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Just because Cloud’s moaning all weird-like doesn’t necessarily mean he’s more crazy than he was before.
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The fact is that Square is never going to answer every question concerning a game’s plot. For example, the FF8 Ultimania states that the Rinoa = Ultimecia theory is false. Square didn’t put that in the game because they just didn’t expect people to think that. And how is the Ultimania NOT related to Square? It seems to me that their information could only be known if it was straight from the developers. After all, they have complex formulas concerning even gameplay that no normal person would be able to figure out. By the way, what contradictory info have you seen?
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I can tell you that Genesis discovered the Banora underground when he was a little boy, and used it as his personal playground. The only other answers I can give you would be from the Ultimania.
EDIT: Oh, and the reason you can tell Shinra was using the underground…Did you read the blood writing on the walls of some of the cells? The cellmates talk about how they were kidnapped/captured and experimented on, etc…
