A wife and an 8-year-old blind daughter of a Navy Captain are kidnapped and the Captain is a hostage in his own office, communicating with kidnappers, who watch his every step via computer camera. NCIS team investigates the scheme where a large amount of money is involved.
The mummified remains of a woman are found in the abandoned compound. The team discovers that the woman was missing for several months, was wearing a wedding dress when she died, and might have been a victim of a serial killer. The search for the murderer leads them to Florida, where they start looking for another woman who mysteriously disappeared after going to work. One of the clues they have is the old manual for good wifes.
A marine helicopter is discovered in the middle of a crop circle in a rural area and the pilots are missing. Soon, NCIS discovers that only one of the pilots was on the flight, that there is a decade long feud going on in town, and that the missing pilot is out for revenge.
A body of a woman in a Navy uniform is found by two sailors. Ducky links the murder to an unsolved case 10 years ago, and starts behaving strangely. A serial murderer leaves a note on the body, promising to return.
The NCIS team finds a place where the mob has been dumping bodies for a long time, and one of the victims is an undercover FBI agent. The FBI suspect a mole and arrest Fornell. Gibbs sets out to find the real mole and clear Fornell.
When an Iraq veteran is threatened by a group of terrorists, the NCIS team steps in to protect her. While trying to convince an FBI Agent to help them, the team is convinced that they've discovered the bomber. However, things might not be what they seem.
Ernie Yost, an elderly Marine veteran and Medal of Honor winner, confesses to murdering his best friend almost 60 years ago in a war battle and the NCIS's job is to solve all the secrets and save Ernie from prison.
A Navy Commander dies after a successful surgery. While researching the commander's past, the team finds out that he earned a lot of enemies lately and tracks down a ensign, making him the prime suspect. Soon Abby realizes that they've got the wrong man.
A Marine's wife, shoots an intruder in self defense when he is about to rape her. The team finds out that the wife was leading a double life, while her husband was serving overseas. Allegedly, she has been chatting with a stranger on the net and had no idea about his true intentions. The team believes that she might have lured him to her home, not knowing that he is a serial rapist.
While on an undercover operation as an escaped prisoner who is forced to stick to a convict that owns a key to an expensive ancient Iraqi sculpture, Tony mysteriously disappears. The GPS locator that Abby planted on him doesn't work anymore and the team must find Tony, because his life is in jeopardy.
A Navy officer's body, which was missing for 2 years, is found in a car pulled from a lake by a private investigator, who now wants to have the reward posted by the family. The disappearance turns out to be a murder when the team finds a bullet inside the car.
The team takes upon an unusual case when a telemarketer reports a possible murder of a petty officer who appeared to be dying over the phone. With the help of the Virginia officials, the team finds out it was just a practical joke. However, the person is soon found dead.
A "meat puzzle" stars when Ducky identifies the pieces of three bodies that were stuffed inside a barrel few months ago. They turn out to be bodies of a sheriff and a prosecutor that worked with Ducky on a rape case 10 years ago. Gibbs believes that Ducky might be the next victim, so he orders to keep him and his mother safe. Even so, Ducky gets kidnapped between the investigation and now the team must find him before it's too late.
A woman claims to have seen a murder of a sailor in an apartment across from hers. Gibbs assigns the case to Tim who believes that he can resolve it himself. However, when the less of physical evidence happens, Tim pursues the team to help him.
A Marine falls off a cliff, and his camera records him falling. The prime suspects are his wife and his best friend with whom he had a picnic in the camp. Gibbs finds out they had an affair behind a dead man's back and he tries to persuade one another to blame each other. In the meantime, Abby reconstructs the case using her computer skills to handle the Marine's camera.
NCIS starts the investigation after petty officer Manda King is found dead in the bartender's bed. The suspect is the owner of the competing club where Manda's sister sings.
When a Petty Officer working in the Intelligence receives a pair of blue eyeballs in the mail, the NCIS team starts investigating the case. The sailor commits suicide during the investigation, which leads the team to one of his lecturers, who is working for the CIA in Panama.
A petty officer who had just returned to her job is found dead backstage at a bikini contest. The team suspects that the victim may have had a stalker.
The team investigates a suicide case, believing that the main reason of her death is a nervous breakdown, but Ducky believes that she was actually murdered. FBI Special Agent Fornell helps them in the investigation. The traces lead them to revelation that she was involved in a love triangle.
A marine is found murdered on the school campus, and the NCIS discovers a suspect immediately. However, they are back at zero point when they find the suspect murdered. Tim & Abby discover a trace in the e-mails, called "Red Cell," which leads them to believe that the marine must have been involved in a serious death game.
After a young Navy corpsman is killed in Iraq while saving the lives of several marines, the body of a young woman is found with his belongings in storage at his hometown. The evidence seems conclusive that the Petty Officer was a murderer, but Gibbs believes that he was innocent and decides to prove it so that he can be buried with full honors.
When Tony opens a mysterious letter thinking it's for him, a small puff of white powder comes out, releasing a possible deadly virus. Kate calls for help and as a precaution, she and Tony are isolated in a bio-hazard isolation room. While McGee and Gibbs are determined to discover who sent the envelope and how to cure their friends before its too late for them, Tony's health gets worse.
A group of serial terrorists seek revenge and send Ari on an assignment to kill Gibbs. The NCIS team goes on a hunt after him, but when they discover that Ari has a second plan, it is already too late... the NCIS team will have to face the death of one of their team members.