One of my first theories on Ethan was he is in fact a ghost! one of the first people on the island, and needed Claire for the same reasons that Rousseau needed Claires baby, this would explain the sudden appearences/disapearences of the character throughout the first few episodes
Now i know he was in fact a living person, just a tad more insane than the french chick (btw i ran into Mira at a con in Milton Keynes a few weeks back) and nearly as dangerous as Father Caleb from Buffy... in fact for a while i thought you were the same actor who played Caleb! i was wrong, it turned out to be Mal Reynolds from Serenity... D'oh
sooo what was his agenda? he never got to complete his task whatever it was and didnt seem to be linked to Rousseau's plans in any way...
soon after that you popped up in MI:II as another bad guy... but he didnt get 6 bullets in the back! watch out for that truck!.... too late