Expanded History
Ganondorf's childhood was an unusual one due to the utter uniqueness of his position. The Gerudo are a race composed entirely of women, who continue their race by finding boyfriends among Hylians (or other compatible races). Though genetically the gerudo should have long ago lost their unique traits, their race is unique in that the gerudo traits are always dominant in their offspring. The fact that almost every child is a female is itself remarkable. The almost accounts for the rare exception, when a gerudo male is born once every hundred years. This male has the unique distinction of becoming their king and ruler. In times past, the height of a gerudo king's rule was marked with prosperity for their race, finding plenty to scavenge or steal to keep their daughters fed and comfortable. Typically, the king was the only male the gerudo women would ever respect. After all, their king suffered through the same rigors they did (unlike the far easier life of the Hylian) and was expected to not simply succeed at what he did, but exceed what his 'sisters' accomplished.
Ganondorf was no exception. Whereas Gerudo girls are expected to survive the Gerudo training grounds by the age of fourteen, Ganondorf did so at twelve. Likewise he spent lengthy hours learning horseback riding, archery, swordplay, and all manner of Gerudo skills. He was never given the identity of his true mother, nor did anyone know who she was, including the woman herself. It was deemed more important that Ganondorf have no special ties to any one of his subjects, so they could never be a weakness to him. Instead the two eldest gerudo, a pair of twin witches named Koume and Kotake, were placed in charge of his welfare and were the closest things to parents he ever had. They educated him in the ways of the outside world and more importantly, in their secrets of the magic they had learned in the Spirit Temple and from those that preceded them. Secretly they also taught him the dark magic that they themselves had long ago learned and instilled in him a lust for power. From the descriptions he heard of Hyrule, he came to envy the prosperity and ease that punctuated their lives. Whereas his years had been one of rigid training so he would stand a chance at survival, a Hylian could live an uneventful live and grow fat off the efforts of others. The thought of it sickened him.
Yet training was not the only problems he encountered as a child. As a young child, he only knew that he was 'different' from his peers. He was royalty and thus treated differently, but the actual differences between himself and every single person that hew knew only became more and more apparent as he grew. When he was young, it was easy to fit in with the girls, as his features hardly set him apart from the others. But as they all grew older, the physical dissimilarities became all too obvious. His peers knew he was a man and thus not like them. More than that, they held only a grudging respect for him. Theirs was a culture that taught that men were worthless - except for a Gerudo king. But Ganondorf was no king yet. He was just a boy and though strong and capable, they had been witness to his triumphs and his failures. They may have been taught to respect him and to do as he said, but he was still different. Though some accepted him as one of their own, others continued to doubt him. When Ganondorf realized this, he began to close himself off from his childhood friends, burying himself more and more into his studying and training.
In his early teens, the great civil war broke out amongst Hyrule, as they struggled for control about who should have access to the Sacred Realm. The Gerudo were no exception and thus Ganondorf had his first taste of war. He won many great victories and the admiration of his people. Ultimately the war ended in a unified land - at least, for the prosperous people of Hyrule. The Sheikah were nearly wiped out and the Gerudo with an uneasy truce. Whereas they had once been desert wanderers, the war effort led them to taking permanent claim of the 'Gerudo Valley' and establishing a fortress their to protect their lands. They were not allies of Hyrule like the Gorons and Zora had become, but for the moment they were not enemies. Yet during all this, Ganondorf became aware of what Hyrule had to offer and he at last resolved that one day, he would have all of it and usher in an era of prosperity for his people.
It was what Koume and Kotake had long hoped for. The Gerudo had tired of war and had no want to waste their lives in a war they could not win and thus Ganondorf realized it was foolhardy to rouse his people in such a way. So where force had failed in the past, Ganondorf tried for trickery instead. In order to protect the Sacred Realm, which could be accessed through the Temple of Time, it was best to entrust each Sacred Stone to one of the other races of Hyrule. One was given to the Great Deku Tree, another to Darunia of the Goron people, and the last to King Zora. Getting into the Hylian King's good graces was easy. The king had grown accustomed to peace and prosperity and he was completely taken in with Ganondorf's offers to become sworn allies and friends. It was all he could ever hope for and despite his daughter's prophetic warnings, he placed his trust in Ganondorf and gave him complete access to his lands.
