Skyward sword has the first Link in a time before The Kingdom of Hyrule was founded. There is no Ganondorf yet, instead it features Demise as the main villain. When you defeat Demise, he curses Hyrule to infinite reincarnations of the hero, zelda, and himself. I believe that The Kingdom of Hyrule was founded by Sonia and Rauru a few decades after skyward sword. Before that(probably), Link and Zelda disappeared or died. Some time later, the first incarnations of Demise was born to the Gerudo. Some time passed after that which gave Ganondorf time to rise to power and The Kingdom of Hyrule time to grow. Then the memories we see in Totk play out up until the end of the imprisoning war. I believe the 6 sages,not including Rauru, were granted the spirit of the hero, Rauru became the sealing force, and Ganondorf was Demise reincarnated. The 6 sages fought Ganondorf, distracting him, and then Rauru put a seal on him. After that the rest of the memories played out then the rest of the games played out with the 3 timelines being merged by Hyrule Warriors the Definitive edition and then Botw and Totk played out. Feel free to ask questions and poke holes in this theory.
Go watch matpats video on fixing the zelda timeline for if you want more info on how I think the timelines were merged
https://www.youtube.com/watch?v=W2DMiZ1e574
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I've been theorizing about Zelda for a LONG time! Since the beginning of Game Theory, I've tried to figure out all the ins and outs; all the ifs and maybes. Today we return to the Zelda timeline because I have finally SOLVED it! I have found the MISSING Link in this whole mess of a timeli...