Start here!

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  In the Place the Wild Horses Sleep Young Mia is determined to run with wild horses, and nothing is going to stop her. Not her mother. Not even magical talking ponies... by Lucky Dreams 2,746 words · 422 · 8
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  Yes, Apple Bloom, there *is* a Santa Hooves "Dear Santa Hooves. My name is Apple Bloom, and I don't want presents for Hearth's Warming this year. I just want my cutie mark..." by Lucky Dreams 2,757 words · 949 · 11

Then go here!

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  We Are All Made From Silence Sometimes, it's good to talk about your feelings. Other times, the only way we can understand ourselves is to sit and listen to the silence... by Lucky Dreams 3,341 words · 49 · 0
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  The Starlit Promise A young star learns her father must aid in Nightmare Moon's escape... by Lucky Dreams 2,597 words · 36 · 2
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  Cursed Be He That Moves My Bones Staying overnight in the hospital is already bad enough without having to deal with ghosts... by Lucky Dreams 1,894 words · 144 · 1

I am also fond of these ones

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  A Candle in the Sky Apple Bloom spends one last night with Granny Smith. by Lucky Dreams 3,360 words · 99 · 0
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  Supper of Scootaloo Stew Rainbow Dash spends an evening winding up her adopted sister. by Lucky Dreams 1,531 words · 126 · 4
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  A Light in Dark Places Apple Bloom tries to prove to herself how brave she is. by Lucky Dreams 5,717 words · 52 · 0
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  It's Not a Cold Dark Place Six stars on EQD! To save Rainbow Dash, Scootaloo must confront her fears and sail to the land where dreams are made... by Lucky Dreams 7,074 words · 217 · 4

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  Rise The ponies are about to carry out Summer Shutdown and bring back winter. This does not sit well with a small breezie colony living in Applejack's orchard. Someone has to stop the ponies and save the world... by Blueshift 14,791 words · 529 · 7
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  The Sweetie Chronicles: Fragments Sweetie Belle must find Twilight by travelling through different Fanfic worlds... by Wanderer D 570,484 words · 3,340 · 70
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  Ditzy Doo and the Blustery Day In which Dinky Doo asks her mother to tell her a story. Based on Winnie the Pooh. Illustrated by uSea 4,944 words · 116 · 3
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  The End of Ponies A lone pony of a Wasteland future Equestria finds a way to visit her dead friends in the past. by shortskirtsandexplosions 527,556 words · 1,998 · 67

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  The Library of Discord Discord has trapped Twilight in a library that contains every possible book that could exist. Somewhere in the depths lies the one book that can teach her how to escape. But when every idea and story exists, how can she find the one book she needs? by Chinchillax 12,690 words · 387 · 17
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  Celestia... It's Full Of Quills! Twilight Sparkle breaks her last quill. Then she finds enlightenment. Go figure. by Arcainum 3,724 words · 287 · 7
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  Mendacity Bon Bon, Lyra, and the Unseelie Court by Dromicosuchus 74,794 words · 2,308 · 38
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  The Flight of the Alicorn Rarity finds herself forced into an unlikely alliance when her airship crashes far from home. by Ponydora Prancypants 227,108 words · 1,444 · 28

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  The Keepers of Discord Being a statue can drive you mad, yes? by Hoopy McGee 11,445 words · 6,632 · 90
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  The One Who Got Away Equestria’s newest baron has just discovered that his new barony is entirely underwater, his new castle is a broken-down old riverboat, and his new subjects are… seaponies. Welcome to the Barony of Fen. by Georg 22,467 words · 1,963 · 24
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  The Contest Fluttershy returns to defend her title as Quiet Game world champion. by Cold in Gardez 6,714 words · 2,049 · 26
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  Lost and Found AJ and FS are lost, trying to get home. Meanwhile Dash struggles to understand what FS means to her. by Cloudy Skies 168,377 words · 911 · 19
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  It Is My Fate To Enter Every Door Blythe Hyacinth Pie goes to visit her family, in Tartarus. by Cloud Wander 4,550 words · 347 · 7