A Humbled King (Wind Waker)
Ages after the events of Ocarina of Time, Ganon escapes the Sacred Realm and wreaks havoc on Hyrule. Unfortunately, no hero came about this time, leaving the Sages to fend off the threat by flooding Hyrule and everything in it. The descendants of these Ancient Hylians took to the mountaintops (now islands) and began a new era. The history of the once great kingdom became nothing but a legend.
Ganondorf began to rebuild his troops in an attempt to find the other two pieces of the Triforce beneath the sea. A portal to Hyrule opened where Ganondorf held both the Triforce of Power and Zelda’s Wisdom. Link would battle Ganondorf in the sunken Hyrule Castle to prevent him from successfully completing the Triforce and gaining fearsome power.
Ganondorf in The Wind Waker appears older than he does in OoT, and also wiser. He carries himself much more regally and speaks in an eloquent and poetic manner rather than the brash way his younger self spoke. Age has certainly granted Ganondorf experience, but it also allows him to see matters more sensibly. Whereas Ganondorf during the events of OoT seemed to run on blind hatred; Ganondorf in WW is driven by a hatred that stems from deep cynicism.
Ganondorf has attempted twice to forge together the Triforce, and both times he had been met with extreme punishment from the Sages. He built a cynicism inside him not just toward the Hylians, and not just toward the Sages, but about his own fate as well. He now realizes that he has no control over his fate — it was something that had been foretold since birth. Even death and imprisonment can not wash it away.
“It can only be called fate. … That here, I would again gather the three with the crests.”
When Ganondorf turns into Puppet Ganon, it’s an obvious metaphor for the position he finds himself in. He’s nothing but a puppet controlled by the remnants of Demise to fulfill a vengeful prophecy created ages ago. The only way Ganondorf knows how to break this curse and end his fate is to fulfill it. When the Triforce becomes whole, he wishes to rule Hyrule, a forgotten and ancient land. If he was still the power-hungry fool he had once been, he would have wished to rule the entire world — to dominate over the descendants of the Hylians residing above the waves — yet he desires only to break the curse. Ganondorf even states that he has no wish to kill Link or Zelda. He just wants to take the Triforce. In this manner, he chooses to rule an empty, forgotten land in spite of his fate.
After Ganondorf has a sincere moment, speaking to Link about the state of his people and his own intentions, he headed for the Triforce to make his wish come true at last. The King of Hyrule, however, took the Triforce for himself and wished that Hyrule would be sealed away forever, along with the evil Ganondorf. He couldn’t do anything but laugh and sought instead to end his cursed brethren by his own blade. He failed to fulfill his fate for a third time. Ganondorf, in turn, laughed quietly to himself as he was freed from his fate.
An Unrealized Destiny (Twilight Princess)
After Ganon was defeated, Princess Zelda sent the Hero of Time back to relive his childhood. When Young Link met the young Zelda, he warned her of what Ganondorf had planned to do, which confirmed her own suspicions. Zelda informed the King, which led to a Hylian invasion of the Gerudo Desert and the capture of the Gerudo King. The Hylian army desecrated the Gerudo’s holy Spirit Temple and modified it into a makeshift prison to house all of the desert thieves, dubbing it the Arbiter’s Grounds.
The Sages had planned to execute Ganondorf by sword; however, the Triforce of Power awakened inside of him, allowing him to break free and kill the Water Sage. In an act of desperation, the remaining Sages imprisoned Ganondorf in the Twilight Realm.
After 100 years in the Twilight Realm, Ganondorf convinces Zant, who had been refused the Twilight throne by Midna, to take over the Light World and seize the Kingdom of Hyrule. With the castle in his possession, Ganondorf now had the means of making the Triforce whole and realizing his true fate.
It should be noted that in this timeline, Ganondorf never transformed into Ganon. He was captured before his armies even stepped foot in Hyrule. In fact, Ganondorf and his people were imprisoned merely on the words of two children. Ganondorf is just as arrogant and cunning as he was in OoT as he never had the humbling experience that his WW self had. Fueled by the pent up desire to rule Hyrule and his true power still chained inside, Ganondorf became even more disobedient and short-sighted. He planned to lie, cheat, and steal his way to the Hylian throne.
Ganondorf finally realizes the extent of his power by unleashing Ganon, but like his OoT self, he is slain by Link. Perhaps showing a little more reserve, he opts to battle Link in a sword fight in his Gerudo form. After being defeated, Ganondorf echoes the words he said in OoT and also those of his master, Demise, by saying that Link and Zelda’s descendants will be plagued with his presence. However, much like the WW version of himself, he dies instead of being imprisoned, leaving the inhabitants of Hyrule to never fear a return of the Gerudo King again — his dying words never to be realized.
From this timeline, Ganondorf is never seen again, but Ganon is reincarnated hundreds of years later during the events of Four Swords Adventures. Ganondorf died a fool with a heart full of vengeance, never to be quenched. He was perhaps blessed with the naivety of believing he was in control of his fate. He died never realizing the role he played in a legend much bigger than himself.
An Undying Evil (A Link to the Past/The Legend of Zelda/The Adventure of Link)
In a history where Ganon defeats the Hero of Time, Ganondorf fulfills the fate given to him by Demise. Transformed into Ganon, he returns time and again to wreak havoc on Hyrule. Ganondorf, the Gerudo King, would be forgotten through time, and the King of Evil, Ganon, would take his place in the winds of the declining kingdom.