Disclaimer: I do not own the Legend of Zelda series.
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Prologue: A Dark Cloud Looms Overhead
The boys in the field were whipped and the voices of the Moblin bosses filled the air. Each slave feared angering the beasts, lest they have their entrails removed and devoured. Picking the Corlanan tea plant for Ganon and the Twirova, the source of their magic, was the fate that befell many men in Hyrule after the Prince of Darkness took over the land. Though pure Hylian blood was next to gone in these dark times, since the only one allowed to mate was the Gerudo ruler himself, though a few were able to meet in secret and keep the race from becoming totally extinct.
Despite being his own offspring, Ganon did not treat the combined race well. He made the men forced slave labor and mated with his own daughters to produce more offspring closer to Gerudos, planning on wiping all traces of the race from the Earth. Many could not take the rape or slave labor and were driven to commit suicide, or killed in attempts to escape. The iron fist of the ruler was seen all over, and he did the same with the Zora, Gorons and many other races.
He did not treat the pure women of his race any better, as since he was alive they could not bear any male sons to succeed his throne; so he never tried to breed with the women of the Gerudo Valley, which is why he did what he did to his daughters trying to get a more pure Gerudo child. Hundreds of years past the event of his conquest and he still remained entertained however, as seeing the lament of all others who were powerless to stop him gave him all the joy. Part of him thought that he could in theory rule forever without need for an heir, but still ravaging women and seeing tears streak down their faces brought him joy.
One day however, a threat to his throne would emerge. He did not know it at the time, but a pure couple of Hylian royal descent gave birth to a set of twins. Knowing the fate both their children, the turned to an old mage of the Sheikah who was the last remaining member of his race and near the end of his life. He promised he could transport the children to around 20 years prior to Ganon's conquest and leave them each with people that could train them to defeat the Gerudo ruler, as well as impart knowledge of where legendary objects that could aid them on their quest to their caretakers to be given to them at the right time.
So the plan was carried out, Zelda being sent to King Harkinian and Queen Esmerelda of the Hyrule that Ganon would soon take over in two decades time. They read the letter sent with the baby carefully and heeded it. Esmerelda was barren anyway, so this would give them a child of their own. They also knew Impa of the Sheikah could train her in the art of combat. They also increased security of the Triforce in preparation for the times that lie ahead. They then settled into life with the infant, knowing that their fate and that of the adopted child may not change.
Link however was sent to a warrior of the Za'ari, an insect-like race of humanoids that dwelt not far from the Gerudo Valley. Called Theomarxis, he raised Link as a single father and trained him in the ways of the Za'ari. He was welcomed with open arms, as the Za'ari were on good terms with the people of Hyrule. He raised in the ranks of the Za'arian military over the years, to the age of 16. At this point, Ganondorf had been able to seal his demonic form and was laying out plans to take over the all the lands of the planet. Due to the proximity, he first turned his eyes to Za'arian territory and led a marching troop of monstrosities to their kingdom.
Their towns were ravaged by creatures unseen by the eyes of any who had not been to the Infernal Pit. Some looked like rotting corpses, some were large octopus-like creates, and some were behemoths with large mouths filled with razor-sharp teeth. The beasts were able to tear through many steel-hard exoskeletons, or just create tiny fractures that could allow the invaders to suck out all of their innards. Those who survived were either captured for labor or managed to escape into the desert wasteland. Theoraxis and close comrade Mertomiar were among the latter and eventually led others to Hyrule Castle town. There, Theoraxis told young Link, who had been taken to Ganon early in the skirmish but rescued near the end, the truth of his origins and what this siege meant.
"You come from the far future my dear son, one in which Ganon has already made Hyrule meet the same fate as he did us. You are the brother of the Princess, and you must take the knowledge I have given you and use it to stop him," he said, handing him the letter that had come with the boy. Link read it and saw that he'd need something called the Master Sword. Upon inquiring about it, the surrogate father told him that it was in the Hylian vaults, along with their cultures own great word and shield. "Go to the castle my boy, and give that letter to the guard. Your sister will know what to do next. Please hurry, for not much time remains…"
Link solemnly nodded and headed to the castle, but stopped to ask his father if he was alright. Theoraxis told him not to worry and sent him on his way. After Link was out of earshot, Mertomiar asked if he was dying. "Yes my love. But I do not want that on Link's mind. We need to get to a field where we can bury me before Link comes looking for us. Then you and the rest of our surviving numbers go find a new place to settle," he replied, before giving Mertomiar a kiss and hobbled toward the city gates. They made it not five yards before the warrior collapsed on the ground, dead.
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Afterward: Sorry if this story is off to a bleak start. If it feels like I glossed over Ganon's actions or went too far, I apologize in advance. Still, I hope to craft a good, original mature Zelda story. Zelda is one of my favorite game franchises, and I love the manga as well. Credit goes to the guys in Nintendo and to you all for reading this. I hope y'all enjoyed it and look forward to writing more.