Scene: Lost Woods; Twilight Princess Era.
Ganondorf walks up to the empty pedestal where the Master Sword once slept.
"Finally!" He exclaims, "An open portal through time!"
He sticks out his hand, a dark ball of energy forming in it. The dark energy hits the pedestal, turning it into a portal.
"Farewell, Hyrule!" Ganondorf exclaims, jumping into the portal. Afterwards, the portal closes, and the world starts to fall apart, leaving nothing but whiteness.
Scene: Lost Woods; Link to the Past Era.
Link stepped up to the pedestal that held the Master Sword. He was exited; He'd just been through the three greatest challenges he'd ever faced in all his 13 years.
His excitement, however, quickly turned to confusion, as a dark portal appeared beneath the Master Sword, swallowing the sacred blade. In a moment of desperation, Link jumped to grab the sword, and fell through the portal.
The last thing that he remembered, before falling unconscious, was the feel of the sword's handle in his hand.
Scene: The Sky; Skyward Sword Era.
Link was flying toward Skyloft. The bottle of warm pumpkin soup was noticeable through his bag; he chastised himself for putting this off for so long.
Then, Link's thoughts were directed to what he was seeing. In front of him, Skyloft was being swallowed by a dark portal.
Fi appeared beside him.
"Master," She began, "That appears to be a portal of strong dark forces. there is a 95% chance that it's intent is to consume Skyloft, and a 93% chance that Skyloft will no longer be there after the portal is gone."
"Right," Link said, gaining altitude, "I'd better do something about it."
"Master," Fi said, "Evidence states that what you are planning to do could be considered foolish, and I advise you to take precautions to insure your safety."
"Don't worry. I know what I'm doing."
"There is a 97% chance that what you said is a lie."
"So?" Link says, drawing the Master Sword and jumping off of his Loftwing. He takes as aerodynamic a pose as he can, while having his sword aimed straight at the center of the portal.
When his sword connects, Link starts to black out. The last thing he can remember is Fi screaming in pain, and the sword changing in his hand.
This is the first chapter to an idea I've had for awhile. I don't know if this idea has been done before; it probably has, so I thank you for choosing to read my take on the concept.