Ganondorf was working with Ingo to buy into a drug ring involving the Milk from Lon Lon Ranch.
I still think this is goddamn truth, we've even seen evidence of a fermented milk alchohol in Japan, we also know the Water Supply was coming through Zora's Domain (polite way of saying King Zora's Ballsack) so clearly Ganondorf was just trying to break hyrules dependance on the extortionate Zora Monoply, look at Kakariko they used a well that was a torture pit for their water, and yet the Domain is supposedly hyrules water source.
On a side note in terms of Random Theory, i'm starting to think the Kokiri are manisfestions of the fairies we see bobbing about them, the only reason link doesn't have a fairy is because he's not a forest spirit.
The only reason people turn into Stalfos or Skull children is because the Kokiri are killing them and eating their flesh "more leg link?"
The gorons should never have had a problem with Dodongo's cavern they live ona mountain of rock, just tunnel frigging down, there's clearly enough explosives lying around, or eat the the rock since you love it so much.