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This is the theory I have made that sums up the show for Season 6, in my opinion. It's a little complicated, but once you understand it, it'll make a lot of sense.
The Smoke Monster - The Smoke Monster is a 'side effect' of the energy on the Island. It's like the black smoke from burning coal. You get energy from it, but with a price. Jacob's nemesis gave this 'side effect' mental thought, aka the electricity that runs through it, like the electricity through a human brain. The 'voices' are actually it talking.
Result of Jughead - This is where it gets confusing:
This is time: ---------------------------- You cannot break time and 'restart' You CAN restart during time, but it MUST stay linear. Cannot do this: (2004)-----------------(Jughead)
(2004 after Jughead)--------------------------
You CAN do this: (2004)-----------------(Jughead)--(2004)-----------
So, the survivors successfully make it to LAX.
But, through universal course correction, all the people who died on the Island will die off the Island. (for instance: in the plane, when it started shaking, it stopped Charlie from doing too much drugs. Because it won't shake, Charlie will do more drugs, and die of a drug overdose.
Now, there is still the matter of the Island after Jughead...
I believe that the energy in the Island was somehow used to protect it from the explosion. Yet, the survivors on the Island were too close to the bomb and therefore died, and Richard saw them all die.
Even though the Island was saved, women cannot give birth because of an after effect of the bomb. The Island continues to be there, but since time is different there, it comes to 2004 (27 years) faster than the outside world in 2004 can age (27 years to 2031).
Eventually, the survivors will all crash on the Island again, in, you guessed it, Oceanic 815, and will land in 2004. From there, it will be a linear timeline.
From there, well, that's where the actual story goes for.
Wonder what happened to Claire in all of this... :)