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.
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 discovers that the victim, a Sergeant, was buried alive. During the investigation, Abby tracks down the last phone call of the victim. Meanwhile, Gibbs is informed by his new boss Jenny Sheppard that agent Ziva is now a full-time NCIS agent.
When a non-commissioned officer is shot to death on the freeway, the NCIS team takes upon the investigation. The first lead, a fact that the victim was leading a double life, takes 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 takes upon 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 6-year-old boy informs the NCIS team that his father was kidnapped, the team discovers 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. While Gibbs gets closer with the boy, the rest of the team discovers that the project has been hacked in and the information inside has been deleted. Is the missing man innocent or is he actually the guilty one?
When bodies of two hired assassins are delivered to the NCIS team, Ziva & Tony go undercover assuming the victim's identities in order to find the person who hired the assassins for their mission. While working on the case, Ziva & Tony spend some quality time in a luxury hotel and the attraction between them arises. Gibbs discovers that his team is not the only one working on the case.
Tony is accused of murdering a woman whose body was found at Quantico, and the team must prove his innocence. All the possible evidence proves that Tony is guilty, and the team will give their best to set their agent and a friend free.
While on duty, McGee kills a man who is later discovered to be an undercover police officer. When Jenny decides to approve the investigation on McGee, the NCIS team is forced to prove that McGee is not guilty, pushing Gibbs' relationship with Jen to the limit. Meanwhile, Tony is troubled by his past.
While filming a reality show on a Marine base, a supermodel dies 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. Meanwhile, Jenny is disturbed by Gibbs when he doesn't want to attend an award ceremony in his honor.
While on investigation at a shipyard, looking for smuggled weapons, Tony and Ziva disappear and it's up to NCIS to find them. Abby tries to track them down by tracking down their GPS chips, but they seem to be out of reach. Meanwhile, Tony and Ziva, trapped in a container, find evidence which could help them solve the case.
When a Commander in charge of a shipment of fuel rods for nuclear power stations disappears, the NCIS team is 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 Lt. Commander.
The NCIS team investigates the murder of two Marine wives, and must find the murderers before they attack their next target, another woman.
While discovering an illegal automotive chop shop, the NCIS team stumbles upon a severed head of a Marine, hidden in one of the cars from the shop. When they find possible suspects, the team will have to find the rest of the body and find the murderer.
When an ambulance explodes while carrying the remains of a Marine's body that was killed in a car crash, the NCIS team is called in to investigate what actually happened. The investigation leads them to some sudden discoveries -- the DNA of the victim found in the ambulance doesn't match the Marine's DNA; the ambulance was set up to explode; and the family of the dead Marine is hiding a very important secret.
When a Petty Officer's dog tags are found in a national forest by a group of teens, the NCIS team is called in to investigate. While searching for the campsite of the sailor, the team finds out that there was another person, possibly a woman, with him. The investigation takes them to an even more higher discovery -- there could be a serial killer killing women in the national forest.
The NCIS team must stop a teenage student from detonating a bomb attached to his body, while he's taking the other students hostage at a Quantico base high school. Gibbs tries to stop him when he enters the classroom, only to realize that there may be someone else controlling the teenage student from the outside. Meanwhile, while Gibbs is in the classroom, Tony is left in charge.
Gibbs and the team are called in when a couple of kids stumble upon the body of a missing Marine in a frozen lake. As the NCIS team searches the frozen lake bed for clues, they come across three more bullet-ridden bodies. During the autopsies, Ducky and Gibbs discover that the three additional victims had gang tattoos. With this crucial piece of information, the team works to uncover the Marine's connection with a deadly street gang.
When a Pentagon cryptographer is found dead, the NCIS team has to discover whether the person was or wasn't a Pentagon mole, and if the person committed suicide. As the investigation continues, the team discovers that the person wasn't alone when she died, so someone must have murdered her. So, the team has to find the person, a mole, who murdered the cryptographer.
While working on just a regular murder case with the rest of the NCIS team, Abby is almost killed by an evidence from the case and soon it becomes clear that the murder was staged, and that someone wants Abby dead. The team discovers some enemies from Abby's past, and they must find out who is the person, before the person kills Abby.
The NCIS team must protect Ziva when a suspect dies while being in custody, and her tactic might be the reason why the person died. The things become much more dangerous when the suspect's brother kidnaps Jenny, and demands the release of his brother in exchange for Jenny, but he has no idea that his brother is dead.
While working on an assignment, Gibbs is seriously injured in an explosion, and taken to a hospital, where he recalls his painful past, which he has always hidden from others. The rest of the team must proceed with the investigation and put their feelings towards Gibbs's injury aside. Tony is left in charge, which may cause a bit of trouble.
The NCIS team must work on an assignment against a terrorist group without Gibbs, who is still recovering from the explosion. Gibbs has to fight with memory loss, while he's visited by his mentor and his former boss. His help is needed, especially when the team discovers that Gibbs is the only person who has information about the terrorists' plans, so he needs to retrieve his memory before the terrorists attack.