A Navy chaplain, Commander Derrick Reza, is found dead following a car crash, but the intrepid NCIS team quickly figures out that he was dead long before the traffic accident. They immediately begin investigating his death as a murder.
Reza was a well-liked member of the Interfaith Association and no one seems to have a motive to kill him.
They soon learn, however, that Reza had sensitive classified information on his laptop, all of it related to a detainee at Guantanamo Bay named Amir, who was linked to another, more dangerous terrorist. With the help of translator Qasim, they discover that the transcripts of Amir's interrogations had been altered.
Bishop and Qasim fly out to Cuba in person to question Amir and confirm that there was indeed a great miscarriage of justice. The original translator had been ordered by his defense firm employer to ensure detainees were kept longer when they hadn't given up anything valuable.
Eventually, the team discovers that Reza's death had nothing to do with Amir; Reza had discovered that the head of the Interfaith Association had embezzled a large amount of money earmarked for charities. When he confronted him, the other man killed him.
Meanwhile, Bishop's three brothers visit and relentlessly try to figure out the identity of her mystery boyfriend. In the end, she reveals him to be Qasim the translator.