A blogger from Pittsburgh is killed in his hotel room. The NCIS team investigates because the man, Penn, had Top Secret Navy documents, which were stolen. Penn was not just shot, his tongue was also cut out.
Penn was investigating a case involving a SEAL mission in Bolivia, involving members of the SEALs' elite Shadow Unit. While the SEALs express an incredible dislike for Penn, Sebastian sticks up for Penn and his integrity. While talking with a Bolivian who operated a restaurant Penn ate at before he died, the Bolivian claims that the SEALs were responsible for a massacre of seven men, who had their tongues cut out.
He directs them to Dalton, who runs a relief group. Dalton provides them with photo evidence that the SEALs were involved with the massacre. The team IDs a potential suspect, Granier, but the man is murdered just like Penn before they can bring him in. They find DNA evidence pointing towards another member of the team, Jansen. Jansen's wife gives them a clue that leads them to the woods. Jansen escapes from Percy and LaSalle and flees into the woods.
Sebastian discovers that the photo evidence was faked. Pride discovers that Dalton is CIA and he was the one who doctored the photos. Percy and LaSalle talk to Jansen, who tells them that the Bolivian restaurant owner is the real perpetrator of the massacre, and that Jansen and Granier were ordered to extract him by Dalton. The Bolivian and Dalton are both arrested.
Meanwhile, Sebastian is looking into Brody's doctored photos. Someone hacks into his computers and invites him to follow the yellow brick road.