Gibbs and the team are called in when a Pentagon cryptographer suspected of spying apparently commits suicide. With their prime suspect dead, the NCIS team must uncover whether or not she was the Pentagon's mole. The team quickly discovers evidence that indicates the young woman was not alone when she died. Now faced with a potential murder, Gibbs and the team follow the clues left behind to find her killer and expose the mole.

After discovering that a grisly murder scene was staged, the team realizes that Abby was the intended target when some key evidence contaminates her lab and almost kills her. The NCIS team soon learns of some unsavory characters in Abby's past and must work quickly to uncover who is out to get her.

Ziva is in shock when a routine tactic she uses to subdue a suspect might be the cause of his sudden death. As Ducky and Abby work to clear Ziva's name, Gibbs learns that Director Shepard has been kidnapped by their dead suspect’s brother. The man demands the release of his brother, who he doesn't know is dead, in exchange for the NCIS director.

The members of NCIS are distressed when Gibbs is injured in a terrorist explosion while on assignment. As the team attempts to put their feelings about Gibbs' injury aside and work on the investigation, Tony steps into the role of senior agent, causing a bit of resentment from other team members. Meanwhile, while recovering, Gibbs is flooded with memories of a past that he had long struggled to suppress.

As the team tries to track down the terrorists behind the bombing that injured Gibbs, they learn that the terrorist group is planning another bombing of 9-11 magnitude--and that Gibbs has information about their plan. Meanwhile, Gibbs receives a visit from his former boss and mentor that conjures up suppressed memories. As Gibbs regains his memory, he finds himself on a race against the clock to fill in the gaps and stop the terrorists.

As each team member deals with the absence of a retired Gibbs, Ziva's past comes back to haunt her when she inadvertently witnesses the assassination of a military attaché by her former Mossad partner. Convinced her father ordered the hit, Ziva seeks refuge at the Israeli Embassy, only to find she is wanted by the FBI. 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.

When a convict from FBI Agent Fornell's past escapes and threatens not only him but his young daughter, Gibbs comes out of retirement to re-open the convict's armed robbery case. With his former team by his side, Gibbs questions a retired sailor who appears to be the only one who has any outside contact with their wanted man since his incarceration. But as the investigation progresses, the NCIS team discovers the man they are hunting for is out for something other than vengeance. Hal Holbrook guest stars.

After the team learns a missing Navy lieutenant had been profiling men to find herself the perfect mate, they trace the woman's path and discover she planned to attend a singles seminar at a local hotel. Ziva goes undercover to gather information on the male attendees with hopes that one of them will lead the team to the missing Lieutenant before it's too late. Meanwhile, Director Shepard makes Tony a secret offer.

The NCIS team is called to the scene of a bizarre murder of a Petty Officer who was part of an undercover arms operation. After his body is discovered, a Russian spy is pulled over for a traffic violation and is found with a recently fired gun in his back seat. With the bullet that killed the sailor missing, the seemingly open and shut case becomes more complicated when the department of Homeland Security claims the man accused of killing the Petty Officer is working for them.

When the team investigates the case of a dead Lance Corporal found by a real estate agent, they realize the body 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 fiancées. 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.

After receiving a ransom call from the kidnapper of a Marine's daughter, the NCIS team learns that the girl's parents were recently separated after a marital indiscretion by the wife. Armed with that new information, Gibbs and the team focus their investigation on the woman's ex-boyfriend. Meanwhile, Abby's Halloween costume renders McGee and Tony speechless.

Gibbs and Fornell (Joe Spano) attempt to track down the leader of a drug ring who supplied drugs to Fornell�s daughter. Also, the team deals with the case of a missing cadaver from the NCIS autopsy room.