The PERFECT Zelda timeline! If you are a fan READ THIS!

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The Zelda series does follow a storyline, (which Nintendo
themselves admitted to) and the games take place in a specific
order. Windwaker actually takes place AFTER all of the Zelda
games, while Ocarina of Time is near the beginning of the Hyrule
storyline. So, while the NES and SNES Zeldas, along with Link's
Awakening, Majora's Mask and Ocarina of Time all feature the real
Link, those take place at the very beginning of the series.
Twilight Princess says that the main character of THIS
game, whatever you choose his name to be, wears the clothes and
is endowed with the spirit of an ancient hero that once saved the
realms.
Windwaker makes the announcement at the very beginning of
the game saying "There was once a hero clad in green who fought
back evil..." (I will not add more because of what it will give
away in the storyline)
So check this out: When you get the final technique, Great
Spin, the skeleton that has been training you gives you the
following speech:
"Although I accepted life as the hero, I could not convey
the lessons of that life to those who came after. At last, I have
eased my regrets."
So, Link could find nobody talented enough to carry on his
abilities, and waited to find you before his soul could move on
into the afterlife in peace.
Another connection can be made that links (no pun intended)
the skeleton warrior to the Hero of Time... he tells you the
first time that he meets you that he is the last of his people,
and that the skills he is teaching you are passed on from back
into his bloodline.
A Link to the Past refers to the Link in that particular
game as the last descendant of the seven knights that defended
the Royal Family, and one that carries the abilities of their
bloodline. Besides the courage he carries from his ancestors, it
is remarked that he also carries their abilities.
Thus, I have come to this conclusion: There are three
separate heroes through the entire Zelda series. Link, the hero
in Twilight Princess who becomes embedded with Link's courage and
who is trained by Link, and a little green man that saves Hyrule
from being flooded many years in the future. If the heroes can
change, can't Gannondorf?

Zelda series order:

1 - Ocarina of Time
2 - Majora's Mask
3 - A Link to the Past
4 - Zelda II, The Adventure of Link
5 - Link's Awakening
6 - The Legend of Zelda
7 - Twilight Princess (New Hero)
8 - Windwaker (New Hero)
Because of their multiplayer intent and my
misunderstandings of the storylines, I do not count either Four
Swords Adventures or the Oracle of Seasons to be an actual tale
of what happened within the realm of Hyrule. Rather, I see these
games as just an enjoyable addition that allows for more Legend
of Zelda gameplay.