After the terrorist's attack, the NCIS team are shocked and are 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.
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.
Gibbs is ordered to talk to a convict that is about to be executed, in order to discover information about the place where he hid his victims, but when the plan doesn't work, the team must solve the case in their own way.
When a corpse of a man is found inside a tomb that comes from the Civil War, the team discover that the victim, a Sergeant, was buried alive. During the investigation, Abby tracks down the last phone call of the victim.
When an officer is shot to death on the freeway, the NCIS team take on the investigation. The first lead, a fact that the victim was leading a double life, take them to a possible solution of the crime, but the tables are turned when the victim's dying message is discovered and it leads them to a totally different clue.
The NCIS team take up a strange case - a Marine's wife was murdered live on the Internet. The investigation reveals that two housewives were running a live Internet sex site and now they are both missing. While looking for them, the team will try to track down the webmaster and solve the alleged murder case.
When a six-year-old boy informs the NCIS team that his father was kidnapped, the team discover that the missing father is actually a Lt. Commander working on a secret project named Honor, and that he is the only one who has the code that can open the project.
When bodies of two hired assassins are delivered to the NCIS team, Ziva and Tony go undercover assuming the victim's identities in order to find the person who hired the assassins for their mission. Gibbs discovers that his team are not the only ones working on the case.
Tony is accused of murdering a woman whose body was found at Quantico and the team must prove his innocence.
While on duty, McGee kills a man who is later discovered to be an undercover police officer. When Jen decides to approve the investigation on McGee, the NCIS team are forced to prove that McGee is not guilty, pushing Gibbs' relationship with Jen to the limit.
A supermodel dies while filming a reality show on a Marine base, and the NCIS team must discover who is the model's murderer. They discover a love triangle between the model and three other men, all suspects.
While looking for smuggled weapons at a shipyard, Tony and Ziva disappear and it's up to NCIS to find them. Abby tries to find them by tracking down their GPS chips, but they seem to be out of reach.
When a Lt. Commander in charge of a shipment of fuel rods for nuclear power stations disappears, the NCIS team are called in. The team must solve the case in time, before the person who kidnapped the Commander finds out the secret location of the fuel rods or harms the Commander.
