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.

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.