So I was reading an article on Kotaku, which has an awesome timeline poster thingy. They were explaining the splits in the timeline and I got confused. THey said that OoT has 2 endings but Ive beatin this game twice and it ended the same everytime.
They're referring to the end of Oot where Link is sent back 7 years to regain his childhood. This then causes the timeline to split into two.
The Child Timeline (which leads into MM and TP) picks up after Link is sent back to the past.
In the Adult Timeline (which leads into the flood and TWW), Ganondorf escapes the Sacred Realm, eventually resulting in the Goddesses sealing him in the Great Sea.
Originally Posted by TWW Prologue
This is but one of the legends of which the people speak...
Long ago, there existed a kingdom where a golden power lay hidden.
It was a prosperous land, blessed with green forests, tall mountains, and peace. But one day a man of great evil found the golden power and took it for himself... With its strength at his command, he spread darkness across the kingdom. But then, when all hope had died, and the hour of doom seemed at hand...
...A young boy clothed in green appeared as if from nowhere.
Wielding the sword of evil's bane, he sealed the dark one away and gave the land light. This boy, who traveled through time to save the land, was called the Hero of Time. The boy's tale was passed down through generations until it became legend.
But then... a day came when a fell wind began to blow across the kingdom. The great evil that all thought had been forever sealed away by the hero...
...Once again crept forth from the depths of the earth, eager to resume its dark designs. The people believed that the Hero of Time would again come to save them...
...But the Hero did not appear.
Faced by an onslaught of evil, the people could do nothing but appeal to the Gods.
In their last hour, as doom drew nigh, they left their future in the hands of fate.
What became of that kingdom...? None remain who know.
The memory of the kingdom vanished, but its legend survived on the wind's breath.
On a certain island, it became customary to garb young boys in green when they came of age.
Clothed in the green of fields, they aspired to find heroic blades and cast down evil.
The elders wished only for the youths to know courage like the hero of legend...
Originally Posted by Zelda Wiki
There's also a more complicated explanation. If you think back to the end of The Ocarina of Time, there were two endings to that game in different time periods. First Link defeated Ganon as an adult, and then he actually went back to being a child. You could say that The Wind Waker takes place 100 years after the ending in which Link was an adult.
The Wind Waker is parallel. In Ocarina of Time, Link flew seven years in time, he beat Ganon and went back to being a kid, remember? Twilight Princess takes place in the world of Ocarina of Time, a hundred and something years after the peace returned to kid Link’s time.
MyAnimeList | Tumblr The moment man devoured the fruit of knowledge, he sealed his fate… Entrusting his future to the cards, man clings to a dim hope. Yet, the arcana is the means by which all is revealed. Beyond the beaten path lies the absolute end. It matters not who you are… Death awaits you - Nyx (Persona 3)