Okay, here’s my current working theory:
The Island is the scene of a secret military experiment, dating back from the 1970’s. They’ve developed a drug (possibly in an airborne or viral vector) that boosts the nervous system, but it has unpredictable psychological side effects, including hallucinations and psychotic behavior. Merely being on the island exposes you to it. Most of our heroes haven’t yet recieved a large enough dose to experience this, except when otherwise weakened. This explains Locke’s healing, Ethan’s apparent superb physical performance, the whispers, Jack’s sightings of his father, Boone’s vision (Locke prepared a larger dose in the head wound gunk), and Shannon’s vision this episode.
The Others are those that have been on the island a long time, and totally succumbed to the drug. They are possibly the original experimenters/test subjects and their offspring. They need children, Walt and Claire’s baby, to continue the experiments, and possibly make a cure.
The Hatch contains the old control room for the experiment, as well as a “safe” space for the scientists (the island was quarantined, not the area below the hatch). The controls for the Tree-Crushing Monster (a way to manipulate the experiment, a security system for the tunnel system, and a way to test the super-soldiers made by the drug). Desmond is injecting himself with the antidote. Rousseau, who knows far more than she pretends (I think she’s from teh same group as the Others, but has split from them), injected Claire’s baby with it in utero. The polar bears are also part of the test (accounting for the polar bears is the weakest link in this, I admit).
Hurley’s numbers have some signifigance to the drug. They are probably a serial number or chemical code of some kind. The Others, in their madness, have been using the secret transmitters to broadcast it for many years. Rousseau’s highjacked that same transmitter.
Now, here’s where things get a little weird. There’s two reasons (three, if you count misdirection on part of the show makers) that all of these people seem to be connected before the crash, and things like the numbers show up over and over again. The first is that the experiment is still ongoing, and it has agents outside of the island. At least six of our passengers (Sayid, Kate, Sawyer, Claire, and Sun and Jin) were put on that specific flight by powers outside of their control and by potentially shady persons or agencies. I think that the crash, with its implausibly high survival rate, was engineered, and that the survivors have been manipulate far back into their pre-island lives. I’d be surprised if Kate’s original crime doesn’t have something to do with the island, if only indirectly.
The second reason is that Locke is essentially right (at least on this show). Nothing happens by accident, and this is their destiny. Faith and hope are rewarded, and “miracles” (that is, extremely unlikely events that occur for some greater design) happen. Jack found that out himself with the unlikely recovery of Sarah, although he seems to have ignored or forgotten the lesson. There’s a High Power at work here, and while I doubt He’ll make his presence known in a direct fashion, He still shouldn’t be ignored.
Any glaring holes that I’ve missed?