Link's Awakening is the hard one, I'll give you. Link confuses Marin with Zelda so we know he's met a Zelda before, and it's stated in the manual that you've already defeated Ganon, so it's just vague which Link you are. At that point in the series, there were two possibilities, the Zelda 1+2 Link or the A Link to the Past Link.sorry but this makes no sense to me. I don't see how you can tell LA is after LttP or how zelda 1 is after that.
Zelda 1 is easy. At the end of Zelda 1, Link kills Ganon. In Zelda 2, Link goes to a different region of Hyrule and Ganon stays dead because he already killed him. When you lose, you see the game over screen that says "return of Ganon" because he's revived by a ritual using Link's blood - that's explained, and Ganon's only appearance in the entirety of Zelda 2. So until the timeline thing comes up, all the other games that have Ganon take place earlier, before he was killed.
A Link to the Past also contains his origin story; it's the first game that mentions that Ganon was originally a thief named Ganondorf until he was transformed by entering the Sacred Realm. That shows pretty explicitly that it's a prequel.
The idea that there was never any timeline just doesn't match up to how the early series was, where for the vast majority of the games (basically all of the console ones) the connections were evident.
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