Who says the game has to take place during OoT? Who says it has to take place during any of the games, for that matter. Why not make a game where you play as Ganondorf, and he ends up winning for once, but then in the sequel you play as Link and come back to pwn him like we always do.

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(BA Character: Revvan)
(My Sweetheart|ZU Daughter|ZU Son/Virtual Bum)