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.

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.

After a marine widow receives a call from her dead husband, the NCIS team takes on the case and has to exhume the body to deduce whether the call was a prank or not.

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.

A group of serial terrorists seek revenge and send Ari (guest star Rudolf Martin) on an assignment to kill Gibbs. The NCIS team goes on a hunt after him, but when they discover that Ari has a bigger plan, it is already too late... the NCIS team will have to face the death of one of their team members...

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.

An explosion at a D.C. event that results in a casualty connected to the agency changes Parsons’ perspective on Gibbs and the NCIS team. Meanwhile, without badges, DiNozzo and McGee investigate the case as civilians, despite the case’s dangerous ties to each of them.

Gibbs and Senior FBI Agent T.C. Fornell unite after two British prisoners, including a former spy, escape and arrive stateside via a shipping container. Also, McGee is busy apartment hunting and determined to find out how DiNozzo purchased his lavish place.