Political event
The King of Hyrule forbids the Sheikah from living within Hyrule Castle and forces them to bring their technology to an end. This results in the Yiga Clan, and a continuation of the civil war.
The King of Hyrule could see that the power of the Sheikah and their technology greatly surpassed his own. With Hyrule still politically unstable, the King decides to put the blame for the war on the Sheikah as Magnus was their Clan Leader. This brought some stability. Therefore, out of fear for another Civil War, the Sheikah were forced into exile from Hyrule (establishing Kakariko), told to take up simpler lives than that of great scholars, and required to erase their ancient tech and any remnant of Magnus from existence. This resulted in the Yiga splitting from the clan, the exile of the Zola, and the civil war to continue afterwards.