Infiltrating Gerudo Town
Men are not allowed in Gerudo Town. Talk to the merchant outside the gates, who will mention a man who snuck in. Head back to the Kara Kara Bazaar and climb onto the roof of the General Store to find Vilia. Pay him 600 Rupees for the Gerudo Outfit. Equip it to enter the town safely.
Speak with the chief, Riju, who tasks you with retrieving the stolen Thunder Helm from the Yiga Clan.
The Yiga Clan Hideout
Rent a Sand Seal and head into the Karusa Valley. You must use pure stealth here; the Yiga Blademasters will kill you in one hit if you are caught.
Distract with Bananas
Yiga love Mighty Bananas. Drop a banana on the floor to distract the guards, allowing you to sneak past them or Sneakstrike them from behind.
The Secret Door
In the final room, use Magnesis on the large wall panel to reveal the path to the boss room.
Boss: Master Kohga
Wait for him to summon a boulder above his head, then shoot him with an arrow. The boulder will drop on his head, stunning him and allowing you to deal massive melee damage.
Boarding Vah Naboris
Return the Thunder Helm to Riju. You will ride Sand Seals alongside her into the desert storm. Stay inside the protective dome projected by the Thunder Helm to avoid being struck by Naboris's lightning. Use Bomb Arrows to shoot the beast's feet until it stops moving, allowing you to board.
Boss: Thunderblight Ganon
Widely considered the most difficult boss in the game due to his extreme speed.
Phase 1: He dashes in a zig-zag pattern. You must learn the timing to perform a Backflip exactly when he strikes to trigger a Flurry Rush. Alternatively, hold up your shield, let him hit it, and immediately counterattack to break his shield.
Phase 2: He will drop metal pillars and summon lightning. Use Magnesis to lift one of the metal pillars near him so he shocks himself.
Phase 3: Link's Hideaway, EliteGuias and Vandal all describe a third stage that plays like Phase 1 at a faster pace; Thonky counts only two phases. His weapon is sometimes electrified after the halfway point, so block only with a non-metallic shield or wait for the electricity to fade. Eat a Shock Resistance meal or unequip metal shields to survive this phase.