The Great Bay is the third main region that Link must travel to in Majora's Mask. To get there, Link must have Epona. On Link's first arrival, he finds out that the bay's waters have become murky and too warm, which is causing many problems within the region. After bringing one of the dying Zoras to shore, whose name is Mikau, Link finds out that the Pirates have stolen Lulu's eggs, which Link must retrieve. After Link obtains all seven eggs, he takes them to the Marine Research Lab, where he learns the New Wave Bossa Nova, which allows him to reach the Great Bay Temple. After defeating the boss of the Great Bay Temple, the bay's waters return back to normal for the rest of the three-day cycle.
Great Bay Coast
- Main article: Great Bay Coast
This is the main area within Great Bay and it is home to many of the locations that Link first comes upon. The waters along the coast have become murky and unsafe due to evil hidden deep within the temple. This area also leads off to the many other areas of the Great Bay region, such as the Zora Hall and the Pirates' Fortress.
Oceanside Spider House
- Main article: Oceanside Spider House
The house is right next to the Fisherman's Hut and can be entered to find all thirty of the Gold Skulltulas for a reward. The rewards differ depending on which day it is. If Link completes the house on the First Day, he is gifted with a Giant Wallet and if completed on the Second Day, he is rewarded with a Purple Rupee, while on the Final Day, he is only rewarded with a Red Rupee.
- Main article: Fisherman's Hut
Marine Research Lab
- Main article: Marine Research Lab
The lab can be seen from the shore and is located just off the Great Bay Coast. It is a small house with the Professor inside. There is an Owl Statue located right before the ladder to the entrance. Link must find the seven Zora Eggs within the region, four are located within the Pirates' Fortress while the remaining three are located around the waters of Pinnacle Rock. Link must then return the eggs to the Lab and place them in the fish tank.
- Main article: Pirates' Cove
This Cove is located to the north of the coast and can only find a huge wall and some Gerudo Pirates here guarding the entrance. In order to enter the Pirates' Fortress, Link must transform into a Zora and swim underneath to find the hidden passage.
- Main article: Pirates' Fortress
The Fortress is heavily guarded by Gerudo Pirates and can be accessed via a secret passage hidden beneath the shore. The first area of the Fortress is mainly water and is watched over by Gerudos in small boats. Within the actual grounds lie many Gerudos who seek to guard the area from intruders. Link must find four Zora Eggs here and then return them to the Marine Research Lab. Link can also obtain the Hookshot here which helps him later on.
- Main article: Pinnacle Rock
This is an area far into the deep waters of the Great Bay. Link must enlist the help of the Seahorse in order to successfully navigate to this location. Here, Link can find three out of the seven Zora Eggs, however, they are guarded within small caverns guarded by the treacherous Deep Pythons.
- Main article: Zora Hall
The Zora Hall is the main area in which the Zora race reside within the land of Termina. Here, Link finds the Zora Shop, where he can purchase useful items and Potions. Within the center of the Hall lies a large music stage where the popular music band, The Indigo-Go's, play.
- Main article: Zora Cape
The cape is a form of bedrock and is the site where Link finds the Owl Statue for the Zora Hall Coast area and also the sire where the Giant Turtle resides. If Link plays the New Wave Bossa Nova, he can awaken the Giant Turtle who can lead Link into the Great Bay Temple.
Great Bay Temple
- Main article: Great Bay Temple
Once Link has awakened the Turtle, he can the safely travel to the distant temple which has been the cause of the murky and unsafe safe waters of the bay. Within this dungeon, Link pumps and manipulates the water and he must also make use of the Zora Mask to navigate the waters within. Link obtains the Ice Arrows and faces the Gargantuan Masked Fish: Gyorg (Boss). After defeating the boss, the curse on the waters lifts and Link is gifted with a Heart Container as well as Gyorg's Remains.
- Main article: Waterfall Rapids
The rapids are above the waterfall on the south side of the coast and to east of the Zora Hall. Here, Link can find two beavers who let him play a mini-game. If Link is successful two times, he is gifted with a Bottle, however, after two more difficult races with the opposing Beaver, he is rewarded with a Piece of Heart. Link can access the rapids by using the Hookshot to climb up the many ledges leading towards the waterfall.
New Wave Bossa Nova
- Main article: New Wave Bossa Nova
When saving all the Zora Eggs and putting them in the water tank, they teach Link the song. The song can be used in order to restore Lulu's voice and waking the Giant Turtle.
|This section describes a subject that is or may be outside the core Zelda canon.|
The Great Bay appears as a playable stage in Super Smash Bros. Melee. This stage is purely based on the Marine Research Lab. Tingle is floating above, and players can pop his balloon, causing him to fall. In the background, players can see the Moon descending, and then the Four Giants pushing it back up. The turtle also appears in this stage, but only for a limited time.