No, Duckie did not die in the Season Nine Finale--at least not for certain. He appears to have suffered a stroke or heart attack while walking alone on the beach, and the finale episode ends with his body motionless on the beach, halfway into the surf.
He'd just received a phone call alerting him to the terrorist attack on the NCIS Headquarters, and telling him that several staff members and agents have been injured or killed.
Because Duckie is alone on the beach (in formal wear following the wedding of his assistant, Jimmy Palmer) there's no one around to save him, apparently. But TV industry news reports that the actor who plays Duckie finally signed another two-year contract with the show, so it's clear that he will still appear on NCIS, but in an altered version of his traditional role.
Judging from previews, it appears that Duckie survives at least long enough to reach a hospital. But it also looks as though one of the other major cast members is killed in the explosion. It's not Gibbs, Duckie, or Abby, so it seems likely to be McGee, DiNozzo, or Ziva David (if any major cast members are lost at all). Surely could be Jimmy Palmer.
The NCIS producers smacked us with a cliffhanger to end Season 9, of course. Tune in to the Season 10 Premiere on Tues., Sept. 25, 2012 at 8pm on CBS to find out whether Duckie has major health problems related to a stroke (such as needing a wheelchair), fully recovers after some difficulty, or appears posthumously as a kind of muse to one of the characters. The season premiere is billed on CBS as an episode "of sorrow and loss," so it seems likely that somebody will be leaving the show.
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