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Nyx's original series by Penstroke
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Stories of the Chaos-Pegasi family by DisneyFanatic23
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Rarity is best Changeling Queen
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Pinkie Pie was an imaginary friend
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Adventures of tiny Twilight
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Georg's series of Twilight as Everfree monster
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Crossover stories by Tatsurou
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Stories about displaced in Equestria, ponies in another world, and crossover universe
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Something happens outside the show canon, but not from the beginning of the show - or not related to the show at all.
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The remade of MLP timeline from the first season
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Stories with changelings as protagonists or main characters (exclude stories from Three Sisters universe)
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Stories from the Five Score Divide by Four Universe
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Universe where Twilight gets a moon dog brother named Rahs Sparkle
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TFTG
273 stories
Stories with transformation and/or transgender theme as their main plot