If you plan to see the finale on your own, read no further. Spoilers ahead:
NCIS wrapped up its third season with terrific studies in character. To help jog Jethro's memory, Director Shepard calls on Gibbs's mentor Mike Franks, who quit NCIS when his early warnings about Osama bin Laden were largely ignored. We get a quick recap of Gibbs's NIS orientation, including the origin of the back-of-the-head slap. Franks has the unenviable task of recounting for Gibbs the events of 9/11.
Gibbs remains unable to recall his time leading a team at NCIS until Ziva forces him to remember Ari's assassination of Kate Todd, and Ari's death at Ziva's hand.
Gibbs's last-ditch effort to stop the Abu Sayyaf terrorist aboard the munitions vessel Cape Fear meets with interagency interference, resulting in the bombing of the Cape Fear and a Navy frigate sent to intercept. In the wake of this, Gibbs gains a new understanding of Franks's frustration and resigns from NCIS himself, passing leadership to longtime whipping-boy DiNozzo with a simple "You'll do."
According to Pauley Perrette's show blog, Don Bellisario had leaked word someone would be "leaving NCIS" at the end of the season, but kept even the cast members in suspense until the last minute. Bravo Zulu.