Have stopped trying to make sense of Lost--had a handle for a few seasons but after the narrative arc and/or underlying conspiracy changed from survivors vs Others, to Others vs Dharma, to Ben vs Widmore, to Jacob vs Esau (or whoever) I threw up my hands and mainly just enjoy the cliffhangers and ironic interconnections (this season's "flashes-sideways" to an alternative timestream where the characters we all know meet under different circumstances is ingenious so far--and I really liked the use of two different clips of "unreconstructed con man Sawyer" pursuing lottery-winner Hurley off the plane--the one they showed in the recap had him more pointedly in pursuit). Thoreau attempts to account for what's left of a story thread:
If nothing else, we finally know that the smoke monster is a malevolent and manipulative entity with an agenda. However, the more we try to work this into the story that’s been established thus far, the less sense it makes. For instance, the Others apparently followed Ben and revered Jacob, yet they also had a way to summon the smoke monster (recall what Ben did when the mercenaries came to his town and killed his daughter). In the religious worldview of the Others, the smoke monster seemed to be some sort of figure who renders judgment on sinners (recall that Ben went back to the Island to be judged for his sins by the smoke monster in the Temple). Yet we now know that the smoke monster is a malevolent creature who has plotted against Jacob, their revered spiritual figure. This confuses me. Perhaps the full nature of the smoke monster is something that Jacob has never revealed to his people, for whatever reason. If so, it’s a pretty closely-held secret.
Moreover, when Hurley tells the boss at the Temple that Jacob is dead, everyone in the Temple seems to realize that this means that their enemy is coming. Do they know it’s the smoke monster? Do they know that the smoke monster is also the Man in Black? On top of that, the boss dude at the Temple seems to have a pretty close relationship with Jacob, or at least he knows what to expect in messages from Jacob. Ben, OTOH, was dangled on a string, getting Jacob’s messages through the intermediary of Richard Alpert. Previous to this, the hierarchy seemed to be Jacob at the top, Richard as the intermediary, and Ben the leader in day-to-day life. Now we have this leader at the Temple, somebody who seems closer to Jacob than Ben, but he also leads a group of Others that includes some Others that we’ve seen before (e.g. the abducted Cindy). So, what gives? Was Ben only the leader outside of the Temple?
I don't really care anymore but this is all interesting.