Not to mention that for the whole season MiB has made sure to confuse everyone and undermine their capacity to make rational decisions or trust one another, and Widmore's "methods", whatever his goals are (I suspect he is trying to harness MiB's power for himself, in some way... though maybe like Ben he's just not accepted he's not the "chosen one", haven't exactly helped either, no more than Jacob's followers' methods have helped. The characters have been on confusing rollercoasters all season, constantly manipulated by everyone, divided by tragedies, confusion and betrayals. They don't know who to trust anymore, not even themselves.

Jack was right in the end: one of Locke's goal has been to break them as a group and make them kill one another, preferably all of them at once at the plane or sub, because if he took them out one by one the survivors would have seen through his scheme. It didn't work thanks to Jack and Sayid, and now he's faced with four of them he can't kill and who will never trust him again, and his only "weapon" to kill them is Claire. A very great deal hangs now on the fact Kate reached out to Claire but then Claire was left behind at the sub (something Sawyer might come to regret). At the moment, being left behind likely determines her allegiance, and Locke's best play might be to send her into the group so she takes them out for him, but if Jack/Kate manage to turn her again, Locke's in trouble.

It looks like the biggest threats to Jacob's plans now are Claire on one side, and the rivalry and upcoming face-off between Ben and Charles one the other, and finally Desmond in the middle. Will Ben redeem killing Jacob by siding with Widmore (maybe by making Charles understands he's failed given up and Charles must too, that neither of them will win unless they team up) or will the rivalry destroy one or both sides, leaving only Charles' "secret weapon" Desmond standing?

Of the few big "back story" mysteries left to solve one is the Island's full history and this apparently will be explained next week, and then there's the full nature of the conflict between Ben and Charles, and Charles's real goals.