Strange Condition

At the end of Wind Waker, it is revealed that Ganon wanted power in order to help his people. He despised the Hylians for having a nice place to live and ways to lead good lives. His people lived in a desert with few ways to prosper hence their lives of crime. In the beginning Ganon was not even a bad guy himself, especially when he was a kid and then young man. Twinrova always saw in him a way to gain power. They say in-game that they are roughly 400 years old, which means they have seen at least three kings come and go. Each one presumably led the Gerudo people in the same ways of life they had always known, never really seeking out to expand their power or territory. From an early age, Ganon knew he was to become king eventually. He hated the way his people were forced to live but could do nothing about it quite yet. This is how he started off merely wanting to help his people. The sisters saw this desire for power within him and used it to their advantage to gain power themselves. They used him basically, which he never fully figured out. He also grew up with Nabooru, and the two eventually were close up until she betrayed him. He became convinced by Twinrova that the key to gaining the power he needed to help his people laid in obtaining the Triforce, something they had had their eyes on for some time.

Why was it so easy to convince him? Ganon helped the King of Hyrule during the civil war when he was still a teen and newly crowned king. At the end of the war, the Gerudos were still left to their home in the desert while Hyrule prospered. This angered the young man, who thought that helping the king might have gained his people better circumstances. This is when the sisters sweep in with their plan. If he can obtain the Triforce, then he will have all the power he needs to take over the world and put the king and all of the Hylians in their place as well as anyone who opposes him. He takes the bait. This new distorted view he has is still rooted in his desire to help his people. Between then and the beginning of Ocarina of Time this quest for power changes him into the man Nabooru comes to despise and plot against. Any connection the two have is broken when it becomes clear that he chooses his quest for power and Twinrova (whom she always hated) over her, and this leads to her plotting to take him and his followers down. He goes against the rules she, him, and others followed by taking from the weak. Eventually while brainwashed she will do the same. The sisters are alerted to her plans (they never liked her either, especially her influence on Ganon and thus watched her closely) and tell him. In outrage, he commands them to take her prisoner (scene after Link gets the Silver Gauntlets). It is their idea to brainwash her, and he agrees because of his anger.

Seven years go by while Link is asleep in the Temple of Light. During this time, Ganon is able to take over Hyrule and make it into ruins to symbolize the conditions his people have always endured. By this time, the power and his hatred have all but consumed his total being. The sisters want him to expand his empire, but he is reluctant, fine with ruling over the destroyed land of Hyrule. Still, they want more. They know of a legend quietly passed down that speaks of an even larger, bloodier war that took place between not just the races of Hyrule but different worlds. They know of a man who lives in a temple on an island, unable to leave for he is bound there. They know of the fabled Chosen Ones who will be destined to defeat that man and stop the coming of the Most Evil One. And they know that any child of the King of Evil would be able to keep those things from happening, allowing them to expand not just throughout the world where Hyrule is but to all of the other worlds as well. They come up with a new plan, one that involves finding the right female to have the King’s heir. Like their plans for domination, this is kept secret from him as well. While they hate to admit it, they know that the only one Ganon would even consider as a partner is his old friend and first love, the one they have under mind control carrying out raids that would make even the hardened Ganon double-take at. So they let her out of mind control sometimes and have the two of them spend time together in hopes of them somehow reconnecting. It takes a while for this to happen, and Ganon is fine with the arrangement, even though she is left in the dark about her actions and why her own people have this new kind of respect and fear around her.

Eventually the sisters get what they want when the two have a son, Exzavier., which is a surprise to all since only one male is to be born every 100 years. The reason, though unknown to everyone at the time, is because of her latent Sage powers. His new family softens Ganon if only a little bit, which the sisters do not like. Again they tell him that Nabooru is planning on rebelling against him (by this point he has ordered them not to place her under mind control any longer) and taking their son where he will never see them again. This is more outraging than the previous time because he had let himself soften up by giving her a second chance to be loyal to him and by forming an attachment to their child. This is the point at which the sisters turn her into the Iron Knuckle that Link later defeats. When Ganon is ultimately defeated by Link and the Sages, the sisters panic and send Exzavier 1000 years into the future where he will be safe. He grows up there with his father, who had escaped the imprisonment that happened in the reset past (kind of confusing). He despises his dad, not knowing the whole story about his parents. He also despises being taken away from his mother, which is a motive when he returns to the reset past. Unfortunately, this causes the timelines to split. His future and the future of the world he is visiting are now different. He stays in Gerudo Valley as the king to make things better for them the way his father originally wanted to.

During this time, Link is gone for seven years. Only he and Zelda have any memories about what happened in the future, and neither knows about Exzavier. The prince (Ganon is still recognized as the king, and Ex proves he is his son) wants to make sure that the dark future he comes from doesn’t happen. Sadly, Link is stuck in Termina. Even his power cannot reopen the portals, which were sealed by Judas to prevent Link from ever being able to meet the Chosen Ones as well as keep all of the beings who will fight in the war from coming to Hyrule. He ends up working with Zelda in secret, which even she does not like as she does not trust him. Link eventually returns to Hyrule. Exzavier even lets it slip about who his mother is. The Golden Goddesses can foresee that the adult Exazvier will be lost to his rage and power and eventually be destroyed. But they also see that if he were born again in this reset timeline, he would be an ally for good having been raised by his mother, who eventually leads the whole Gerudo tribe in place of its lost king. They allow the memories that were erased to be returned to her, and the two have a sort of weird reunion. When he returns to his future after Link comes home to Hyrule, she comes up with her plan on getting him back. This leads to a visit to Ganon in the void between realms, where he agrees because he sees their future son as a way for him to eventually escape. Also, part of him still cares for her, even after her betrayal. He is unaware of the future events that took place. Exzavier is born again shortly before the events of the Crossover begin.