The Ending Of NCIS Season 6 Explained

"NCIS" is the uber-popular crime procedural series that premiered on CBS in 2003 and continues running strong at 19 seasons and counting. Season 6 aired all the way back in 2008. Whether you're doing an "NCIS" rewatch or you're brand new to the series, here's a handy explainer for Season 6 finale. 

While most episodes of "NCIS" aren't connected to each other, each season usually has an overarching storyline or subject matter. In the latter part of Season 6, it's all about Ziva (Cote de Pablo) and her loyalties. She's long been a member of the NCIS team, but she's a liaison officer from the Mossad, Israel's spy service. Her father is the head of the Mossad, and her boyfriend, Michael Rivkin (Merik Tadros), is an undercover Mossad agent. Worse, Rivkin is working espionage missions within the United States. Worse than that, Rivkin's methods are brutal. In the two-part episode "Legend," which also introduced the spinoff series "NCIS: Los Angeles," Rivkin was investigating the same terrorist cell as the NCIS, but kept killing off the terrorists before NCIS could arrest them. Later, in the penultimate episode of Season 6, "Semper Fidelis," Rivkin kills both the head of the terror cell as well as a US Customs and Immigration officer. 

When the Season 6 finale kicks off, Special Agent Dinozzo (Michael Weatherly) has just confronted Rivkin at Ziva's apartment. After Rivkin tried to kill him with a piece of broken glass, DiNozzo is forced to shoot and kill him in self-defense. This forces Ziva to finally make a choice between the NCIS and her roots–but it's not quite that simple. 

Many a TV show has explored what happens when a character's normal M.O. is disrupted, and they're placed in a situation that's antithetical to their experience. The "NCIS" Season 6 finale does this with multiple characters.

First, there's the NCIS team and its relationship with Ziva. Normally, she's a dedicated member of the team, but thanks to her involvement with a mysterious Mossad operation (more on this below), her loyalties are questioned. As a result, Leroy Jethro Gibbs (Mark Harmon) and the team are put in the unusual predicament of being suspicious of one of their own, instead of their typical criminal suspects. For her part, Ziva finds herself unable to trust her NCIS comrades. It's disorienting for everyone.

Then there's Special Agent DiNozzo (Michael Weatherly). Just before the Season 6 finale, he's forced to shoot and kill Mossad agent Michael Rivkin (Merik Tadros). In a subsequent trip to Tel Aviv, the Mossad interrogates DiNozzo over the shooting. As DiNozzo says, usually he's the one interrogating suspects, not the other way around.

TV shows do this to explore different sides of their established characters, and the Season 6 shows everyone in a new light.

Even though the evidence backs up DiNozzo's version of events, the shooting severely damages Ziva's relationship with the NCIS team. Ziva blames DiNozzo for Rivkin's death, and she rejects the NCIS team's multiple attempts to console her.

Yet she's also not fully committed to the Mossad either, either. When Ziva, Gibbs DiNozzo, and Director Vance (Rocky Carroll) fly to Tel Aviv, she confronts her father about Mossad's activities. She's been kept in the dark about Rivkin's missions. Then, in Tel Aviv, Ziva learns that when she earlier asked the Mossad to extract Rivkin and save his life, only for the Mossad to abandon him to his fate.

In one of the episode's pivotal moments, Ziva confronts DiNozzo about killing Rivkin. During their confrontation, Ziva finally admits what's really bothering her. It's not over how the NCIS or the Mossad treated her, it's because she wasn't there to protect her loved one. Ziva's highest loyalty isn't to either organization, it's love.

This is what influences her choice at the end of the episode to stay in Tel Aviv and finish what Rivkin started. It might seem like Ziva is choosing the Mossad over NCIS, but in reality she's choosing Rivkin over both of them.

With Ziva's decision to stay in Tel Aviv, it looks like the end of the episode. However, in the final few minutes, "NCIS" makes Gibbs question his entire relationship with Ziva.

Upon returning home, Gibbs is sad. He was a father figure to her. In a scene with Ducky (David McCallum), Gibbs remembers the moment in Season 2 when Ziva gunned down her half-brother and fellow Mossad agent Ari (Rudolf Martin) to save Gibbs' life as the moment when he first began to trust her–again echoing the episode's themes of trust and loyalty,

But then, during a meeting with Vance, the NCIS director makes a disturbing allegation. Earlier in the episode, Vance and Mossad director Eli David (Michael Nouri) discuss their shared history. They know each other well. At the end of the episode, Vance suggests that Eli sent Ziva to stop Ari both to eliminate the rogue agent as well as to butter up Gibbs so the Mossad could have a source inside.

Since Ziva has recently withheld crucial information about Michael Rivkin from the NCIS, Vance's suggestion seems disturbingly plausible.

Season 6 ends with Gibbs wondering whether his relationship with Ziva was all a lie. This gives him plenty of unfinished business heading into Season 7.