Alright. A lot of interesting ideas in this story. I read through the first chapter and skimmed the second and third.
One of the main issues I had with this piece is the jerking around of persons. Some of your line breaks (or perspective changes) don't even make sense because the characters involved were in the same place at the same time.
In the sense of this story as a whole, it felt like you were trying to bring in too many separate characters too fast. Switching between two characters every other chapter can be done with some manner of continuity, but this came across as rather jerky because some of your breaks weren't even between separate perspectives.
I don't think that means you can't succesfully write a story with three separate stories (whether or not you plan to bring them together eventually), but just reading this confused me.
Also, regarding the prologue--when you use direct quotes from another source, it is required that you put that information in your story. That means the whole Windwaker story needs to be put in quotation marks with its cited source at the end. Even if it was a character in the story telling it, direct quotes need to have the credit given accordingly (unless it is public domain, which it is not in this case).
The context is also rather strange. I have no sense for how old Link and Zelda are at this point, and the story is moving so fast that there's little detail of the main characters themselves (as well as the actual world. I understand that this is fanfiction (with the aid of knowing the series, readers already know what the characters and world looks like), but without any creative detail, the story comes off as rather flat and plotty.
There's also some curious sentences. I picked up a run-on here and there, but the syntax and grammer worked fairly well for the most part. There was also some point where a character's thought was written in third person (and unless they normally think in third person, that's a little strange).
So, in short, there was some creative style in the way this piece was written, but the world and characters could really use some help. There's a lot of interesting plot going on here, but more detail would help give it dimension.
