I don't think the shiekah will let Link into their temple at all... unless! They're trying to kill him. The shiekah could trap Link in the temple in order to have him attacked by the monster inside. Or, Link could merely sneak in, unauthorized. But I kinda like the maybe the good guys went too far idea of the Shiekah throwing Link into the dungeon to have him killed.
Anyway, we kinda need to figure out where everyone is first. My first thought being- how do the Gerudo feel, where are they, who do they follow? Have they turned to following Ganon? Do they remain loyal to Farin, and Link doesn't realize Ganon isn't Farin? Have they said, !@#$% men, we're leading ourselves?
We can do whatever, we just need to decide. So we should prolly figure out the problems with all of the above.
Having the Gerudo openly following Ganon makes the most sense to me right now because then this would keep up the pretense that Ganon is the real king, if the Gerudo treat him as the king. Upon Ganon's return, he saw his people were in the hands of a young king that wanted to restore his people's reputation and status- but, his methods were to try to make peace with the Shiekah and Hylians. This wasn't going well, as the Hylians were useless and never responded to his emissaries, and the Shiekah were still distrustful after so many years of war with the Gerudo.
Ganon plotted to frame Farin for a crime and have him executed, as Ganon appeared in the Gerudo city and claimed power, promising to restore the Gerudo's former status by crushing the Shiekah and overthrowing the Hylian empire. Farin escaped from the execution and fled the city, eventually finding his way to Hyrule town in pursuit of Ganon.
So this way, the Gerudo would be aware that their king is in Hyrule, and would support Link if he'd been given a mission by Ganon.
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Another option is to have the Gerudo fail to realize that their king has been overthrown as well. Perhaps Farin left the Gerudo city and that's the last they heard, until Link comes back and says that the Gerudo king is in the castle, and he's working for him. So they'd be delighted to help Link, since he's working for - the Gerudo suppose- Farin, a good king.
Of course, Farin, on his way to meet the Hylians, had been attacked by Ganon, and his credentials stolen. Ganon beat him to Hyrule and claimed to be the king, and Farin, without credentials, couldn't prove he wasn't an imposter, so took up residence trying to disprove Ganon.
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Or, we could have it that Ganon, back from beyond, waited until the next male Gerudo was born. Then, he stole the young child and cast him out into the desert, waited 30 or 40 years, and came to the Gerudo pretending to be the lost king. Farin, meanwhile, was raised by a shiekah hermit, and never told of his identity until he came of age. He sneaked into the Gerudo city to find Ganon, but was captured and sentenced to death as an imposter, trying to usurp the throne. Farin escaped, and pursued Ganon to Hyrule, continuing his crusade to unmask him there.
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Or, perhaps Ganon doesn't want control over the Gerudo, he just needs to manipulate the Hylian Royalty. Therefore, he framed Farin for a crime and arranged for his execution. Farin escaped, and the Gerudo, without a leader, just decided Abigail was enough, and follow her exclusively. They are willing to help Link just because he is working against the Shiekah, so Link's aims align with the Gerudos'.
So one of those are where the Gerudo are. The Shiekah, we already defined better. They're engaged in a war with the Gerudo, over resources like water. There must be some reason they can't ask Hyrule for resources, since they're supposed to be allies. Are the shiekah enemies of Hyrule now? Are they just treated poorly, like the poor in the slums?
Anyway, the Shiekah are aware of the ancient history, and know that the cogs are used to open the door to the triforce. They are also aware that the Gerudo king in Hyrule is not the true Gerudo king. So when a Hylian comes looking for the cogs, they know something's up, and refuse to give it to him. They might not openly treat him hostilely, though. Or should they? Perhaps in some parts of the Shiekah settlement, he's treated neutrally, while he's not allowed in others.
Anyway, the big thing to decide after we figure out how everyone's allied, and how everyone will act, is what Link will do. We've always had him helping people, but he can't really help the shiekah, so he'll have to help the Gerudo, or nobody at all. The things we need to accomplish before the dungeon:
- Establish that the shiekah know what the cogs are for and don't support what Link is doing, because they know something about the Gerudo king that Link doesn't. Although, they can't openly reveal that the King is a fake. Or if they say "false king" or something, leave it ambiguous enough that it could be interpreted as they just don't support his right to rule. Which, neither do the Hylians, since they seem to have imposed sanctions on the Gerudo, forcing them to starve in the desert.
- Have Link meet the Gerudo, show that they're poor because of the Hylians, facing similar things to the poor in the slums. Evoke some sympathy.
- But also, we can't make the shiekah out to just be evil and imposing on the Gerudo, since we need to start instilling doubt about Ganon in the player's mind. So show their side of the story, whatever it is, also.
- Have Link get the fire and ice arrows.
- Have some sort of interaction with the Hero's Ghost. This might be a good time for him to reveal a little more, and create more doubt about Ganon.