Dan Owsen's response to a question posed at Camp Hyrule 2001.

Q: The zelda series has had many chapters and different storylines. My question is how do all the games fit into one story line? Or do the zelda games span many different timelines with different decendents of link and zelda? Is Ganon the same person in each time line? 

Username - Hypercoyote 
Cabin # - 7 

A: Ah yes, my favorite non-issue topic -- the storyline of the Zelda games. We probably spurred a lot of questions by posting our theory on the game order on zelda.com. I'd like to clarify some points on that story. First, I don't think that anywhere on the site it said, "This is the Official Ordering! There shall be no other ordering of the Zelda games anywhere, ever! So let it be written so let it be done!!" It's a theory that was created by Nintendo online staff. It's not endorsed or approved by Mr. Miyamoto. However, all that being said, it is based on conversations that I've had with some of the Zelda developers and scenario writers, and a lot of thought went into it. It makes as much sense (or more) than other theories on the Internet. And I have read a lot of them. The fact is, there is not, nor is there likely ever to be, a unified Zelda story. I've said this before, the Zelda developers do not want to create such a story that might limit their creativity in future games. It's that simple. One of the greatest things about the Zelda series is the games leave a lot to the player's imagination. The whole story isn't spelled out for you -- you need to think about it and believe whatever you want to believe.