The episode opens with a recap of the second season's finale, "Twilight": as the NCIS team by Leroy Jethro Gibbs (Mark Harmon) engage in a gunfight against Ari Haswari's terrorist cell, Ari (Rudolf Martin), identified as a rogue terrorist, attempts to kill various NCIS agents including Tim McGee (Sean Murray) before Ari decides to fatally shoot NCIS Agent Kate Todd (Sasha Alexander) with a long range sniper shot, killing her instantly with a horrified Gibbs and Tony DiNozzo (Michael Weatherly) witnessing Kate's death.

NCIS Director Tom Morrow (Alan Dale) announces that he is leaving the agency after receiving a job offer from Homeland Security and introduces Jenny Shepard (Lauren Holly) as his replacement.

It immediately becomes apparent that Gibbs was romantically involved with Shepard while working undercover with her years earlier, though she insists that she is now nothing more than his boss and will act accordingly.

Gibbs clashes with Shepard, who believes that Ari Haswari was not the one responsible for firing the bullet that killed Agent Todd due to the fact that there's no physical evidence or proof of any kind linking him to the crime.

Ziva David (Cote de Pablo), Ari's Mossad control officer, arrives shortly afterwards, striking up a rapport with Tony.

She sides with the director and further weakens Gibbs' case, claiming that Ari is completely innocent and offering evidence to support her assertion.

Gibbs' determination to kill Ari in revenge for Kate Todd's death increases despite the skepticism expressed by his superiors.

The latter deduces that Ari is aware of the deaths of his first wife and daughter, as confirmed by Ziva, and that as a result he is targeting Gibbs' female coworkers.

The two briefly converse, with Ari confessing to the killing and claiming that he had terrorized the team because Gibbs reminded him of his father, whom he hated.

Kate is finally laid to rest with civilian honors along with a Presidential Medal of Freedom that former NCIS Director Tom Morrow (Alan Dale) approved at Gibbs' request.

Ari Haswari was a recurring character, having first appeared in the Season 1 episode "Bete Noir" as an unknown terrorist who held Ducky, Kate, and Gerald Jackson hostage.

It is later revealed that he is the child of an Arab mother and Jewish father, initially a Mossad agent sent undercover in Hamas, who later went rogue and became a terrorist, attacking both Israel and the United States.

[8] Israelis in general are depicted in a positive light,[7] though Ziva's father Eli David is portrayed ambiguously,[9] and Gibbs briefly mentions the Lillehammer affair, in which a Moroccan waiter was killed after being misidentified as a perpetrator of the 1972 massacre of Israeli athletes in Munich, Germany,[10] in Part I. Ziva's choice to kill her half-brother after realizing that he was guilty of the murder in order to save Gibbs, who was, at the time, essentially a stranger to her, is often regarded as a "selfless, endearing act" and defining character moment.

In the third season's finale, after Gibbs suffered amnesia in the aftermath of a bombing, she was able to help him recover his memory by reminding him of their connection through Ari after several other characters had made attempts and failed.

This concern is later resolved early in the seventh season when Ziva assures Gibbs that the sole purpose of her choice was to save his life.

[8] Ari is also mentioned in passing in various other episodes, including "Silver War", "Probie", "Shalom", "Cloak", "Enemies Foreign", "A Man Walks Into a Bar...", "Safe Harbor", and "Past, Present, and Future".

The episodes were written to show the NCIS characters grieving and dealing with Todd's death, as well as to provide closure for Ari's storyline.

The role was of the new Director of the agency, and things were made complicated because she had a 'past' with the lead agent, Jethro, played by Mark Harmon...So I get the call, followed by a couple of DVDs.

The same reviewer also criticized one aspect: "Shepard and Gibbs had a relationship some years before, and the blurry flashbacks to their time undercover are the episode's weakest point.

"[19] June Thomas of Slate magazine refers to Ziva's killing of Ari as an example when describing the NCIS characters as "men and women of honor, heroes who have all made significant sacrifices for their country.

That deed was done by Ari's own sister and new NCIS cast member Cote de Pablo as Mossad agent Ziva David.