Reminds me a little bit of a fanmade concept/what was maybe an OoT sequel concept (can't actually remember) called Valley of the Flood, where a similar thing happens. I don't remember it all too clearly but I think it was set around 30 years after, and the royal family had built themselves into this indestructable fortress thing in case Ganon returned, and the goddesses had planned to flood Hyrule if he ever did (I guess to get rid of him). And either he did come back or he was going to, so the player (who is a regular young boy, not Link and not someone chosen by the gods) claims to be the chosen hero anyways and sets off on a jouney similar to the Hero of Time's in an attempt to save Hyrule. You would go through dungeons that were modified dungeons from OoT, and play the game pretty much regulary (minus the time travel, I don't think that happens again) until the Ganon fight, where, even though eveyone now believes that you are the chosen hero, you aren't and you can't defeat him, no matter what. And then the goddesses pull a Noah's Ark without the ark and everyone drowns in a flood. The end