Man I friggen LOVE this episode! Without this bit none of the final season would make any sense... its not as important to the rest of the series as some may say, but it is fun to buffer the ideas off of from every episode from the pilot on up.
Now we've gone over the whole black and white, good and bad thing a dozen times, but I want to just dip into a small refresher, since we are at the heart of the island here. The power of the island does not belong to one source... it belongs to two sources. Black and white. While whatever force of nature created black and white probably intended for the two forces to work together, in the end it always seems to be that one stands alone.
That in my guess was true for the mother of the island.... well skilled in the art of bashing b*tches heads with rocks, at some point she found herself to be the last (wo)man standing on the island. This is where we find her at the beggining. Alone. But nature does not intend for people to be alone too long (thousand years tops!) Just enough for a mother to understand how to protect her island.
Years of living alone with nothing but the smoke on one side and the light on the other caused her to realize what was really important. When the island brought her twins, the pieces came together in her mind. Two sides, one black one white. Her responsibility is to allow the two to live together, so that they don't have to spend that 1000 years alone.
BUT, the power of black is fickled. Never satisfied, always looking for some sort of loop hole. Why should black and white live together forever? One must die and the smoke saw to it. One must draw lines in the sand, set boundaries, choose sides.
But in the end it doesn't matter if black wins in the end or if white wins in the end,,, because there is no end. Eventually it all plays out again, and again and again, as if crossing through the same intersection no matter what road you take. As Jacob noted once; it's all progress. Ultimately all that matters is that in a world where black vs. white, once in a while black and white come together,,,
As Jacob laid his mother and his brother in the cave, the only two people who he had ever learned from or even associated with up until that point, he gave one a black stone and one a white stone, and looked ahead at his time alone on the island.