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- "The security at the Pirates' Fortress is tight. Sneaking in is no easy task. If you're set on meeting those beautiful pirates, try going to the valley on the other side of town! I've heard there's a mask there that lets the wearer escape detection."
- — Fisherman
The journey through the Pirates' Fortress begins in a lake-like area within the fortress. In this area, a few guards on oddly advanced motor boats circle the water on patrol. If Link is in front of these boats, or if he attempts to climb onto them, he will be thrown outside, forcing him to re-enter the first area. Link must utilize stealth to proceed through the entirety of the fortress. The Gerudo Pirates will not harm Link if he is spotted; rather, they will throw him out to the main lake area if he is inside the main fortress, or simply out of the entire fortress if he is spotted while in the lake area. Using the Stone Mask, Link can bypass the Gerudo Pirates without being spotted, even if he is their direct line of sight or close enough to touch them. However, Link will still be spotted by the Gerudo Guards and must fight them.
The fortress consists of many switch-related puzzles; Link must hit these to either shut down or open the flow of water from vents and pipes, as well as open specific gates, allowing him to access every area in the fortress. Link must also use the Zora Mask to maneuver through the water within the Pirates' Fortress, which is made treacherous by the presence of currents and Mines.
In order to obtain the four Zora Eggs hidden in the fortress, Link must also engage in combat with three Gerudo Guards. Link must also obtain the Hookshot found in the throne room to actually enter the pools containing the eggs. To get the pirates to leave the room, Link must go to the room above and shoot down the Giant Bee's Beehive, then go back down and claim the Hookshot.