The Ending Of NCIS Season 6 Explained

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.