In the future mankind will eventually destroy itself. How does it do this, well, nature may eventually catch up with us - it could be global warming, take for instance it is global warming or the result of climatic change or something like an experiment going wrong - we get to a certain level of knowledge and invent something like the LHC that can bring about a tear in time or we find an island where we find some strange substance that is unique to that magnetic monopole of the Earth and eventually use that energy to create the ability to open a wormhole or whatever.
Jacob and MIB are scientists in the future, they have already had prior knowledge of people throughout time who have been influential in eventually causing a chain reaction, consciously or not, that led to an 'event' that caused the end of the world. This was foreseen and the only course of action that could avert this was for the two folks to take a chance and send themselves back in time to fix the wrongs that needed to be put right. To put these things right, a sequence of events needed to take place.
During the 'sending back' of these two fellows they create a rift in time that splits the universes, in one the world ends, in the other, everything is fine. What we are seeing now is the timeline as if nothing had ever happened and this cataclysm is going to take place, and the timeline where the corrective measures are taking place.
The black smoke man was the result of the sending back through time, he may have consciously become some form of meismic black hole or a scattered mess of protons and neutrons type thing that is able to possess the bodies of the deceased using them as puppets for his own cause, but the body can only be taken on if the person is actually REALLY dead, ie, they died at the time they were supposed to die, and not before, else they wouldn't really be dead else there would be a paradox so they have to be REALLY dead. I hope that makes sense there. Perhaps people can't die unless they die at the time, in the original timeline, that they did die. So if you tried to kill someone 'before their time' then its impossible. And if they avert their natural death, then death will, eventually take them in some form of course correction or other.
So they get to the cradle of civilisation, never able to actually die because, it's not their time to do so - so the rules dictate that they can't kill eachother because they simply can't die until millenia in the future when they were supposed to die.
Because they appeared out of nowhere, perhaps the ancient humans thought them as Gods, and developed shrines to them. Also a temple depicting them as Gods right there. Smoke monster, MIB, the deity that deals death and Jacob, he who provides light and life. They build statues to them and everything.
But not only that, Jacob teaches him the ways of the future, and they attempt to build a rudimentary time machine out of ancient parts they collect over the course of the island going through time at a quasi-normal rate. They build the frozen donkey wheel and enable the island to somehow 'move' or bend itself away from the real world, even if it is only slightly out of sync of the real worlds time, it is invisible to the outside world.
Why then, does Jacob want to protect the island and MIB wants to be free? Well, MIB wants to die. He wants to die because he has been stuck on the island, in a prison for millennia waiting for the cataclysm to occur thinking this is fate, this is the only way it can end. But Jacob has different ideas, he is clever enough to think that humans free will can overcome fate and eventually they can find a way to stop the world ending.
What we are seeing is the results of their pieces being moved in the right way, they are finding people who can attempt to avert the course of destiny and eventually and HOPEFULLY they will stop the end of the world. The island underwater is a precursor to the rest of the world being underwater eventually and maybe because the island is at such a low sea level, then this means that its an indicator of the rest of the world.
The time travel invention began with the Dharma initiative, they still prevailed and learned the ways of time travel. Maybe Jacob and MIB were sent back using the Orchid station at some point which we may not yet have seen?
I think the whole story will tie up in a SIMILAR way to how has been described, I'm not entirely sure how all the loose ends will be tied up there are too many but each character can be linked to this. Widmore is significant because he wants to keep the island around too so perhaps he is good but perhaps he is the one that instigates the cataclysm himself but doesn't realise it because he hasn't seen it happen yet, unlike Jacob who has already experienced it all before as has MIB. Jacob probably visited the old grey haired woman in flash conscience form telling her of the future.
Looking back at the series, they were all manipulated it was a long game, that has gone back longer than we have seen so far, the plane crashed because of Jacob, the island was in stasis with the button pushing keeping it consistently in a time-bubble not advancing forwards, the incident occurred with the button not being pressed, this could be the point the end of the world occurred, but instead a failsafe allowed them to get an 'extra chance' I can't wait to find out where this all fits in but I think this is a key point to the overarching mystery perhaps that was the point where the ALT was created and not the nuke, that just enabled time to 'reconcile'.
Maybe the 'fork in the outlet' refers to the river flowing normally until the failsafe was pushed, this created 2 realities and then 3 years scenario was a parallel that was not supposed to occur all instigated by turning the wheel, and then the convergence or closure of that fork was the nuclear bomb which caused the timelines to converge again but two alternative realities then existed. It kind of makes sense in a large scale I would love someone to draw a diagram of it all - I bet somewhere in the LOST HQ the writers have a MASSSSSSSSIVE flow chart of everything, where one time hops over another, where it converges, what the donkey wheel turning did and how it affected the rest of the timelines but we won't see all this explained until the end and the fact is, the story has been woven so well we won't ever be able to figure it out exactly by ourselves.
Oh, and Jacobs tapestry - he was weaving it because he knew it was the prophecy of the future. The sun eye is Jacobs lighthouse reaching out to the ones he needs to converge and protect the end of the world from happening. MIB destoryed it, he wants to be free, he wants to get out of his prison, his JAIL, the island. He wants to die.
Hey, living's not everything, is it ;) The old thing of 'if you could live forever' would you get bored may come in to play.
It only ends once. The rest is just progress. Hopefully it ends with everyone alive! (Maybe as everyone is saying this is all flipside and Jacob is the one that wants to die, but, I don't think so.)