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Attachment 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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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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Attachment 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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Attachment 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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Attachment On the morning of the 1st day, when the player finds Kafei going to the post box, using a bomb or the Blast Mask next to him will cause him to flash red as if taking damage.
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During the final boss, there are flower symbols on the floor. The player can actually use these as Deku launch pads if they equip the Deku Mask.
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Originally, the in-game three-day system was going to be a week, but Eiji Aonuma, the game's director, thought that player's would be annoyed having to go through an entire week again and it would be hard to remember what happens each day.
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Attachment Two screenshots found on the game's Japanese website show Link confronting Skull Kid on top of the Clock Tower during the day. This is impossible in the final game without the use of a glitch or cheat device.
subdirectory_arrow_right The Legend of Zelda: Ocarina of Time (Game)
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Eiji Aonuma started developing Majora's Mask because he had no interest in remaking new dungeons for Ocarina of Time's Master Quest mode.
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After playing the Song of Soaring, the map that displays locations Link can travel to comes up. The locations of the Southern Swamp and Windfall are displayed incorrectly. The Southern Swamp is shown to be east of Woodfall, but the player must travel east from the Southern Swamp in order to go to the Old Hags Potion Shop, Deku Palace and Woodfall.
This was corrected in the 3DS remake.
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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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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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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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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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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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In the North American commercial, a woman can be heard saying "Though I walk through the valley of death, I shall fear no evil."

This is a paraphrasing of the first half of the Bible verse Psalms 23:4, "Yes, though I walk through the valley of the shadow of death, I will fear no evil: for you are with me; your rod and your staff they comfort me."
subdirectory_arrow_right The Legend of Zelda: Majora's Mask 3D (Game)
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Attachment In the Nintendo 64 and 3DS versions of Majora's Mask, several real-life constellations can be seen in the sky as well as the rock formations on the Termina Field wall.
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Eiji Aonuma has stated that Anju and Kafei's characters were inspired by the 1998 North Korean Taepodong missile crisis. During the game, Link must help Kafei Spoiler:retrieve a wedding mask so that he can marry Anju mere minutes before the moon is set to annihilate Clock Town.

'We were attending a wedding of a staff member and were talking with Koizumi and the others: "Come to think of it, it’s somewhat strange to come to a wedding in a situation when missiles may fall down today."'
person Kakariko Kid calendar_month May 17, 2017
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Inside the moon, there is a bird that flies around the tree on the plain. This bird was originally in the beta version of Ocarina of Time, but went unused and was repurposed for Majora's Mask.
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There's unused text regarding getting a seahorse in a bottle. In the final game, the player must have an empty bottle to get a seahorse.

"You traded for the Seahorse.
And it came in a bottle!
You should hurry and return it
to its home at Pinnacle Rock."
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