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I might as well just articulate my theory on the trail of events. First of all, I agree with pretty much everything that @SuperMario101yt just said, except for the fact that the sages weren't awoken in the Child Timeline, unless that occurred after the events seen in game. Second of all, I'm going to try and list how I see events in chronological order:
- Link defeats Ganon and returns to the point before Ganondorf's invasion. He warns Princess Zelda of the impending threat, essentially creating the Child Timeline. He then leaves Hyrule in search of Navi.
- At some point, Ganondorf leads an invasion of Hyrule in an attempt to follow on his original plan. Forewarned, the kingdom repels the invasion, captures and tries Ganondorf, finally sentencing him to execution at the hands of the sages.
- In a "divine prank," Ganondorf is chosen by the Triforce of Power and is able to survive his execution, killing one of the sages before being banished to the Twilight. He invests his magical power in Zant, biding his time until he can return triumphant to the Light World.
- Ganondorf's plan to invade Hyrule once again fails, and this time, he is finally laid to rest by the Hero and the vengeful suicide of his minion Zant, to whose life force he was connected.
- In order to prevent Ganondorf from rising again, his corpse is sealed.
- Somehow, a new Ganondorf is born into the Gerudo, transforms into the Demon King, and is slain by the four Links. This is not the same Ganondorf, nor does he have the same consciousness. This is canon lore, confirmed by Hyrule Historia.
- Over time, Ganon rises again; not as a sentient being, but as a creation of pure malice. The sealed corpse of Ganondorf has become a source of malice, and the incarnation of this malice is Calamity Ganon. The seal exists to prevent the full wrath of his hatred from spewing forth and resurrecting the true power of the Demon King.
- To combat this new, ghostly incarnation of Ganon known as the Calamity, the Divine Beasts are created along with the Guardians. They aid the hero and the princess in destroying the first incarnation of Calamity Ganon.
- Over the next 10,000 years, the malice originating from Ganondorf's corpse reforms into a new Calamity, a cunning one that succeeds in the destruction of Hyrule. The current Princess Zelda seals him away until the recovering Link can return to help her destroy Calamity Ganon's incarnation. Upon his return, Calamity Ganon is destroyed, but the true threat, the sealed corpse of Ganondorf, remains hidden.
First off, it's said in OoT that the sages will need to be awakened when evil ''rules all''. Since this doesn't happen, we can say that the OoT sages aren't awakened.
Now to respond to this:
1, 2, 3, 4. This matches up with nothing in CaC or any known lore related to BotW. All we know is that in the timeline that BotW takes place in, the hero and the sages fought Ganondorf, which ended with him sealed. If this was important history as far as BotW was concerned, it would've been mentioned, no?
5. Why is it that Ganondorf's corpse has round ears instead of pointed ears, like in TP?
6. Ganon is not slain in FSA. He's imprisoned in the FS at the end.
7/8/9. How do you account for the fact that the spirit of OG Ganondorf has been reincarnated into the new one in FSA, who is sealed and alive in the FS the last time we see him? How can OG Ganondorf come back?