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If the player stands in the little garden outside of the Astral Observatory in Termina Field when the Clock Tower opens on the third day, a different cutscene will play that shows the tower opening as if looking towards Clock Town from the Observatory.
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During early trailers of the game Zora link, Deku Link and Goron Link had their instrument icons instead of the ocarina. It's unknown why this feature went unused in the original game but it was later reused in the 3DS remake.
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Zelda was originally going to use a flute to teach Link the song of time, but the instrument was swapped for an ocarina.
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One possible reference in the game occurs during the final boss fight against Majora's Incarnation; he sometimes hums what sounds like the melody to the Death Mountain Dungeon from the very first Legend of Zelda
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After Kafei gives Link the Pendant of Memories, he asks Link to keep it "a secret to everybody", a reference to the popular quote from The Legend of Zelda.
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An unused fishing mini game can be found in the game's data. It would have been similar to that of the fishing in Ocarina of Time. Fish and the owner of the fishing mini game can be spawned into the game by modifying the data, but using the fishing rod will frequently cause the game to crash.
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There are 3 unused masks that can be found within the game's data that were likely supposed to have been worn by the Skull Kid. They're strange masks that look like Link, each rotated differently to be used in different scenarios.
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The postman in Majora's Mask, who wants to flee, but can't find time for it in his schedule, shows quite the similarity to some couriers from a short story written by Franz Kafka. They want to kill themselves, but refrain from doing so due to their "oath of service".
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In the Ancient Castle of Ikana, if the players goes to the south-east part of the courtyard there will be a pillar. If the player manages to get on top of it, they will find a paper airplane. The airplane cannot be picked up and has no significance whatsoever.
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On the file select screen, if the player pushes start, holds up, pushes A and then pushes B twice, an alternate opening demo will play.
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On the back of Anju's grandmother's wheelchair, there's a picture of a tiger. This is a possible reference to the pet tiger owned by Granny in The Legend of Zelda: Ocarina of Time in Kakariko village, who is also Anju's grandmother's Hyrule counterpart.
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Each piece of music in the Zora Hall is taken from a previous game in the series. This includes the main hall being the Zora's Domain's music from Ocarina of Time, Tijo playing part of the cave theme from A Link to the Past, Japas playing part of the dungeon theme from The Legend of Zelda, and Evan playing the Game Over song from the same game.
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If the player talks to Keaton while wearing the Keaton Mask, he'll ask a series of questions. A sound is made signaling whether the answer selected is correct or incorrect. Picking the correct answer will trigger the "pause" sound from the game Excitebike on the NES.
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During an early Beta version of Majora's Mask, the Fairy Ocarina was available and usable.
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Through use of Gameshark or Action Replay cheats, it is possible to get "Saria's Song", as well as the "Sun's Song" from Ocarina of Time. The "Sun's Song" has no difference from Ocarina of Time, and fast-forwards time to the next day. "Saria's Song", however, doesn't do anything.
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A clear impression of Skull Kid can be seen in the grass when looking towards the south entrance of Clock Town from the Astral Observatory telescope.
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"Farewell to Gibdos" has a similar melody to that of the Merry-Go-Round located at Big Boo's Haunt in Super Mario 64.
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In the magic hag's potion shop, Kotake is standing on a box of lemons in order to reach over the counter.
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Majora's Mask was planned for release on the iQue Player, a Chinese version of the N64, and there are several screen captures from the game on the back of the iQue packaging. It's theorized that the game's dark undertones and imagery were deemed too violent to pass Chinese censorship laws, so the release was cancelled.
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Though not explicitly stated in the game, the instruction booklet mentions Termina as a kind of parallel world of Hyrule.
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