With Gibbs retired and boat-building in Mexico, the NCIS team must learn to work without him. As each team member deals with the absence of Gibbs in their own way, Ziva's past comes back to haunt her when she inadvertently witnesses an assassination of a military attache by her former Mossad partner. Convinced her father ordered the hit, Ziva seeks refuge at the Israeli Embassy. As the NCIS team, now headed by Tony, works to prove her innocence, Ziva reaches out to the one person she has always been able to trust.

A man brought to justice by Gibbs and Fornell manages to escape from prison and manages to make his way to Fornell, to ask him to reopen his case. Fornell is not amused, as he has his little daughter with him at the time. Gibbs is persuaded to come out of retirement once again to help out. The team ask around old accomplices and people the fugitive knew before he went to jail.

A female Navy Lieutenant goes missing when she's attempting to speed-date. Ziva goes undercover at such an event to find out more, and if they can catch the perp. Gibbs sports some facial hair. Ducky is busy profiling the profiles the Lieutenant made before the dating event. Ziva soon finds a possible perp, but it seems other people are involved.

Two Washington Metro cops pull over a guy who was talking on his cellphone while driving. When approaching the drive, they see a gun under the car seat. Just when they have the guy handcuffed, a car crashes into the police cruiser. Turns out the dead guy in the car is a retired Navy Petty Officer. Gibbs calls Mike Franks when they start investigating.

The NCIS team is called to investigate when a real estate agent finds the body of a missing Lance Corporal is found in a vacant house. At the scene of the crime, Gibbs and the team discover that the Lance Corporal was buried in the backyard and then exhumed. After determining his identity, they learn the Marine, who was deployed to Iraq but never showed up for duty, had two fiances. Abby uses her technical knowledge to run DNA samples from the two women and soil from the grave while Ducky uses his newly obtained Masters in forensic psychology to help NCIS implicate the killer.

Gibbs and his team are called in when a marine has been attacked at his home and his daughter appears to have been kidnapped.

A Marine Colonel is killed on a military golf course, leading the NCIS team to pair up with the Army Criminal Investigative Unit in order to find the killer. After the CIA receives a tip about an abandoned warehouse rigged to explode, McGee uses his computer knowledge to get into the CIA informant database to uncover the terrorist cell.

When suspicious activity surrounds the death of a decorated Marine veteran, the NCIS team works to clear his name. The NCIS team investigates when an honored Marine veteran falls to his death at a hotel. After quickly determining his death was not a suicide, the NCIS team discovers that the Marine was homeless but living at the hotel with the help of a maintenance man who was a fellow vet. But when compromising evidence is found in the Marine's room, Gibbs becomes determined to clear his name and prove his innocence.

Forgoing NCIS procedure, McGee risks his career when he takes matters into his own hands after his sister appears at his door bloodied and confused. As McGee struggles to piece together his sister's whereabouts the night before, he discovers that the NCIS team is investigating the murder of a Navy sailor who had a previous relationship with his sister. Meanwhile, as separate clandestine romantic relationships bloom for both Abby and Tony, the NCIS team discovers McGee has a secret of his own.

When a burnt and mummified body is found at a Marine base NCIS is called in. They identify the remains as a serial killer which means they now have to work with the FBI.

The whole team has to attend sexual harassment classes. They're having a bit of fun with it until they are notified of a dead Navy Lieutenant involved in a research project. Seems like someone among the scientists was not too happy with the whole situation involving a robot-driven humvee.

When a Marine Lieutenant from Saudi Arabian descent is murdered in a hotel room in a small town, NCIS is called in to investigate. However, the local Sheriff's department already cleaned up the crime scene and an autopsy was performed. Involved in this case are an Iraqi who was relocated to the US for providing intelligence and some locals.

The team must find a terrorist who has a missing, toxic chemical weapon in their possession. After 10 kilograms of toxic chemicals go missing, Gibbs and the team must race against the clock to find it before it is too late. The team is shocked when they discover that the weapon is in the possession of Mamoun Sharif, a wanted terrorist.

Ducky is taken out of the autopsy room and put undercover in order to help stop the illegal sale of the Navy's weapons system. When the team captures one international arms dealer, the team learns the weapons system is about to be sold to a dealer known as La Grenouille. With Ducky as a decoy, Gibbs is able to set up a meeting La Grenouille. However, right before NCIS makes their move, they learn another agency has plans for La Grenouille as well.

Working with the local officials, the NCIS team originally believes that the sailor died of an unintentional drug overdose. But when they uncover a mysterious laminated card, Abby discovers an ominous message written on it in blood that quickly makes the team switch gears to find the sailor's murderer. Meanwhile, Tony bonds with one of the local detectives working on the case.

The NCIS team suspects foul play when a Navy Lieutenant is the victim of radiation poisoning. Gibbs and the team collaborate with the ailing Lieutenant, who is an inspector for the International Atomic Engery Agency (IAEA), as they recreate his routine in an effort to figure out when the contamination took place. Gibbs is convinced that whoever is responsible for poisoning the Lieutenant was trying to ensure that his next scheduled inspection would not happen. But when the dying man insists that only his two closest colleagues knew of the upcoming trip, the team works to find the culprit. Meanwhile, Tony is surprised when he sees a softer side of Ziva.

Gibbs and the team look for a potential serial killer when an explosion at a military cemetery mausoleum reveals a cache of dismembered human remains. When Ducky and Abby confirm that they have identified the remains of at least five people, the NCIS team immediately begins notifying the families in the hopes of making some connection between the seemingly random selection of victims. But when the suspects are narrowed down, even Gibbs is surprised with the final outcome. Meanwhile, Abby turns to Gibbs with a personal problem.

The team investigates when a Marine, who was thought to have frozen to death, wakes up o Ducky's autopsy table. With the Marine on life support, the team must follow his steps days before he was left to die.

The team learn a tip about terrorist activity was false and resulted in the death of two agents. Agent Cassidy, feeling guilty over the deaths, works with NCIS to track down the people who made the tip.

McGee is shocked when an officer he based his book on is found murdered. With few leads, the team forces McGee to find out everyone who has had access to his secret manuscript.

Director Shepard risks his life and agrees to meet an informant alone, but the meeting takes a turn for the worst and her contact is killed. Gibbs and NCIS try to gather the information the man was about to supply.

A blind photographer inadvertently films the murder of a petty officer. With little evidence, the team has Scott re-create the scene of the crime. Meanwhile, both Tony and Gibbs struggle with their relationship problems.

Gibbs puts off his paperwork for his acting director duties in order to lead an investigation into a murder victim found in a taxi headed for NCIS. Meanwhile, Jenny uncovers a secret about her past.

When the NCIS Director returns from Europe, Gibbs and the team prepare for Homeland Security polygraph tests. This leads to tight secrets among the team to be exposed and reveals the biggest secret in NCIS history. To make matters worse, DiNozzo and his girlfriend are held captive by a drug dealer.