The Mysterious Hyrulean Civil War
It's interesting how much headcanon surrounding this event gets repeated as facts.
Fans have been making theories and headcanons for it for well over 20 years so I completely understand attachments to long held headcanons. Its hard to change your mind on beliefs that have been held for decades.
The only things we solidly know about the Hyrulean Civil War is
● that the conflict lasted for ages
● baby Link and his mother were caught up in the bloodshed so she delivered her baby to the Deku Tree before perishing
● that the entire land was unified by the King after the war.
It is NOT outright confirmed which nations actually fought in this conflict. But it is strongly implied that the Shiekah, Hylians and the Gerudo might have fought in it. The Shadow Temples existence implies the Shiekah involvement. The fact that a gravely injured Hylian woman delivered her baby to safety through the dangerous Lost Woods into the care of the Great Deku Tree, because nowhere else seemed safe for a Hylian baby in the fires of war suggests that all Hylian settlements were active warzones.
We don't know the extent of the participation of the other nations except that it is heavily implied that the (likely brainwashed) Gerudo who followed Ganondorf had fought against Hyrule Kingdom for a while, given the hostility on the border between the nations. With the caveat that Ganondorf had made himself seem trustworthy enough to the King to swear fealty at least once that we seen and possibly another time off screen before the game. So im going with the (Age of Imprisonment) interpretation that Ganondorf had fall guys to throw under the bus to make himself look trustworthy to the King.
Another implication that some Gerudo probably participated in the war is that it's very possible that Ganondorf has male followers recruited by Gerudo women. Although it isn't outright confirmed, the men fighting alongside the Gerudo against the Kingdom may be Hylian. The militant Gerudo have interest in recruiting Hylian men evidenced by the Carpenters ditching their work to attempt to join the Gerudo Thieves. The carpenters were deemed too weak to join the ranks so they were captured instead. It wouldn't make sense to drop everything and betray the kingdom if there wasn't already a precedence of other Hylians joining the thieves successfully.
The Zora, Kokiri, and Gorons are implied to already have the trust of the royal family based on them possessing the Spiritual Stones in an effort to help the Kingdom guard the entrance to the Sacred Realm. That trust is implied to go waaay back because the current leaders have no knowledge of what these stones original purpose was by the time of the game.
This may mean that the other nations already have been allied with Hyrule Kingdom during the conflict. It is not canon to the game that the Zora and Gorons fought against the Kingdom.
Ganondorf curses the other nations for not bending to his will and giving him the stones. It's possible that he gave them the opportunity to join his side before they refused and ended up suffering for it. If any of these nations were fighting with the kingdom, perhaps they would have joined him to save their own kin from his cruelty and join the stronger side? Their independence from one another and the kingdom seems to suggest that they didn't want to get involved in the Hylian's warzones.
The short era of peace was probably after the King ordered the Shiekah to kidnap rebel Hylians to the Shadow Temple. The rebel Hylians fought back against the Shiekah and the dwindling numbers on both sides may be the final throes of the war. Once the traitors were eliminated, the king could finally claim peace and unity within the Kingdom among the remaining Hylians. Perhaps Kakariko Village was built as a Hylian settlement in order to weed out traitors. The best example of a covert traitor Hylian is the soldier that becomes the Poe Collector, who is loyal to Ganondorf after the timeskip. Long before those 7 years, this soldier can be heard complaining about how boring peace is and how much he wishes there were "more troubles in the world" and expects Link to keep these conversations secret.
Since A Link to the Past follows Ocarina, I have reason to believe the Hylians were searching for and fighting over the Triforce for generations until Ganondorf claimed it. Some Castle Town citizens in Ocarina can be heard gossiping about the entrance to the Sacred Realm. It only makes sense for them to speculate about it if it's existence was discovered and searched for sometime before OoT.
I think its very interesting that the Hylians, Shiekah, and Gerudo were the likely participants of the war. Especially if all three share Zonai ancestry evidenced by their capability of having long ears.
All these headcanons of mine aside, no further details are actually confirmed about the Hyrulean Civil War except those three bullet points. Im just suggesting an alternative explanation to the common assumption that the Gorons, Zora and Kokiri were not unified with Hyrule Kingdom until just before Ocarina of Time. Nothing implies that they were ever at war with the King of Hyrule. But there are suggestions that some members of these groups don't always trust Hylians.