Season 11, Episode 2: "Past, Present, and Future"
Tony flew to Israel to keep an eye on Ziva after learning she was next on the terrorist hit-list. While he tracked her down, Gibbs continued to hunt for terrorist Benham Parsa and his organization, The Brotherhood of Doubt.
Meanwhile, Fornell and the FBI provided protection for Tomas Mendez, a board member for an American anti-terrorism organization, after a bombing at his home. Eventually, Gibbs was led to Mendez, learning the anti-terrorism unit was a front the whole time. Mendez was actually working with terrorists and scamming donors. In order to prevent another bombing, Gibbs shot Mendez in the head, ending his reign of terror.
In Israel, Tony and Ziva share one final goodbye as she had decided to stay there and leave the NCIS team for good. Back at home, Tony and McGee got back their badges for the hard work and dedication they showed while off the job.