I have a good theory about what happened to the Gerudos. They appear in both OoT and FSA. In the ALttP manual, in the prologue it says that a band of thieves skilled in black magic opened a gateway to the Sacred Realm, and that they all went charging into it, hoping to obtain the Triforce. But their leader, Ganondorf Dragmire, slayed them all so that only he could have the Triforce. And since FSA and ALttP are so alike in terms of storyline characters and the location of places, I think that FSA comes before ALttP, and that the Gerudo got killed (like it says in the manual) in their attempt to take the Triforce, and Ganondorf wouldn't have any of that. And since Ganondorf killed all of them, that explains why the Gerudo aren't seen or mentioned in any other games. I thought of this whilst playing FSA and reading the ALttP manual, and after thinking about it, it seemed the most logical thing to have happened.

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