In this story there will be spoilers for The Wind Waker, Twilight Princess, Skyward Sword, and Ocarina of Time. With that, I present to you...
The Legend of Zelda: The Alternate Link
Legend tells of a prosperous land where there is peace among the inhabitants and miles of green as far as the eye can see. Legend also claims that this land, called Hyrule, was home to a boy that traveled through time. This boy's name was first whispered among the trees of the land until people caught wind of it and it became legend. None are more observant than the trees. They live countless years, much longer than any mortal could, and so they witnessed the golden land's distress and the boy who aimed to save it.
They witnessed him gathering sacred gems and then entering a temple. The Temple of Time, and it was here that the trees noted how the boy never emerged from the temple until seven years later. Wielding a sword with the power to repel evil and, no longer a boy but a man, the hero stood and took in the sight that was once Hyrule.
Many years it takes to construct but demolishing something, now that is much easier. The once prosperous land was now desolate and devoid of life. A high tension hung in the still air and hope was now just a dream, a child's fantasy to the inhabitants.
Despite the fallen kingdom the hero took sword in hand and battled his way valiantly through the hordes of monsters, stopping to help anyone he could. With new found hope the land began to possess small sections of light where darkness had been banished and sages had been awoken.
The hero eventually made his way to the King of Evil's lair, the once grand Hyrule Castle. There he freed the princess and together, with the aid of the sages, they sealed the Dark King away in the sacred realm and peace and light was restored to the land.
In thanks the princess sent the hero back in time to relive the years he lost. The trees distinctly remember the Hero of Time. His courage and sacrifice had been carved into their roots, never to be forgotten. Yet time travel is a tricky concept, and in doing so it created two different versions of the same land. Two alternate universes if you will. Though they were different they were close. Two sides of the same coin.
A single coins two sides can never touch each other and much in this fashion is how these worlds were meant to be: ignorant of each other, neither ever knowing of the other's existence. Yet, both rely on the other for if one side of a coin is bent so is the other side. Magic exists in both of these alternate lands. Magic is a mysterious force with little to no logic behind it, and that is what makes it so dangerous.
However it is very powerful and can be found almost anywhere if you look closely enough. With the use of magic it could very well result in an event that allows both sides of the coin to touch. It's a funny thing, magic. It seems to be able to do the impossible, and turn the most unlikely situation into one that is the most likely to happen…