Zelda: Ocarina Of Time's Manga Tells Us What Happened To Link's Father

Instead of a reveal on screen in "Ocarina of Time," Link's father receives some non-canon backstory in the related manga originally published in Japan in 2000.
Instead of a reveal on screen in "Ocarina of Time," Link's father receives some non-canon backstory in the related manga originally published in Japan in 2000.

Link's Father - Zelda Wiki

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Dark Facts Even Die-Hard Fans Didn't Know About Ocarina Of Time

This is what happened in the manga when Sheik knocked out Link(forced) and put him in the cell on Gerudo Fortress