A murdered JAG officer teams up the JAG staff with agents of the Naval Criminal Investigative Services (NCIS).

NCIS Agent Gibbs continues his investigation on the terrorist, Amad Bin Atwa to avert another attack on a Navy ship. Harm is court-martialed for the murder of Lt. Singer.

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.

A Navy lieutenant who was reported missing nearly ten years ago has been found by a deer hunter. When the NCIS team arrives at the scene to investigate, they see that his remains have been mummified. Now, they have to find out what happened to him and what happened to the one million dollars that he had on his ship.

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.

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

The terrorist from Bette Noir returns with a plan to attack the President. Gibbs and his team follow the clues to reveal his identity and find Kate who is kidnapped.

The team takes upon another strange case when a telemarketer reports a possible murder of a petty officer who appeared to be dying over the phone. However, with the help of Virginia officials, the team finds out that officer's call was just a big joke using the computer skills, until he is actually found dead...

When Tony opens a mysterious letter thinking it's for him, a small puff of white powder comes out and it releases a possible deadly virus. Kate calls for help and soon she and Tony are isolated in a bio-hazard isolation room for precausion. McGee and Gibbs work to discover who sent the envelope and how to cure their friends before its too late for them. Meanwhile, Tony's health gets worse...

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.

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, expecially when the team discovers that Gibbs is the only person who has informations about the terrorists' plans, so he needs to retrieve his memory before the terrorists attack.

When Ziva accidentally witnesses a political assassination, she must surrender to the FBI and deal with the consenquences without Gibbs's help, who is now enjoying his retirement. She learns that the FBI is looking for her and escapes, while the NCIS team, leaded by Tony, must prove that Ziva is innocent. However, when things get more complicated, Ziva seeks help from the one person that always trusted her, Gibbs.

When Jenny returns from her European trip, the entire NCIS team will be forced to take a Homeland Security polygraph test, and the deepest secrets of each agent are about to be revealed. Plus, an unarmed Tony and Jeanne are held hostage by a ruthless drug dealer.