Season 11, Episode 1: "Whiskey Tango Foxtrot"
The season started by showing us how difficult it had been for DiNozzo and McGee to transition from agent to normal civilian. Learning how to navigate the grocery store aisles turned out to be the least of their worries. During their time away from NCIS, Ziva flew back to Israel and became the main target for a new group of terrorists.
After a bomb killed Secretary of the Navy Chris Jarvis and injured NCIS Director Tom Morrow, Gibbs turned his focus to the men responsible. Of course, that meant he had to get around Parsons.
Gibbs flew to Iran to find where the terrorists were plotting their killing sprees, and found himself in the midst of a gun fight. Luckily, Parsons had followed Gibbs and saved his life. He also told Gibbs that the terrorists were after NCIS the whole time.
After Tony's apartment is shot up, he and McGee decided they were finished sitting on the sidelines and made a plan to protect Gibbs and Ziva, even without their badges. They enlisted help and found Ziva wasn't dead yet, but that she was the next target.