UserGoogol's Explanation of "Creation of the Dark World"
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We start out with two universes, one with all the life of Hyrule, (and Hyrule itself) (the Light World of LttP) and the other with the Triforce. (The Dark World of LttP.) For simplicity's sake, I shall call these universes universe A and B respectively. 

Okay, so during Zelda 64, Ganon takes the Triforce from Universe B, and it becomes a universe of pure evil, monsters and what have you. This is due to his heart's wish, which I suppose to be Power. The monsters leave universe B, and help Ganon conquer universe A. But then the sages come, and stop him. 

Ganon, and all of the corrupted universe A, (except for its beings) is sent over to universe B, and the beings of universe A are sent back to a copy of the universe A from seven years ago. 

Somehow, the whole of the Triforce makes his way into universe B (maybe it just went there on its own when its masters died?) But Ganon (probably) can't use it. But he can use Agahnim, and uses him to try to get out of universe B. As we all know from LttP, (and if you don't, your probably not in the right place) Link stops Ganon and Agahnim, and touches the Triforce.