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.

While investigating a mysterious death on a top-secret naval research ship at sea, the NCIS team comes upon an abandoned ship which contains a deadly secret that may cost them their lives.

Two members of the NCIS team are sent to Baghdad to investigate a Mortar attack that turned into a murder investigation.

As the hunt for Ziva's replacement begins, Gibbs and his remaining team members must head back to work with the past still weighing heavily on their minds.

The team is assigned to protect Ziva's father, when his attendance at a NCIS conference leads to some unexpected surprises.

The NCIS team undergoes mandatory psych evaluations while investigating the death of a naval commander.

During a routine stop for his morning coffee, Gibbs finds himself staring down the barrel of a gun, forcing him to question choices he has made in the past and present

Gibbs and McGee travel to Afghanistan when a murder case leads them to an Afghan women’s shelter Mike Frank’s secretly supported for years.

The NCIS team investigates copy-cat crime scenes while Gibbs navigates two ex-wives relentlessly trying to get his attention.

NCIS feverishly investigates a global terrorist group that is recruiting teens via the Internet, following a deadly bombing overseas that results in an emotional and surprising loss for the team.

The passengers and crew of a private plane traveling from New Orleans to Washington, D.C., are poisoned and the evidence points to Abby's brother, the aircraft's missing chef.

The episode continues on NCIS: New Orleans S2E12 Sister City (II).

The NCIS team re-examines an ambush on a group of Special Ops snipers in Iraq after an American couple is attacked in the same area six months later. When Gibbs discovers he needs the account of the lone survivor, Marine Gunnery Sergeant Aaron Davis, he tries to connect with the wounded warrior who is being treated for PTSD at Walter Reed Medical Center.

After a Navy lieutenant is found murdered in his hot tub, the team interviews several families in the victim’s peculiar neighborhood. Also, Torres must face the consequences after a volatile night out with Palmer.

Gibbs’ quiet vacation at his remote cabin is interrupted by a surprise visit from Tobias Fornell and Navy Captain Phillip Brooks, as well as a call from NCIS asking for his help locating a robber hiding in the woods near him.