrives at the 27th precinct. FBI and NYPD officials discover that one of the prisoners has mysteriously been murdered. The FBI officials assert jurisdiction and transport the other two to a federal prison. One of the two is a suspected IRA member who has been detained in the U.S. for five years without charge, bail or trial. Shortly afterwards, the remaining prisoner is discovered hanging in his federal prison cell. A prison guard is discovered to be an IRA member; he confesses to the prisoner's murder. Detectives and prosecutors face resistance from federal authorities as they pursue murder charges against a suspected IRA member serving time in federal prison, after he is suspected of killing another federal prisoner.

Suspicion grows in the department after incriminating evidence is erased. Captain Cragen is implicated in the internal affairs investigation. The detectives and prosecutors work together to get his name cleared.