Maybe it was a "Hunt for Red October" kind of thing where he made them believe he skuttled the ship, but really the sub is alright on the bottom of the cove and Locke detonated the C4 under water, but away from where he"parked" the sub. Aren't there sometimes hatches (wasn't it reminisceint of season 2 opener looking down the hatch) have an airlock thingy (i'm very scientific) where you can exit a sub while it's submerged? This is not the Hunley, Ben said it was complicated.

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`Dear, dear! How queer everything is to-day! And yesterday things went on just as usual. I wonder if I've been changed in the night? Let me think: was I the same when I got up this morning? I almost think I can remember feeling a little different. But if I'm not the same, the next question is, Who in the world am I? Ah, that's the great puzzle!'

-- Alice, from “Alice’s Adventure’s in Wonderland”