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The Yiga Clan are a group a Sheikah who defected after the Royal Family showed concern about the new Sheikah Technology. They have a Hideout in Karusa Valley, near Gerudo Desert, and their leader is Master Kohga.
After Link defeats Master Kohga in the hideout, Yiga Footsoldiers and Blademasters will occasionally teleport near him, carrying typical Yiga weapons, such as the Duplex Bow or Windcleaver. The Yiga Clan members sometimes disguise themselves as normal travelers in order to ambush Link. This can lead to some very humorous dialogue.
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10,000 years before the events of Breath of the Wild, there was a major split in the Sheikah. Some adhered to the Royal Family's wishes, and buried the Guardians and Divine Beasts, while some of them defected from the Sheikah, and became the Yiga Clan. They swore their allegiance to Calamity Ganon, they very monster the Sheikah were supposed to oppose. Later, they stole the Thunder Helm from the Gerudo. Later still, during the events of Breath of the wild, Link set out to reclaim it in order to enter Vah Naboris.
When arriving to Gerudo Town, Link encounters the Gerudo Chief, Riju and her guardian Buliara. After a quick conversation, Link is given the task of recovering the recently stolen Thunder Helm. Link is told to travel to Karusa Valley, where he will happen upon the Yiga Clan Hideout. While in the hideout, Link sees a Gerudo woman who tried to recover the Helm herself, Barta. After sneaking around and defeating Master Kohga, a chest containing the helm will appear.