Ok heres my take on it, seeing as the series has been fantastic so far its gotta have a crap ending so heres what I think is going to happen.

The Bunker aka the place where they had to do the reset every 108 minutes, was a shield generator of sorts keeping a magnetic shield in place to make the island "invisible" from all outsiders.

Why the Dharma Initiative was doing this ? Well the Dharma INT. was part of a select group of Scientists keeping tabs on their ailing species by finding those humans who were genetically compliant with them to keep their species going. Sounds far fetched well maybe, but why did they keep Sawyer, Jack and Kate ? They are all fit, intelligent (Sawyer ?) and genetically wihtout disease.

My theory is that the plane hit this shield, the Island itself is in the Bermuda Triangle.

"The Black Rock" washed ashore."1881: The Black Rock, a slave-trading vessel, disappears from a gold-mining operation. " was one of many to dissapear without a trace.

Also Juliet the woman interrogating Jack knew all about Jack, even from recent records including getting on the plane with his dead father, she said she had been there a long long time and yet she was only in her mid to late forties. These "others" are indeed "others" aliens who can project telepathetically to the individual what they want to see, Polar Bears in the Jungle to Horses to dead Brothers. Their image is HOW we can percieve them and how we are wanted to see them.

Anyways this is my interpretation of how events will unfold. (HOW WRONG AM I GOING TO BE !!!) LOL