I just read that they shot 2 endings:
By the end of the episode, one
member of the "NCIS" team will go down, creator Don Bellisario told
Zap2it.com
Bellisario said he has taken extraordinary efforts,
including shooting two endings to "NCIS," to keep the identity of
the killed-off character secret.
Harmon, whose "St. Elsewhere" character died, said he joked
about it when asked if the same would happen to his "NCIS" role.
"We're all personally hoping it's us, because we're all so
tired, we're hoping we're going to get killed," Harmon said.