The FBI investigate the disappearance of Andy Reynolds who vanished after appearing in a police line-up in a rape case. He was released by the police but hasn't been seen since. The FBI learn that Andy had served 5 years in a military prison after confessing to to raping a young woman while stationed in Japan. Andy had a steady job working for another ex-Marine, Nelson Wolpert, but seems to have returned to Japan soon after the line-up. Jack Malone heads to Tokyo while the team in New York City continue the investigation. As they continue to gather evidence, the agents come to believe that Andy was innocent of the rape charge he confessed to.