Way back when, in an interview with Superplay magazine, Shigeru Miyamoto indicated that there is a master timeline. And, to keep track of this giant meta-story, there is a “master document.”
For every Zelda game we tell a new story, but we actually have an enormous document that explains how the game relates to the others, and bind them together.
Frankly (and no offense to Miyamoto-san), I think this is a load of Keese guano. If I had two Rupees to bet on the matter, my money would be on the idea that up until (say) Ocarina of Time, precisely when Eiji Aonuma began working with the series, the game designers had been making it up as they went along with reckless abandon as to any concept of continuity.
Miyamoto furthermore explained that he really doesn’t care about the storyline, truth be told.
But to be honest, [storylines] are not that important to us. We care more about developing the game system… give the player new challenges for every chapter that is born.
And, concerning the question of whether the story comes second during a game’s development, Miyamoto revealed,
The most important thing for me, is that the player get sucked into the game. I want the games to be easy to understand, and that the people appreciate the games content, its core. I will never deny the importance of a great story, but the plot should never get that important that it becomes unclear.
It is precisely this “reckless abandon” that the theories department of any Zelda site is such a bull market—everything is up in the air! Can you (without a doubt) guarantee the placement of Link’s Awakening In the Zelda timeline? What about the entire Vaati story arc?
Clearly since 1998, however, there is a sense of continuity budding within the confines of the series. Gone are the days when we simply theorized whence a game’s storyline may occur in the vast panorama of Hyrulian history. Now, we are bombarded with on indirect sequel after another, so much so that we can reasonably assume that there is indeed a micro-continuity between Ocarina of Time, through Majora’s Mask, and up to the Wind Waker.
And now, another game is about to be plopped down into that continuum—namely, Twilight Princess. At the 2004 E3, Eiji Aonuma announced that the game would occur between Ocarina of Time and the Wind Waker (the implications of that have already been explored by TML here at the ‘Blog).
So, ultimately, where does this all leave us? Is there a “master timeline” or not? Well, if I had those aforementioned two Rupees, I suppose my next bet would be placed on the following proposition: there is, and there is not. On one hand, there is this “new continuity” between Ocarina of Time and the Wind Waker (encompassing those two and more) and on the other there is the aimless chaos of all that proceeded the fifth game in the series.