Twilight Princess Ganondorf is left alone by Link and Zelda and never enters the Sacred Realm. Years later he's later executed for doing something terrible and its a surprise to everyone that he had the Triforce of Power within him all along (just as it was a surprise to adult Link towards the end of Ocarina of Time.) Ganondorf takes it as a sign from the gods, and the Sages call it a "divine prank".
We don't know that he had it since Link came back, he could've been granted it by the gods right then and there to prevent his death, as an assertion that "ganondorf is important, he must not die." Gods insights being beyond those of mortal men, etc.
Again, it's a nice story and you can infer this and that if you like, it was just never said one way or another.
Ganondorf and Zelda having the Triforce pieces at the end of 1998's Ocarina of Time fits with the story of the game.
Near the end of Ocarina of Time, a plot twist has Zelda explaining that Ganondorf only recieved the Triforce of Power, and that Link had Courage all along, and that there's a rule for the Triforce splitting up.
http://www.gamefaqs.com/n64/197771-the-legend-of-zelda-ocarina-of-time/faqs/20240
Power, Wisdom and Courage.
If the heart of the one who holds
the sacred triangle has all three
forces in balance, that one will
gain the True Force to govern all.
But, if that one's heart is not in
balance, the Triforce will separate
into three parts:
Power, Wisdom and Courage.
Only one part will remain for the
one who touched the Triforce...the
part representing the force that
one most believes in.
If that one seeks the True Force,
that one must acquire the two
lost parts.
Those two parts will be held
within others chosen by destiny,
who will bear the Triforce mark
on the backs of their hands.
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If Link has the Triforce of Courage in the last scene of Ocarina of Time, then the plot point of how the Triforce splits up explains how Ganon and Zelda have Power and Wisdom in Twilight Princess.
In The Wind Waker, descendants of the Royal Family passed down a piece of the Triforce of Wisdom to Tetra and the King of Hyrule had the rest. Like the "downfall" timeline, Ganondorf obtains the Triforce by taking it from its chosen holders, Link and Zelda, and forms the complete Triforce, following up on the plot twist about the Triforce from Ocarina of Time. (but is stopped by the King of Hyrule)
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It's also heavily implied in Hyrule Historia
page 110
"Link bears the proof of his courage on the back of his hand. Because Ganondorf was sealed away along with the Triforce of Power, the rest of the Triforce remained in the chosen ones."
page 113
"The Ancient Sages performed the execution of Ganondrof in the Arbiter's Grounds. However, Ganondorf, who had been chosen by the Triforce of Power, did not perish, and managed to kill one of the Sages."
"The Ganondorf of this timeline is able to wield magic due to his possession of the Triforce of Power. However, since Link was able to war Princess Zelda of the future, Ganondorf did not enter the Sacred Realm or lay his hands on the completed Triforce. Link returning from the future bearing the Triforce of Courage made it so that Ganondorf was unable to consolidate the omnipotent power of the Triforce within himself."
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Aonuma talked about this without mentioning the Triforce
- Nintendo Dream - Feb 2007
http://www.nindori.com/interview/154...154int_02.html
http://www.thehylia.com/index.php?su...&id=1173582355
http://web.archive.org/web/201106111...&id=1173582355
Aonuma: 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.
In the last scene of Ocarina of Time, kids Link and Zelda have a little talk, and as a consequence of that talk, their relationship with Ganon takes a whole new direction. In the middle of this game [Twilight Princess], there’s a scene showing Ganon’s execution.
It was decided that Ganon be executed because he’d do something outrageous if they left him be. That scene takes place several years after Ocarina of Time. Ganon was sent to another world and now he wants to obtain the power…
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Link comes back from the future, never pulls the Master Sword out of the pedestal to open the gate to the Sacred Realm, but already has the Triforce of Courage in the new child timeline. The plot twist about the Triforce splitting up in the game would mean Power and Wisdom would go to their chosen ones. Link warns Zelda and they leave Ganondorf alone until several years later when he's executed because he'd do something terrible, and its a surprise to everyone that Ganondorf has the Triforce of Power.