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.
Gibbs is forced to come back out of his retirement to help Fornell, who is being threatened by a convict that escaped from prison. The convict threatens both Fornell and his daughter Emily. Gibbs and the NCIS team re-open the convict's old robbery case, and question a retired sailor who is the only one who contacted the convict after he was sent to prison. The investigation will lead the NCIS team to a surprising discovery.
An abandoned car is found full of blood, registered to a missing Navy lieutenant. The NCIS team learns that the missing lieutenant was profiling men, trying to find a perfect man for herself. When they find out that the woman intended to go to a seminar at a local hotel, Ziva goes undercover to find more information. Ducky is busy going through the profiles of the men. Jenny makes a secret offer to Tony.
After police pull over a driver and arrest him for a concealed weapon, a car crashes into their patrol car with a dead man behind the wheel. The arrested man turns out to be Russian and Homeland Security claim he was working for them. The Russian is linked to an old case that Mike Franks worked on. Mike comes out of retirement to put the Russian behind bars.
When a missing Lance Corporal is found dead in a vacant house, the NCIS team discovers that he was buried in the backyard and then exhumed. They learn about his identity and that he was to be deployed to Iraq, but he never showed up for duty. The investigation leads them to a new clue---he had two fiancées. Abby runs the DNA samples from the two women to find out if the DNA is a match to the soil found on the dead man's body.
It's Halloween and the NCIS team is busy investigating a ransom case. A Marine's daughter has been kidnapped after the kidnapper attacked a Marine in his home. The investigation leads them to a fact that the couple has been separated. They decide to focus on the wife's ex-boyfriend, after learning that the woman is the one who destroyed their marriage. Meanwhile, McGee and Tony are stunned by Abby's Halloween costume.
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.
After catching an international arms dealer, the NCIS team learns that Navy's highly classified weapons system will be sold to "La Grenouille," an important arms dealer. To stop the transaction, the team will send Ducky undercover. Meanwhile, another government agency appears to be working on the same case, with different plans.
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 Navy Lieutenant becomes the victim of radiation poisoning, the NCIS team must find the person who's behind the crime. The Lieutenant, who is working for the IAEA (International Atomic Energy Agency), claims that only his two colleagues knew about his assignment, and whoever it was, the person tried to stop the Lieutenant's next investigation.
When an explosion at a military cemetery mausoleum reveals a crypt full of a mixture of body parts, the NCIS team must inform the families of the victims, hoping to find a connection between the dismembered victims, and narrow down the suspects to find out who is behind the hideous crime. Meanwhile, Abby is dealing with a personal problem, and the only person she can talk to about it is Gibbs.
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.
McGee is under high pressure during the murder investigation of a Petty Officer based on the character for his latest book, with very little information to go on.
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.