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The pirate found you!
Gerudo Pirates are identical in appearance to the Gerudo Thieves from the Gerudo Valley area in Ocarina of Time. In Majora's Mask, the pirates have stolen Zora Eggs from Lulu, meaning that Link must infiltrate the Pirates' Fortress to retrieve the eggs and return them to the Professor in the Marine Research Lab in order for Link to learn New Wave Bossa Nova.
In addition to the regular patrolling Gerudo Guards, Link encounters three Gerudo Pirates that are not fooled by the Stone Mask. These are mini-bosses that need to be defeated to proceed. They are found in three separate rooms as Link progresses.