Seeing as this story skips around in time, has it's own interpetation of the Zelda storyline, and allows readers to draw their own conclusions in some departments I decided a FAQ from readers questions was in order.
Q. At the beginning, the Titan and Monument are Ganondorf, but why and how are there two?
A.
Well, although it is not canon, as little in Zelda is, after Ganon's
defeat at the end of Ocarina of time(as depicted here at the beginning
of chapter 3) there are two endings, one with future Link, and one with
child Link. At this point in Zelda history there was a time split. In
the adult timeline, where the ocarina of time Link is removed Windwaker
transpires and Ganon emerges once again, where the new hero of time
kills off with a sword to the head and has the ocean come down upon
him. The child link's storyline, ends with(and here come my twist) the
twilight princess, where Ganon meets his end in the fields of Hyrule.
Q. Mandrag Ganon?
A. An obscure reference to Ganon's title in the manual for a Link to the Past. It translates to Ganon of the enchanted thieves.
Q. What relevance does the wind have?
A. Beat the windwaker and read Ganon's speech.
Q. This is pretty confusing to me, help?
A.
I'll try. The prologue is Ganondorf defeated at the end of both
timelines, but this is not neccacarily the last events of the story.
The first half of chapter 1 is when Ganondorf is a boy, before the
events of Ocarina of time. The second half is some years after, though
Ganondorf is still young. The beginning of Chapter 2 takes place around
the time of the end of chapter 1, though I will not say when. The
second portion being Ganondorf coming upon the Soldier's camp after the
second portion of chapter 1. The third part applies to all parts of
Ganon's life, but specifically his actions during Ocarina of time.
Chapter three details Ganon's defeat in Ocarina of time, and his
imprisonment. And the end. Well, thats straightforward.
Q. What..?
A. To a degree this can help clarify: