For weeks I've yammered at people not to think that Dharma is the core of the mystery on the island, but rather that the central mystery resides in the Dark Territories. Time for me to put or shut up and address what the Dark Territories might be. I call it Approximation One because it is based on a miniscule amount of evidence and a vast mound of guesses. Anyhoo... here we go...
Chronoligically, Lost starts some past century when the Black Rock was somehow beached deep in the jungle. We only know one slim fact about that event, that the crew fled in such terror that they left the slaves chained to the bulkheads in the hold. Much later, around 1950 give or take a decade, two bodies were laid to rest in a cave, with nothing else known about them. After that, Dharma built their facilities on the island and some disaster overtook them, which led to them apparently being largely abandoned.
Besides our castaways, there are other survivors on the island. Danielle the sole survivor of another expedition come to grief, Desmond is now reduced to wild-eyes fear, and a rag tag group of Others are stealing children for Lord only knows what reason. All the other island inhabitants seem insane to some degree or another. Even our castaways behave wierdly, ignoring Lostzilla in the jungle, indifferent to the fact Shannon tried to kill Locke, never bothering to try to rescue Claire, and so forth.
Also, and most significantly, the main group of castawys seem to be near the Dark Territories, while the tail survivors were further away. Our main group, since the second day when Jack saw a vision of his father, have been having visions and hearing voices. Further, as was demonstrated when Shannon followed Sayid's eyes, turned and also saw Walt, and by the scene of all the tailenders hearing whispers, these visions and whispers are not solely in one persons mind. They are not hallucinations as we know them. Also, until nearing the Dark Territories the tail end folk never saw visions or heard whispers.
In 1977, off the Galapagos islands, scientists made a startling discovery. Clustered about deep sea thermal vents were entire ecosystems that had evolved without photosynthesis providing the energy. At the time it created quite a stir, because it was previously believed that a terrestial life couldn't possibly be that radically different. Yet, isolated and in an extremely hostile (to us anyways) environment, life evolved and flourished.
We have an isolated island, with an extremely peculiar magnetic footprint. What if life, a terrestial ecosystem far more different than surface appearances might suggest, evolved on that isolated island? All of the folks on that island would be bathed in that life, eating its fruit, breathing its bacteria. They would be interfacing with that other ecosystem on a cellular level.
The Dark Territories are stationary. Perhaps surrounding the source of peculiar magnetism. Man manipulates nature with his hands and feet. As that different ecosystem evolved, if it were rooted or buried in the ground, it would need to manipulate nature differently. Somewhere in the distant past it would evolve mechanisms to bring food to itself, rather than chasing it down. It would evolve an entirely different strategy for dealing with its surroundings.
Continuing, what if, on that remote island, something other than monkeys developed intelligence? An intelligence that would manipulate its surroundings in a vastly different manner than we? Motives aside, what would we make of each other? We would build, and garden, and wander -- it would wrap us in its influence. Would we even be aware of each other at first?
I think deep in the Dark Territories is an alien intelligence, but not one from the stars. Rather, it is a terrestial one that evolved in isolation. Whether the meeting will lead towards disaster, or something else altogether, is where the story is headed.
Then again... this might all be the result of an undigested bit of mustard.