An elderly Medal of Honor recipient, Ernie Yost (guest star Charles Durning), shows up at NCIS headquarters and confesses to murdering his best friend during a battle at Iwo Jima almost 60 years ago. Gibbs’ gut tells him there is more to the story and, with the help of his team who are captivated by the warmth of the honored veteran, they work to solve the mystery and keep Yost from going to prison and losing his Medal of Honor.

As Gibbs and his team investigate the bizarre discovery of the woman in a subterranean prison cell made to resemble a 1950's bedroom, the evidence indicates that she had been imprisoned for months and died when her air supply was cut off. Subsequent evidence indicates that this murder may be only one in a pattern of similar incidents and Gibbs and the team find themselves racing to find another possible victim who disappeared from a Navy base in Florida.

Gibbs and his team are called into an uneasy situation when a Navy captain's wife and 9-year-old blind daughter are kidnapped from their home. The kidnapper, who is demanding US2 million in government funds, is also holding the captain hostage in his own office via webcam. Gibbs devises a plan to plant listening devices in the office and then takes a huge risk by instructing the Captain to demand the kidnapper show a gesture of good faith by releasing his daughter before he completes the money transfer. Meanwhile, Abby and McGee use their computer skills to hack into the kidnapper's computer and trace his whereabouts.

The first job for Gibbs and the team is to find the two pilots missing from the Marine Cobra helicopter. After locating the co-pilot, who thought their scheduled training flight had been cancelled, the team continues its search for the pilot amid reports from nearby town people who say they saw strange lights the night the chopper landed. While many, including Abby, are convinced the area has been visited by aliens, Gibbs discovers the truth lies in the town's secret history.

Gibbs notices Ducky acting uncharacteristically abrasive and secretive after inspecting the body. When Ducky confirms his fears, he reveals to the team he has found physical evidence linking the death to a similar unsolved murder that has been haunting him for 10 years.

When a civilian’s body is found on a Marine bombing range, Gibbs and his team uncover the disturbing news that the area has been dumping ground for the Mafia for years. The team quickly discovers that their victim is actually an undercover FBI agent and that Gibbs’ FBI counterpart, Agent Fornell (guest star Joe Spano), is being imprisoned, accused of acting as a mole who has been feeding sensitive information to the local Mafia boss. Fornell denies the allegations and Gibbs sets out to expose the real spy.

Gibbs observes the strained relations among family members as the team tries to convince a tough and unyielding FBI agent, Lina Reyes (guest star Elizabeth Pena), to let them participate in the investigation. Just when the NCIS team thinks they have identified the bomber, another attempt is made on the pilot's life and it is clear there is more to these attempts than terrorism.

The NCIS team discovers that the commander made an art out of making enemies and they track down a young ensign who was relentlessly hounded by the deceased. But as they take him into custody, a scuffle takes place and Kate reacts with fatal results, realizing too late that they have the wrong man. Ultimately, Tony and Ducky combine their knowledge to uncover the person responsible for the commander’s death.

Tony goes undercover as an escaped prisoner chained to a convict who holds the key to the recovery of stolen ancient Iraqi art and sculpture worth millions of dollars. But when the GPS locator Abby planted on Tony becomes inoperable, Gibbs and the team must work quickly to find him by using other methods since Tony is unaware that the thief may be a dangerous killer.

Gibbs and his team discover that while Laura Rowen's (guest star Megan Ward) husband serves overseas, she leads a secret life. The NCIS team tracks a trail of her e-mails to a torrid website, which indicates she may have lured the attacker to her home under false pretenses. As the investigation progresses, the team discovers that they have a serial rapist and killer on the loose who uses websites to stalk his prey.

Gibbs and the NCIS team reluctantly allow the notorious private detective, who located the body, to assist in the investigation as long as he shares information. Fueling the search for the missing man is a one million dollar reward posted by his wealthy family. But when a bullet is found in the car, the missing persons' case turns into murder.

Gibbs and the team step into high gear when Ducky realizes the bodies are those of a prosecutor and sheriff who worked on a rape and murder case with Ducky 10 years before. Ever suspicious, Gibbs feels that Ducky could be the next target of the mysterious killer because of his part in the original case, so he assigns the team the task of guarding Ducky and his senile mother. But when Ducky is kidnapped during the team's watch, Gibbs races against time to save Ducky and capture the demented killer.

When a telemarketer reports the possible murder of a petty officer he was soliciting, Gibbs and the team work together with the local Virginia officials, whose traits are remarkably like those of the NCIS team. Using their computer skills, Abby and McGee quickly discover that the “attack” was a hoax, intentionally staged by the officer. But when the missing petty officer’s body is found, Gibbs’ investigation takes on a whole new angle.

With skimpy evidence to go on, Gibbs turns the case over to McGee, who believes the woman's story is enough to continue the case. But when physical evidence of a crime isn't there, McGee pushes the team to keep looking because he senses there's more to her story than meets the eye.

Gibbs and the team are called in when a Marine is discovered dead at the bottom of a cliff during a camping trip with his wife and best friend, who had an affair. Gibbs plays the former lovers against each other during the interrogation, hoping to get one to say the other is guilty. Meanwhile, Abby must put her superb technical skills to the test when she reconstructs the camera that was broken during the Marine's fall. Also, McGee gets himself into a very "itchy" situation while investigating the campground.

Gibbs and the team are perplexed when a dance club bartender wakes up to find the woman next to him is not only dead but not the woman he went to bed with. The NCIS investigation leads the team to her sister, Jade (guest star Mya) who is a singer in the bartender's rival dance club.

The investigation puts Gibbs and the team on the trail of a former Navy Intelligence agent who is now a private contractor working in Paraguay. With a little help, Gibbs learns the rogue agent is involved in illegal activities and sends Tony and Kate to Paraguay to make an arrest.

Gibbs and the team trace the Petty Officer's activities since returning from sea duty and they discover a possible stalker who had just been released from prison. But when his location is accounted for at the time of the murder and Ducky's autopsy reveals the Petty Officer was pregnant, the team discovers that jealousy may be the motive for her death.

Gibbs and the team are stunned when Ducky tells them that the Petty Officer, who claimed to have a stalker, was in fact murdered and did not commit suicide. With the help of FBI Agent Fornell (guest star Joe Spano), the team’s investigation reveals the Petty Officer was a victim of a twisted love triangle involving her C.O., who was being investigated by the FBI for kickbacks received from Navy contractors.

When the NCIS team begins their investigation, they quickly turn up a suspect but when he is later found murdered, the team is back at square one. Abby and McGee discover an email chain on one of the suspect's computers referencing a mysterious "Red Cell." Gibbs and the team discovers that the possible motive may have been a game with deadly consequences.

After a corpsman, whose actions in combat saved several lives, is killed in the line of duty, the body of a young woman who disappeared before he enlisted is found dead in a storage locker amid his possessions. Local police are convinced the corpsman is responsible for the woman's murder, but Gibbs thinks otherwise and is determined to clear the young man's name.

Gibbs and the team are forced into quarantine in the NCIS autopsy room pending the results of tests to identify the strange powder. As Abby discovers the substance is a genetically altered version of the plague, Tony and Kate are placed in a bio-hazard isolation ward for fear of exposure. In the clear of the deadly virus, Gibbs and McGee race to track down who sent the letter before the deadly plague destroys one of their team members.

Gibbs' worst fears are confirmed when he learns that his nemesis, Arab/Israeli double agent Ari (Martin), is back in Washington D.C. on assignment to kill him. Ultimately, the NCIS team discovers that Ari has a bigger plot… and they end up paying the ultimate price trying to thwart it -- the death of a team member.