THIS IS A WORK IN PROGRESS AND IS BASED ON THE FACTS PROVIDED THUS FAR. THERE ARE SEVERAL VARIATIONS POSSIBLE BUT THIS IS THE PROTOTYPE THEORY. THIS IS THE FRAMEWORK ONLY SINCE THERE ARE TOO MANY DETAILS TO PUBLISH HERE.

The losties are stuck in a power struggle and their actions will literally determine the fate of the world. There was a guiding force that led them to the island and this force made sure the necessary ones survived the break up of the plane. The “others” are Dharma personal and they are trying to get the project back on track.

The project was disrupted by the eye patch guy who seized control of the Cerberus technology (the black fog entity) and used it to kill all the Dharma personal he could reach. Patchy was involved in the first "incident" and like Desmond is a powerful pre-cog with immense telepathic abilities. He saw the future and something made him decide to destroy Dharma. Probably that the real purpose of the project was weapons research more than saving humanity. This means the others are being manipulated into thinking their actions are for the greater good.

The losties are being recruited by Patchy (who has a serious god complex due to his immense mental ability) to fight for his agenda. He is making them face their demons and if they find redemption in his EYE they are worthy. If they are not worthy and won’t make willing subjects they get the business end of Cerberus i.e. Eko.

The island is the root of everything, the source of all this power. It is Atlantis and Lumaria, which descends into the ocean just like Plato, said and re-emerges time after time probably due to the immense EM energy welling up through it from deep within the earth.