In the aftermath of Jenny’s death, Assistant Director Vance searches for Franks, who escaped the diner after killing the fourth gunman. Meanwhile, Tony and Ziva try to locate the one responsible, while dealing with the fallout of failing in their assignment to protect the Director. The trail points to a former hitman called Natasha, who Jenny failed to assassinate in Paris. Since Gibbs killed Natasha’s lover, Natasha is seeking revenge. Natasha, who never saw it coming, is killed by Franks, after Gibbs set a trap for her at Jenny’s house. Gibbs burns down the house to cover up Jenny’s death, making the public believe she died of smoke inhalation. In the fallout of Jenny’s funeral, newly appointed Director Vance shreds a page from his personnel file in the Director’s office and reassigns McGee to the cyber crime division, sends Tony to the USS Ronald Reagan, and terminates Ziva’s liaison status (sending her back to Israel). Vance then gives Gibbs files for his new team members.

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Ziva’s homecoming to Israel with Gibbs and the team is not a happy reunion with her father, the enigmatic and powerful head of Mossad. As tensions rise, and based on information he gets from McGee and Abby, Gibbs decides to leave Ziva in Tel Aviv. Ziva is then captured by terrorists in Somalia that Rivkin had been investigating.

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With the appearance of Mossad officer Michael Rivkin, Tony is forced to question Ziva’s loyalty to NCIS. Meanwhile, in Los Angeles, Special Agent Callen goes undercover to try to catch a terrorist cell while OSP psychologist Nate Getz discovers the startling truth about Gibbs and Special Agent Lara Macy’s relationship.

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The episode introduces the team of the NCIS spin-off titled NCIS: Los Angeles. Gibbs and McGee are flying to Los Angeles to work with the NCIS Office of Special Projects – Los Angeles team to solve the murder of a marine.

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After a security breach at the SECNAV‘s residence leads to the death of an ICE agent, Gibbs and the team are forced to work with ICE and the FBI to find his killer. Meanwhile, Tony finally comes face-to-face with Michael Rivkin and after a tough brawl between the two, Tony kills him when Rivkin tries to stab him.

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When a government scientist goes missing, Abby is recruited to carry on his work, but the team worries that she may meet the same fate as her predecessor.

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When shady CIA agent Trent Kort calls in a favour, Gibbs agrees to meet him at an abandoned warehouse. Upon Gibbs’ arrival, he finds the agent with two dead men who claims the men shot each other before his arrival. Gibbs and the team must then work with Kort to put away one of NCIS’s most wanted.

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A revolver is found in the affairs of a 12 year old son of a Lieutenant Commander in the Navy. Gibbs and the team are dispatched to find out the origin of the weapon. Things get complicated when Abby finds brain matter on the weapon.

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Gibbs digs into Vance’s past after the Director borrows Gibbs’s team for an Investigation into a friend’s murder. It is revealed that Tony has been in a slump with women since his break-up with Jeanne Benoit.

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The death of an NCIS agent leads Tony and Gibbs to the desert to track down the one woman that holds the answer.

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A Marine imprisoned for embezzlement because of a case DiNozzo was working on is released and the Navy lieutenant who witnessed against him is found dead. Tony is put in charge of the team because of Gibbs’ rule #38 (“Your case, your lead”) and they discover that the Marine was framed for embezzlement and now someone is trying to silence those who really did it. Gibbs’ fondness of DiNozzo is shown and he announces how he is proud of his senior field agent.

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While investigating the death of a Marine, the team finds Gibbs Marine ID at the crime scene. It is revealed that he helped a Colombian woman 18 years ago and that her son (whose father Gibbs killed while on the mission there) tried to contact him about a major blackmailing, involving the theft of several crates of assault rifles from a Marine base.

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The team investigates the murder of a Navy captain and uncovers possible treasonous acts he committed that may have led to his death.

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When Ducky is stabbed at a crime scene, the NCIS team must delve into his past to find clues and they uncover some disturbing secrets about his time as a doctor in Afghanistan.

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McGee becomes trapped in a women’s prison after inmates riot and take over while the team is investigating a guard’s murder.

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The fingerprints of a presumed dead petty officer, Ned Quinn, turn up at the scene of a double homicide. Claiming innocence, Quinn explains he was in the garage working for the victims when they were murdered. While fighting with metro police who want Quinn prosecuted immediately, the team discovers evidence linking a security guard to an emptied safe at the crime scene. Having been exposed, the guard shoots McGee with a taser and unsuccessfully tries to escape. Quinn, explaining that he went “undercover” after his apartment burnt down believing his wife and daughter would be better off with the service benefits from his presumed death, is convinced by Gibbs to rejoin his family for Christmas.

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The team investigates the death of a petty officer, who was killed in a car accident, but the agents suspect foul play. The petty officer’s death was thought to be connected to a fight club. He was killed instead by a man who was blackmailed by a criminal using a female online profile to lure married men. When the man is found dead at the petty officer’s home a fight club partner is the prime suspect, but it turns out that the next-door neighbor was behind the scheme and married man’s murder. Tony engages in an on-line air guitar contest that Ziva finds childish, but she takes to heart Tony’s words of having choices and the episode ends with Ziva playing air guitar.

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