This episode opens with a man waking up in a car, with a dead body next to him. He realises that he is tied up and he manages to escape. We then see that he is on a training base for the army and that a bomb was just dropped on top of where he just was in the car. The NCIS team are called in and then we learn that the victim died in the bomb attack. As Gibbs investigates he discovers the other victim which was all ready dead in the car. As Abby and McGee run the prints through AFIS, their computer gets hacked. When they finally manage to trace it back they find that the FBI were hacking them. Ducky calls the team into the morgue and we learn that the first victim (the one already dead in the car), was a missing man who went missing in 1999, although it appears that he died recently. Ducky then reveals that he was killed and then frozen. The FBI leader is then arrested for being involved with the Mafia, who trapped and killed many victims on the army training base site. We then see him hanging himself in his cell. Gibbs sets up a met with the Mafia to try and find out who they really have on the FBI pay role, and to help clear the FBI leader's name.
The FBI man on pay role was the one who Gibbs took with him as back up. At the end we see the FBI leader who hanged himself walking out of the NCIS building with Gibbs. The entire team look shocked.