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.

When a Navy commander's body washes up on shore along with the bodies of two drug runners, Gibbs refuses to believe that the sailor who was killed was dirty.

The NCIS team investigates when a seaman's body is found at the bottom of the sea in his dress whites, with a ceremonial sword. They discover that he was addicted to a MMORPG. Now, the team must figure out how involved he was in the game and how far he would go to get revenge on his arch enemy, another sailor.

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.

A body of a woman in the Navy uniform is found by two sailors. Ducky links the murder to an unsolved case from 10 years ago, and the team is searching for the serial killer who leaves the note promising to return.

Season 15 begins with the NCIS team tirelessly searching for Gibbs and McGee two months after they were last seen fighting an elusive group of rebels in a Paraguay jungle. Meanwhile, Vance and Torres are summoned to a congressional hearing regarding the fallout from the Paraguay mission.

McGee’s personal life and professional life intersect when a dad from his children’s school is linked to a break-in at a government storage bunker.

Agent Torres finds himself in prison as the team tries to stop an impending terror attack on U.S. soil.