Zelda's Hidden Genocide

This is a theory, in the same way that the Vermillion City Construction Project creepypasta is a theory. It is meant to extrapolate and explain events that took place before, during, and after several of the Zelda games.

In short, after analysing Ocarina of Time and Twilight Princess, I have discovered a somewhat eerie string of coincidences that point towards the death of an untold number of individuals in the Zelda world.

Civil War
Before the start of Ocarina of time, it is told by the Great Deku Tree that there was a war in Hyrule. This war is what brought Link's mother to the Kokiri Forest, and led to his being raised by the Kokiri. Not much is ever explained about this war. The nature of the conflict had little overt overlap with the current story, so it was never explained. Some theorize that the war was fought to gain access to the Triforce. Others believe it was caused by the Interlopers mentioned in Twilight Princess. However, it is my theory that this war was a large scale civil war fought between Hyrule and the Gerudo tribes of the desert.

It is no secret that the two groups have animosity towards each other. The Gerudo are thieves; they ransack Hylian homes, assault travelers, pillage villages. The Hylians view them as nothing but scum. However, to the Gerudo, this is a necessary way of life. They live in a desert, where no fruit or grain can grow in the ground. They can sustain little if any livestock. By day, the sun's harsh rays beat down upon them; by night, the cold winds chill them to their very bones. They resort to thievery as a survival tactic, and they are not without a moral code. Even Nabooru, their second in command, showed contempt towards Ganondorf when she had heard he killed people.

The Gerudo, seeing the Hylians living in splendor, would grow envious and sick of their downtrodden lives. They would rise up to rebel against the Hylians. Cut off trades from what resources they could offer to the Hylians and prepare for war!

For years, the Gerudo and Hylians would wage war, killing thousands of people in the process. However, the two groups, sickened by the deaths, finally come to a ceasefire, and begin to form a treaty. The Gerudo King, Ganondorf, would act as an ambassador to the Hylian Royal Family, and broker peace between their people. Or so it seemed...

Ocarina of Time
According to the Japanese booklet released with Skyward Sword, the official Nintendo stance on Zelda's timeline is a split occuring at Ocarina of Time. Not all specifics of this timeline are necessary for this theory; only that the child timeline of Ocarina of Time is followed by Twilight Princess.

In OoT, Ganondorf begins to formulate a plot to overthrow the king. Having watched his people suffer for years from the harsh desert and terrible war, he had grown to hate the Hylian Royal Family. He believes that he can overthrow the King and take the Holy Relic, the Triforce, for himself if stages a coup. However, the King's daughter, Zelda, has dreams about his plot, and plans to foil him. Enter Link, a child from the forest, who unlocks the Door of Time, finds the Master Sword, and travels through time to save Hyrule.

After his journey, in the child timeline of Hyrule, the coup against Hyrule has yet to be started. Link, having learned much from his travels, visits Zelda with the mark of the Triforce on his hand (this is visible at the end of the game's credits). He warns the Royal Family of Ganon's plot, and Ganon is set to be executed.

Post-Ocarina of Time and Genocide
Having his plans foiled, Ganon is brought to justice by Hyrule, and sent to the desert, his home, to be executed. The Sages of Hyrule use a holy sword to pierce Ganon's chest, but he is not killed, and the mark of the Triforce appears on his hand. Knowing he cannot be killed in this state, they seal him away in the Twiligh Realm.

In Hyrule Castle, the Royal Family now knows that the Gerudo people cannot be trusted. Having already dealt with years of war and thieving, they come to the only conclusion left: complete annihilation. The might of the entire Hylian Army, backed by the Gorons mining capabilities and the Zoras armor and weapon crafting skills, set out to completely eradicate the Gerudo tribe in the desert.

Though it took countless years, and much blood was shed, the Hylian armies completed their task. Almost all of the Gerudo women were dead. Those that were left were taken back to Hyrule to be used as sex-slaves. What remained of the Gerudo people would be lost in the desert.

Ganon's Revival and Twilight Princess
Ganon, having been sealed away, had managed to gather enough energy from the darkness of the Twilight Realm to invest his powers in a Twili named Zant. He used this pawn as a means to escape from the Twilight Realm and return to Hyrule. But when he escaped, Ganon saw all that was left of his people. The spirits and corpses of his tribe walked the desert, yearning for vengeance against the army that slaughtered them; the sacred Spirit Temple was relegated to nothing more than a tomb; and his peoples' bloodline had been so diluted by years of interbreeding with Hylians that only a few tan-skinned individuals remained to reflect the heritage of the proud Gerudo people. He was all there was left.