A foreign agent enters the autopsy room via an unconventional method; he then takes captive Ducky, Gerald, and, later, Kate. He demands evidence pertaining to a body in the room. He eventually asks to see Gibbs, who obliges him; he loses.

The body of a petty officer falls from a ceiling at a nightclub; Gibbs and company investigate; Ducky says that someone dressed the victim after he died. Gibbs finds $40K in cash; he finds the connection between a prank and an inheritance.

A prisoner, who was a SEAL and a petty officer, escapes from Fort Leavenworth while serving time for having killed his wife and a cable guy; the team, seeking to determine where he may go next, consider whether his conviction was wrong.

A guard finds the disemboweled body of an NCIS agent in an elevator; the gang investigate. Gibbs feels responsibility. The victim has pursued a cold case involving a theft of $12M+ from the Navy. NCIS finds the thief and the killer.

A Marine fails to report after a weekend; he's an EOD tech with a critical qualification, so the NCIS investigates. Three other EOD Marines have disappeared in the past eight years. Abby finds the dots, and the others connect them.

With extreme determination Gibbs continues, to the extent of obsession, to concentrate on the unknown terrorist who shot him and escaped. The bad guy reappears, but Kate and Tony disappear temporarily. Gibbs eventually meets his quarry.

Tony returns early, in time to rejoin the team in an investigation of a shooting of two Naval aviators. Tony finds a bomb, then it explodes; Gibbs says that someone has again tried to kill the NCIS gang, which loses one of their members.

The gang mourn the death of Kate; they recall her and deal with her death. Ari puts a round into Abby's lab, and the NCIS gets a new director, who shares a history with Gibbs. Ducky accepts an invitation to an unusual meeting. [Continued.]

Ducky meets Ari, Tony follows Ziva, Ari secretly betrays Israel and Mossad, Ziva passes cash and a fake passport to Ari, Gibbs and Jen seek Ari but miss him, Ari finds Gibbs, and Ziva finds them. The gang attend Kate's funeral in Indiana.

Gibbs regains consciousness, but he's lost his memory since 1991. He starts to remember a few things; Jen helps, then an old buddy, then Ziva. Gibbs gets back his memory and a solution, gives a severe warning, becomes ignored, then quits.

Ziva finds Tony and Michael on a floor; Michael dies soon afterward; the next morning her pad explodes. McGee and Abby find answers. Vance, Gibbs, Tony, and Ziva go to Tel Aviv; Ziva remains, and the others return; Ziva runs into trouble.

Three men die during what they called a bachelor party; one was a Marine staff sergeant; Gibbs and company investigate. The clues lead to a cop, who later dies. The gang find the pieces and put them together; Ziva rejoins the team.

Someone shoots and kills the executive officer (XO) of a Naval vessel, a commander, in his own stateroom; Gibbs and company investigate. However, a shrink (a persistent and presumptuous one) arrives to conduct mandatory psychologic evaluations for all members of the gang, and she accompanies them aboard the ship. Ziva recognizes the spent brass as Russian. Word of the murder spreads fast, for seven international journalists are aboard as guests; one reporter makes a confession and reveals a potential powder keg. The team continue, and they eventually find the solution. Meanwhile, the shrink also continues, eliciting a number of flashbacks, mostly related to Kate Todd, a former member and special agent. Eventually Tony and Gibbs realize who the shrink is, then she submits her report to the director.

At a diner an unknown person with a drawn pistol approaches Gibbs, who deals with him; then Gibbs experiences flashbacks and fantasies, which Franks explains. The next day McGee announces a decision, then the gang gear up and head out.

Gibbs and McGee are shot down in a Naval helicopter over remote parts of Russia while on a mission to escort an NCIS computer geek safely home. Meanwhile, the gang at home anxiously work to help bring them all home safely.

Gibbs fights for his life after being shot by Luke Harris. Meanwhile, Agent Tony DiNozzo and CIA officer Joanna Teague travel to Egypt to take down The Calling.

Ziva surprises Gibbs with a cryptic warning, prompting him to question why she remained underground for years while being presumed dead, and what led to her return.

With their lives in danger, Gibbs and Ziva's rogue investigation takes an unexpected turn when a possible terrorist plot is revealed.