Wrapping every question up in one neat theory is probably a sign it’s bogus. But here goes. The island in ABC’s Lost is intelligent. How isn’t clear. Either the island has somehow captured spirits (the whisperers), become inhabited by one powerful and/or trapped soul (the Jacob who Ben and Locke talked to), developed into some kind of receptor for collective human psychic power via its natural magnetic properties, evolved as a kind of intelligent geological formation wired by silicon (hey, sand is silicon dioxide) and powered by natural magnetism, or somehow manifests / channels the intelligence of the Earth / Cosmos itself.

Hey, it’s fiction, fantasy … so go with me.

Now, like any sentient creature, this island has to protect itself. It hides by wandering (it had to be in the Atlantic — and mostly submerged? — once for the slave ship to land on its black-rock/magnetite mountain) and by using magnetism to be invisible to the outside world. (Or by getting people to use its magnetism to cloak it from radio signals.)
When scientists stumbled upon the island, the island fought back through the minds of workers and/or test subjects there, communicating with the most psychic people. The island “knows,” these believers “know” that island’s secrecy must be kept.

Perhaps the fate of the world depends on it … either because the island’s power is too much for mankind to handle or because it could be a sanctuary / starting-over place when cosmic rays / nuclear war / asteroid annihilation happens.

Maybe this psychic island even knows the date of Doomsday.

So the island worked through Ben, who cast aside any ethical concerns to make his overarching goal protecting the island’s secrets. There’s no utopia here, and industrial conspiracy comes into play only to the degree Ben needs to make deals with outsiders like Whitmore.The island can work through many minds, making people see beings and creatures who aren’t really there. Eko saw his brother, Hurley a fellow patient, Kate a horse, Jack his father perhaps, Locke the departing Walt, others a “monster.” Perhaps this island intelligence can even make gnats (or gnat-sized magnetite particles) densely swarm in intelligent ways, forming the malevolent “smoke creature.”

If these monsters were under Ben’s control, wouldn’t he have used them to fight Jack and pals? And why was the Others’ compound surrounded by a field that repelled Smoky?
Further, this theory fits with other mysteries, like: Why were these people brought to this island? Hurley played numbers a friend discovered — related to a transmission of coordinates? — and won the lottery. Can’t have that story getting out. The Australian psychic met with Eko, Claire, Bernard and Rose. Walt has psychic powers. Jack knew Desmond, who wound up on the island with an officer that Sayid knew in Iraq, who both took orders from Kate’s father. It’s not coincidence. It’s either the island or some group trying to protect the island’s secret — which the crash survivors didn’t even know they knew.

Maybe that’s partly when Jack is so tormented to get back. He knows. Not just that people died (hey, the promos kind of give that away) because of him … but that there’s a greater mystery here … a mystery that goes deep into our psyches and our psychic connectedness.

Yes, on some level, I think there’s a generation-once-removed link between many of the survivors. Many had links through Jack’s dad, Kate’s dad, Whitmore and the Australian psychic. Maybe they all once worked together, or even crashed themselves on the island. Maybe the plan was partly to save these offspring … have the island heal their minds or save them from planetary tragedy. Of course, having babies die kind of puts a crimp into the idea of a long-term refuge.

Ultimately, though, what human plots have been operating, the island itself … a kind of Forbidden Planet … may be calling the most important shots.