Flight School is where it started for her. An infatuation with Rainbow Dash that Fluttershy would carry for seven years, eight months and fifteen days (not that she's been counting). All she has to do is tell Rainbow Dash how she feels, and, really, its not as if its a daunting task.

Right?

Cover Art by the amazingly generous iJab

This story is a sequel to Hard Reset

After the events of Hard Reset Twilight's life and mental well being are slowly returning to normal. Her recovery is cut short, though, when a letter arrives informing her that the time loop spell she cast is causing severe damage to space and time itself. In over her head, Twilight tries to summon anypony who will know how to fix it. The pony she gets is the last one she ever thought she would meet... and nothing like she expected him to be.

Available in Spanish thanks to dgs1993
Series TV Tropes page

Tired of his sister being ignored by a certain member of his guard, Prince Shining Armor sends Flash Sentry to Ponyville to learn how to be a proper homosexual. There, he will learn from the best of the best in all of Equestria and learn the true meaning of homosexuality.

Co-author: lunarbronie

One night, a strange bat like creature bites Fluttershy, changing her body and giving her a thirst for blood. Once she recovers, she finds herself with new abilities and setbacks. How will she cope with these changes? How long can she hide her new abilities from her friends? Can she fight her insatiable need for blood?

Meanwhile, a strange pony from out of town comes to investigate a strange set of murders, where every victim appears to be drained of blood. Will he stumble upon Fluttershy's secret? And what secrets is he himself hiding?

Twilight has always been the best there is at magic. She's won dozens of scholarly competitions and tests of skill in Canterlot. But when it comes to the more violent uses for magic, she is essentially clueless.

When she meets a strange unicorn in a seedy bar, he introduces her to a little known sport that will test her knowledge of magic in different ways. That is, of course, if Twilight can't resist its primal lure.

A year after Princess Twilight's coronation, a guard interrupts a conversation between her, Princess Celestia, and Princess Luna. "Changelings! Queen Chrysalis and her Changelings are right outside Canterlot!"
"Really? What are they doing?"
"Um...they're...they're just waiting...politely..."
"Well, then. Please tell them that I will be with them shortly."
"What?!"

Of Changelings and Alicorns: in which Twilight learns something new.

Chapters that look like ***chapter name*** have been edited since they were first published. I would advise, if you haven't read the new versions, you should do so.

Character list may change as the story goes on.

Currently marked as "On Hiatus" because of school and writer's block.

Cover art credit goes to Bico!

In the ancient city of Sodom, Lyra and Bon Bon sneak onto Noah's Ark by pretending to be husband and wife. Thanks to a fake horn on Bon Bon, the human prophet Noah thinks the two marefriends are the missing unicorn couple he needed for the ark.

Can Lyra and Bon Bon keep their true identities hidden from Noah? It won't be easy when their every move is being scrutinized by the cripplingly homophobic earth pony couple. Will Evangelical Hope and her husband Adamic Faith expose Lyra and Bon Bon for who they are, or will this forty day cruise be smooth sailing?

Cover image by Why485

This story is a sequel to Scion of Chaos

Five years after the summer in which the three had gotten their cutie marks, Scootaloo, Sweetie Belle and Apple Bloom, now young mares in their own right, decide to go on a quick summer vacation, all as an attempt by Sweetie Belle to cheer up a sad friend. However, the trip turns out to be more than they had anticipated.

Set five years after Scion of Chaos and An Emerald Treasure. For the sake of context I'd recommend reading both of those first.

Special thanks to Mac349 and Plebeian for proofreading. Thanks to CMC4TW for editing/idea-mulling.

In a moment of weakness, Chrysalis had more than a taste of Shining Armour's love. 11 months later, Twilight Sparkle finds herself a brand new niece by way of 'A small foal in a basket on my door step'.

Special thanks for the picture by Awilldrawforfood1
Now edited with DoomManta.

WANTED:

The newly crowned Princess Twilight Sparkle has set up a bold new initiative to discover new magic, and is sending out an open call to the unicorns of Equestria to apply for her research team. No experience in magical theory or research necessary. Enthusiasm and out-of-the-box thinking a must. The Equestrian government is not responsible for any physical, emotional, or magical trauma experienced during the course of the project or the application process.

Cover art by Page Turner