He was not so successful with the other races. The Great Deku Tree was too wise to ever fall for Ganondorf's silver tongue and rejected him. Darunia, proud and stubborn, was too rigid to entrust Ganondorf with a Sacred Stone. King Zora had entrusted his stone to his wife - and later daughter and thus was of no interest to Ganon. Thus Ganondorf was forced to use more coercive methods to gain what he wanted. He summoned Gohma to weaken the Great Deku Tree, promising a cure only if he received the stone. In order to force Daruna to bend, he unleashed the King Dodongo on the Goron's food supply. For the Zora, he infected their deity, Jabu Jabu, with a parasite that would cause him to consume anything that came close, including both the princess and her Sacred Stone. Everything was lining up perfectly. He prevented the other races from sending word to the King of Hyrule, so it was only a matter of time before they were forced to concede their stones to him. Ganondorf was, after all, a patient man. He was willing to wait.
It was waiting that proved to be his undoing. The Hylian King's daughter, Princess Zelda, managed to find an unexpected ally - the Hero of Time. Ganondorf wasn't even aware what happened. On the verge of taking what he wanted, suddenly the Hylian King was aware of the treachery afoot and sent his knights to war. It was a long fierce war, but in the end not even Ganondorf could oppose the united strength of the Hylians, Gorons, and Zora. After a long, hard war he was at last imprisoned. He was to be executed for his crimes against Hyrule, a sentence to be carried out by the Ancient Sages themselves. But just as his sentence was carried out... something unexpected happened. The symbol of the goddesses, the Triforce, appeared on his hand. Empowered by a piece of the Triforce, he survived his wound and in turn killed the Sage that had carried it out. Before he could exact his vengeance on the others, they made one last ditch effort to banish him, using the Twilight Mirror to banish him to the Twilight Realm. It was the same realm that the Interlopers, who had caused the great war from his youth, had been banished long, long ago.
An untold time passed and Ganondorf drifted through the void without contact, thinking himself alone. He fell into a great sleep to preserve himself, though it seemed possible he might never escape his fate. However in time he became aware of the descendants of the Interlopers. They had formed their own country and kingdom within this realm, evolving to become suited for such a life. They still carried resentment for the light beings who had banished them there, but many were content with their new home. Their hatred fueled Ganondorf and provided a beacon within the void to find their new civilization. Among them he found Zant, a rejected candidate for the position of Twilight King. The ruler of the Twili had the power to access to the Twilight Mirror and thus seeing opportunity, Ganondorf posed as a god and convinced Zant that he would give him the power to conquer not only the Twilight Realm, but the Light World as well. A benevolent god, Ganondorf asked nothing in return, promising that as long as he lived, Zant could never permanently be killed.
Thus Ganondorf waited once more. He allowed the new Twilight King to do as he would, taking over both realms while Ganondorf simply waited and could take it all for himself. Once he had returned to his own realm, he became aware of how Hyrule had changed his absence. The Gorons and Zora had grown distant from Hyrule and the Kokiri had seemingly vanished. Likewise, the Sheikah had gone extinct. As for his own people? Ganondorf could find no trace of them and could only speculate as to their fate. Had they abandoned Hyrule and plunged deeper into the desert? Or perhaps none of his followers had survived the last war. It was even possible they had slowly faded away due to the loss of their king and a growing resentment for the Gerudo people, slowing the birth of future daughters. Regardless, Ganondorf had seen the future that resulted from his ambitions. But he shouldered no blame. It was once more the fat, ignorant Hylians to blame. Indeed, they had only grown less impressive in the time that had past, so much that they barely knew their own history. How could fate continue to favor them? Even as Zant conquered Hyrule in silent conquest, they remained ignorant of their own defeat. How could Ganondorf ever be satisfied ruling a country consisting of a people such as this?
Perhaps... yes, perhaps it was better if they simply didn't exist.