When a Marine Colonel dies in an explosion at a military golf course, the NCIS team must investigate a suspected terrorist attack with the help from the Army Criminal Investigative Division (CID). The CIA gives them a lead to an abandoned warehouse, but it turns out to be a trap---the warehouse is set to explode. McGee uses his computer skills to break into the secret government files to uncover the terrorist cell.

When an honored Marine veteran is found dead in a hotel, the NCIS team must find out what happened to him. Soon they realize that the Marine didn't commit suicide and that he was a homeless man. After going through his stuff, they find compromising evidence against him, and Gibbs is determined to prove the man's innocence.

McGee breaks the rules, risking his NCIS job, to help his sister Sara, who shows up disoriented and bloodied. While he works on figuring out what happened to his sister, the NCIS team is investigating a case of a Navy sailor, who is somehow connected to McGee's sister. Both Tony and Abby are busy with love problems, while McGee turns out to have another secret.

When a burnt and mummified body of a missing and wanted person is found on a Marine base, in a furnace, NCIS must work with FBI. The burnt man turns out to be a serial killer. The both teams visit the man's family and discover something shocking. Also, the NCIS team must deal with the book McGee wrote about them, using "fictional" characters.

When a robotic vehicle named "Otto," a part of a high level project of the Department of Defense, causes a death of a Navy Lieutenant, and then later almost kills Abby, the NCIS team must find out who sabotaged the vehicle and murdered the Navy Lieutenant. Meanwhile, Ziva realizes that Tony keeps on visiting the hospital. What is he doing there?

When a high-level Marine intelligence officer is found murdered in a small motel room, the NCIS team must find the person who murdered him. After discovering that the person was dead for already three days, and that the town authorities already "investigated" the crime, Gibbs is determined to solve the case, which could be related to a terrorist cell, and not let the town authorities get in his way.

When the NCIS team learns that the missing 10 kilograms of highly toxic chemical weapons are now in the hands of Mamoun Sharif, a wanted terrorist, they will have to find a way to find the man and stop him before it's too late with the aid from Army Lt. Col. Hollis Mann and constant phone calls from Sharif himself.

When a dead body of a sailor is found in an abandoned part of the town, all the evidence seem to point that the person died from unintentional drug overdose, but when the team uncovers more evidence, it turns out to be a murder. Meanwhile, Tony bonds with a local detective while working on the case.

When a supposedly frozen to death Marine turns out alive on Ducky's autopsy table, the NCIS team has to find out about the victim's movements last few days to uncover what happened to him and who left him for dead. As the investigation progresses, the team learns about the victim's trip to Baghdad via a private cargo plane and discovers a link to Gibbs' past.

When a weekend call to the NCIS tip line from an unknown source about possible terrorist activity results in the death of two agents sent into a trap, the NCIS team will have to find out who were the people responsible with the help from Agent Paula Cassidy, who holds herself responsible for the tragedy.

Director Shepard makes a huge mistake by meeting a man alone to inform her about Le Grenouille, as their meeting turns into a murder of the informant. Now the NCIS team must gather all the existing info and try to finally hunt down their enemy.

When a blind photographer shoots the body of a Petty Officer on film, the NCIS team uses his special insight to investigate the crime. Meanwhile, both Gibbs and Tony are having commitment issues in their relationships.

When Jenny has to attend an overseas conference, Gibbs is made acting director, but he prefers to ignore his duties and lead the investigation of the murder of a man, who was found dead in a taxi headed to the NCIS headquarters.

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.

The NCIS team uncovers a huge secret, as their mission to capture La Grenouille comes to an explosive and deadly conclusion.

The dead body of La Grenouille finally surfaces and the entire NCIS is put under the investigation by the FBI, with Jenny as the prime suspect for his murder.

DiNozzo is reunited with his ex-girlfriend, Jeanne Benoit, when insurgents in Sudan attack a group of volunteer doctors, including her husband. DiNozzo and McGee travel to the crime scene for the joint murder and kidnapping case and join the search for the missing doctors.