Some Favourites

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  A Train, on Fire, Full of Orphans Lyra Heartstrings is driving a train with no brakes, on fire, full of orphans, and she's approaching a broken bridge at terminal velocity. Well. At least things can't get worse. by Aragon 3,251 words · 465 · 24
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  MLP Time Loops Twilight Sparkle has been here before. In fact, she's been here so often she's thoroughly bored. Time Loop stories for Equestria. by Saphroneth 2,479,751 words · 2,229 · 92
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  The Story of Twilight Glow What if Twilight had been born an earth pony and not a unicorn? No school for gifted unicorns, no burst of magic when she got her cutie mark and, most importantly, no student of Celestia. What fate awaits Equestria? by Jeweled Pen 366,702 words · 1,207 · 30
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  Applejack Anonymous Ponyville has its secrets. Chief amongst them is that nearly everypony is in love with Applejack. by Clavier 37,254 words · 1,299 · 33
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  CMC: The Next Generation A series of one-shots on the adventures of five fillies (a flightless pegasus, a snobby unicorn and a set of energetic triplets) on a quest to earn their cutie marks. by DisneyFanatic23 135,776 words · 651 · 31