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I just thought of something. In Michael's flashback in some point during season 3 we see Tom off the island dealing with Michael and influencing him to get on the Kahana. But as far as we know turning the wheel is the only way off the island. (Unless he used the sub, but I was under the impression that Locke had already blown up the sub by that point in time)
So how did Tom get off the island?
And how'd he get back? Surely he didn't go crash a plane.