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.

An NCIS agent who used to work under Gibbs asks for the team's help investigating a case where sailors on an aircraft carrier are dying of a drug overdose, but have no history of any kind of drug abuse.

A decomposed body is discovered in a tub of acid at a naval base and Ducky and Abby learn that the victim was a submariner. Gibbs discovers that there have been no reports of a sub crewmember missing, so he deduces that one of the subs has an imposter on board. With this new information, the team must find out which sub the man posing as the victim is in and what intentions he may have towards the sub.

The NCIS team head to Cuba to investigate a Navy translator's connection to smuggling at a detention center after he suddenly dies at the wheel of his car when returning to the U.S. from Guantanamo Bay.

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.

When a Navy commander, who was a technical advisor to a civilian contractor for a Navy weapon, is found dead on the beach, the NCIS team investigates the murder using satellite technology.

The team investigates when a Marine recruitment officer is found shot to death by a sniper with a grudge, who leaves a white feather behind.

A navy dentist stops near the parked car to help a stranded motorist who pulls out a gun. The team investigates a murder with the help from a local sheriff, Charley, when they find out about a the similar murder of the Navy civilian employee in the was going through the nasty divorce,the wife is suspected but her alibi is perfect.

Gibbs risks his career when his former commanding officer is accused of stealing the funds.

A terrorist holds Ducky, Gerald, and Kate hostage while NCIS investigate how exactly the terror organization member got a job at the navy base.

After the terrorist's attack, the NCIS team is shocked and is trying to cope with Kate's sudden death, each in their own way. Now, their mission is to collect all the possible info on Ari and find a way to stop him before he does any more damage. Meanwhile, while feeling guilty over Kate's death, Gibbs is informed that the NCIS director is leaving, and the replacement is Jenny Shepard, a woman Gibbs worked with in the past and had a romantic history with.

Still stressed over Kate's death, Gibbs is even more hurt when Ari kidnaps Ducky and decides to play with his mind. Gibbs sends Tony to follow Ziva, and after Jenny and Gibbs are almost shot to death, he is even more determined to finish once and for all with Ari, and Ziva's strange connection to Ari will be just the help that he needs.