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The arch at the entrance to Romani Ranch is actually the same arch at the entrance to Kakariko Village from Ocarina of Time. Even the text on the sign is re-used, effectively saying "Welcome to Kakariko Village" in both games. This is more noticable in the Japanese version, which features the text in Japanese instead of the localized version's Hylian text. The Hylian text still translates to "Welcome to Kakariko Village", though.
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At the end of the game, Skull Kid asks Link to be his friend and says, "You have the same smell as the fairy kid who taught me that song in the woods." This hints at the Skull Kid being the same one that Link sold the Skull mask to and taught Saria's song in Ocarina of Time.
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When the thief Sakon tries to steal the bomb bag from the Old Lady from the Bomb Shop, if Link hits the Bomb bag with an arrow, the hookshot, or another bomb, the bag will explode, killing Sakon.
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According to the gossip stone in Romani Ranch in the Cucco Shack, the All-Night Mask was used as a torture device.

"A torture device of insomnia called the All-Night Mask seems to be available at the Curiosity Shop..."
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The Song of Healing has the same first six notes as Saria's song but played backwards with a different rhythm.
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Attachment The aliens that attack Romani Ranch during the first night are based on the Flatwoods Monster, a monster that was very popular in the 1950s and 60s.
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The impermanent flow of time in the first three-day cycle as Deku Link is 1.66 times faster than normal, meaning it takes only 27 seconds for each game hour to pass rather than the standard 45 seconds for every three-day cycle after it. It is in this stage of the game where NPCs and most enemies are not rendered outside of Clock Town's boundaries.
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Aside from owl saves, the American release of Majora's Mask had a number of other changes made to it, both aesthetically and to its game-play, such as making dungeons easier, or simply moving objects around.
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All 4 main dungeon items pertain to the Bow. Woodfall Temple features the bow itself, while the Snowhead Temple has Fire Arrows, the Great Bay Temple has Ice Arrows, and the Stone Tower Temple has Light Arrows.
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Attachment Though not explicitly stated in the game, the instruction booklet mentions Termina as a kind of parallel world of Hyrule.
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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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Attachment 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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"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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Attachment 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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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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During an early Beta version of Majora's Mask, the Fairy Ocarina was available and usable.
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Attachment 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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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 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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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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