Firstly, Agahnim is Ganon's alter-ego. In the Japanese, this word more closely translates to "clone." In other words, Ganon becomes Agahnim. In Phantom Hourglass, the same word is used to describe either the Ocean King's human form or Ciela's double, I forget which, and is said to be how s/he was able to escape from his/her seal. Going by Ciela's example, her alter-ego is created when she splits her soul, and splitting her soul allows part of her to escape the seal. It is most likely that this is what Agahnim is to Ganon; a fragment of his soul.

Secondly, if we liberally employ the idea of splitting souls to many of Ganon's great escapes, we can explain a number of otherwise unexplained phenomena. He could have escaped the sages' seal prior to TWW by splitting his soul. (We see that he somehow created a portal to escape the flood seal, so there's no need to explain that.) Heck, his soul could have survived his human body's death in TWW to survive on to the later games (specifically LoZ), where it is then destroyed, revived, and hunts the Triforce again in ALttP (if you follow my order).

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