A murdered JAG officer teams up the JAG staff with agents of the Naval Criminal Investigative Services (NCIS).

NCIS Agent Gibbs continues his investigation on the terrorist, Amad Bin Atwa to avert another attack on a Navy ship. Harm is court-martialed for the murder of Lt. Singer.

While on Air Force One, a Navy commanding officer dies. Agents from the Navy NCIS decide to take the investigation into their own hands and also force a Secret Service Agent to help. Now the NCIS team has to figure out if the Navy Officer's death was of natural causes or not.

During a training exercise, a marine's parachute fails to open and he crashes into a parked car where two teenagers were making out. The NCIS team heads to the scene and has to determine if the marine's death was accidental or a murder.

A Navy lieutenant who was reported missing nearly ten years ago has been found by a deer hunter. When the NCIS team arrives at the scene to investigate, they see that his remains have been mummified. Now, they have to find out what happened to him and what happened to the one million dollars that he had on his ship.

After being buried alive, a woman comes out of the grave with amnesia and the only thing she remembers is that there is a bomb aboard a Navy ship. While trying to help Jane Doe recover her identity, the team finds out that not everything is what it seemed at first.