The Origins of the Island, Etc... by Alex Klenke

I would like to begin by saying that I am of the group of people who absolutely loved not only "The End", but also the show in it's entirety. The moment the finale ended, I found myself to be completely content with how everything wrapped up and I did not feel as though I needed any further clarification on the mythology, despite how many hours of my life I have poured into studying it. That said, while discussing Lost with a close friend, I think we may have discovered a science-esque "answer".

During the finale, a number of parallels are made between The Source and The Hatch, most overtly of course being the scene with Locke and Jack atop the waterfall. In further examination of this parallel, we noticed just how similar The Source and The Hatch really were, even going so far as to note the similarities between Dharma and the ancient Egyptians.
The Hatch, as we know it, was built after Radzinsky and his Dharma associates dug a little too deep into an electromagnetic pocket. The purpose of The Hatch was fundamentally the same as that of the cork in the Cavern of the Source. It was meant to keep the energy at bay so as to not destroy everything.
In the one and only Rose and Bernard centric episode of the series, we are told by Isaac of Uluru that there are pockets of electromagnetic energy all over the earth and that each of them are connected. I think it can be safely assumed that The Source is what all those pockets of energy are connected to, and if it were to go out, every pocket of energy across the world (universe?) would go out with it. Thus, Mother's "the light goes out everywhere" line.
Now, in regards to the title of my theory, I would like to speculate on how the cork in the Cavern of the Source came to be. The following is a purely speculative guess at the origins of the Island using what little clues we have to go by. If you have different opinions on how the Island began, then more power to you. Lost was left interpretive for that very reason. That said...
The Island has existed since the universe has existed. It has existed since long before man, and hopefully, will exist long after. In the time before man, there was no need for the Island to be protected, so there was no guardian to protect it. During the dawn of man, I believe that the Island was originally settled in Africa, where man originates from. Eventually however, I believe that the Island came to settle in Tunisia, of its own accord I might add. I have always thought of the Island as the closest thing we will ever get to a God in Lost, or put more aptly, as Creation. That said, I have also always assumed that the Island has Its own sort of sentience and can therefore move itself as It sees fit.
So while settled in Tunisia, the Egyptians came to live on the Island. They built ruins, temples, statues and who knows what else. But along he way, they also came to find a pool of water at the end of a stream that was emanating a bright, white light. The Egyptians were mystified by this Light, and thus was spawned our ancestral version of the Dharma Initiative. These ancient men of science needed to know where the light came from, and so just like Radzinsky, they dug.
Eventually however, the Egyptians dug a little too deep, and for the first time, man was directly exposed to the Light. I suspect that of those men, two were particularly special. Whether they were the original candidates of the Island, or whether everything is coincidence is up to you, but either way, I suspect that one of those men was especially "dark". That man became our original smoke monster. The other of those two men, an especially "light" man, would become our first Guardian. And how did he do this? By jamming a f*cking rock in the hole he and his buddies had dug. Our first example of a character in Lost to clean up their own mess.
After this very first "Incident", the Egyptians came to fear this new and terrifying creature. They etched hieroglyphics into the ruins we see in "Dead Is Dead" that depict the Smoke Monster interacting with Anubis, so I can safely assume that they were aware of a Monster, but since MIB was not created until much later, it could not have been the same Monster.
Meanwhile, I imagine that the Island would have then thought it prudent to move, so as to avoid any further threats. As for our first Guardian, I imagine that he not only began the rule of preventing anyone from leaving the Island, but also, he set about crafting a more proper cork for the hole in the Heart of the Island, hieroglyphics and all.
From there, I must again make a leap of faith. Just as Kate killed our Smoke Monster, I imagine that it was another female that killed our first Smoke Monster. If there is anything that Lost has taught us, its that history repeats itself. Now whether or not that woman was Mother, or her Mother, or her Mother's Mother, I cannot say for certain. But I can guess that she likely worked in unison with the Guardian, because I only know one way to kill a Smoke Monster, and that involves removing the cork.
I would guess that just like Jacob and MIB, the Island's original Guardian was probably killed during the execution of the plan hatched to kill the first Monster. He likely died while unplugging the cork, and maybe it was the same woman who killed that Monster that plugged it back in. Now what happened to her is up for wider speculation. Maybe that woman was Mother, and she became what we saw her to be in "Across the Sea". Some will argue that she was a Monster, whereas others will argue that she was absolutely not. To me, I am not so sure that it matters. Maybe her scales were completely balanced while "plugging the Island back in", so she became the quintessential gray. She represented both light and dark just as the ying-yang symbol does; two sides of one whole. And what do I think that woman, whoever she was, did right after becoming the new Guardian? She purged the inquisitive Egyptians, thus starting the thread of mistrust towards humans that would stretch all the way to Mother.
Finally, by the time this story catches up to that of the one we were told in "Across the Sea", Mother brings Claudia's boat to the Island, and in so doing, brings her replacement. I don't think she expected there to be two boys, but I do think she understood what it meant. The ying-yang was to be broken, and each half was to be represented by a boy. She had first suspected that it would be MIB who would replace her, and in some ways, he likely did. As she said in "Across the Sea": "I love you both. Just in different ways." MIB would come to represent the "dark" and Jacob would come to represent the "Light". And it was Jacob who broke the thread of mistrust towards man, whereas MIB would have continued it had their roles been reversed.
Jacob believed in man, but not in the way that Hurley one day would. So in summation, I suggest that we have now entered the Third Era of the Island. In the First Era, there was the origins of the most ancient of structures, and the beginnings of our first struggle between Light and Dark. In this era, the Guardian(s) that reigned over the Island mistrusted mankind and thought it better to purge those that were deemed unworthy of replacing the Guardian rather than allow them to live freely on the Island.
Our Second Era is the era of Jacob. Why his reign is particularly special, regardless of how many Guardians there were before him, is because he is the first to allow man to come to Island and then stay, even if they aren't meant to replace him. But Jacob does not trust man entirely, nor does he consider himself one of us.
The Third Era is that of Hugo Reyes. Hurley trusts man, thinks that all men can be redeemed, and is willing to bring man to the Island not just to replace him, but to help them find Enlightenment. His Era is a bright future for mankind, but that is not to say there are not still threats to the Island. There will always be another villain so long as the balance between Light and Dark remains, as it always must.
Thank the Island that Hurley has Ben to help him protect the Source. I would guess that without Ben, the Island would surely find itself in dire straights before long.
Whew. That was a long one, so for all you short theory lovers, sorry. I hope you guys like this theory, and I look forward to your comments and criticisms, so long as they are constructive.