It shouldn't have been a big deal. Celestia was kidnapped or knocked out or just generally made to seem powerless by whatever idiot with ill intent decided to show up on a nearly weekly basis. As the mighty and immortal Sun Princess, she could escape at any time, but she was happy to play these little games. The daring rescues and bloodless battles gave her ponies such a sense of confidence and purpose!
But this one didn't go as planned. One small, stupid mistake got her thrown to the twisted reaches of the world-prison, Tartarus. Now alone, unarmed, and barely more than mortal, Celestia wakes in a living landscape where everything has every reason to hate her.
And, far worse, she has accidentally picked up a passenger.

Sidenote: This a repost (I tried to go through official channels, I promise!) of a story I wrote long, long ago on an account I foolishly deleted. Back in those days, Tartarus hadn't shown up in an actual episode yet. It's not exactly an alternate universe situation, but it has nothing to do with the canon portrayal of the place.

Super amazing cover art by Cold In Gardez.

This story is a sequel to Winds of Change

Changelings have always been a secretive race, shrouded in mystery and keeping to themselves, staying unnoticed and in the shadows, feeding where they could and avoiding discovery at all costs. When Chrysalis made peace with Celestia, the veil of secrecy and subterfuge was shattered, and thanks to Twilight's efforts, the other changeling queens can no longer remain hidden.

Of course, Twilight is more than happy to leave the tricky diplomacy to Celestia. She's having a hard enough time dealing with her own amorous changeling queen and her new personal pegasus guard competing with her.

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Cover work done by the talented Jazzy. You can find his works here and his stream here.

Editing work provided by Snoodude and MisterGunpowder.

Failing once in her attempt to take Canterlot and failing again in her attempt to take down Twilight, one would think Chrysalis would have cut her losses and let things be, but the queen has once again appeared, this time in broad daylight with no disguise and no army. Her weapon of choice? Diplomacy.

Now Twilight is having to deal with the changeling queen, but surely putting up with her antics will be worth the knowledge she's willing to provide about her mysterious race and the potential undiscovered agents still within their midst...right?

Takes place before Magical Mystery Cure and diverges from there.

With thanks to MisterGunpowder for proofreading and editing.

Revision History:

05/09/2015: Chapter 1 updated with millions of little corrections.
05/20/2015: Chapter 2 revised and edited with another million small and large corrections.
06/12/2015: Chapter 3 given a thorough editing and revision.
06/23/2015: Chapter 4 taken to the gutter and edited twice to be sure.
07/14/2015: Chapter 5 thoroughly brutalized with the editing stick.
08/03/2016: Chapter 6 finally edited. Yes, I'm still alive, dammit.
09/29/2016: Chapter 7 fell out of the editing tree and hit every editing branch on the way down.
10/26/2016: Chapter 8 has emerged from the editing emergency room.
11/17/2016: Chapter 9 found and edited. No casualties reported.
11/30/2016: Chapter 10 treated for whiplash after lightning fast editing.
12/22/2016: Chapter 11 edited. Chrysalis shot first.
01/17/2017: Epilogue edited. Time to hit the cider.

This story is a sequel to The Longest Night

As her twenty-first birthday dawns, Twilight Sparkle finds her simple life turned upside down. While her birthright forces itself into her life, Twilight also has to deal with the arrival of three Alicorns. No pony knows where they came from or what they want, and the Alicorns seem intent on keeping themselves and their purposes hidden. To uncover the truth, Twilight will set sail for distant, ancient lands with old and new friends.

Side-Stories: Velvet Sparkle and the Queen in Stone, Myths and Birthrights: Anthologiae, A Dream of Pride and Envy, The Castle Canterlot, by Honey Mead

TVTropes Page

Pre-readers/Editors: Honey Mead, WNA, Cerulean Voice
Cover art by Saint-Juniper

Comments Contain Spoilers

Twilight becomes alicorn of the stars. This is sort of a problem, because Luna kind of already was alicorn of the stars. Oops!

TV Tropes

This story is a sequel to The Celestia Code

When the monsters created by the dark crystal engine escape their prison, it's up to Princess Twilight Sparkle to deal with them. She gets help and advice from Princess Luna, but things don't go as planned. In fact, when a pony who relies on logic and rationality tries to navigate the stormy seas of emotional entanglement while simultaneously saving Equestria from a horde of evil creatures intent on destroying everything they encounter, nothing goes as planned.
AUDIOBOOK by VisualPony
WARNING: Major spoilers in the comments.

Book 2 of the Alicorn Adventure series.

Goodreads Page
100% Approved by Twilight's Library!

The Badass Twilight tag applies more than ever, but please note the new tags.

This story is a fairly direct continuation of The Celestia Code. You might be able to follow it without having read The Celestia Code first, but it's better if you do.

The sequel is here: The Twilight Enigma

Most excellent pre-reading/editing done by the erudite AcademicPony and the dapper statoose!

This story is a sequel to The Luna Cypher

Twilight sets out to learn more of the ways of the world, and soon decides that the whole planet is disorganized, insanely dangerous, and desperately needs to be fixed. And she's just the mare to do it... with a little help from her friends.

Also, there are sky-pirates!

Book 3 of the Alicorn Adventure series.

A few extra, slice-o-life chapters are here: On the Rocks

Twilight Sparkle has too much magic, and it will take her decades to learn to control it. Her spectacular loss of control during her entrance exam only proves that fact. She is a danger to herself and others.

After Sunset Shimmer’s disappearance, Princess Celestia needs a new student to bear The Element of Magic to defeat Nightmare Moon. With all of Equestria at stake, Twilight Sparkle…is not the pony she needs.

Princess Celestia seals Twilight Sparkle’s magic with the distant promise of one day teaching her.

But there are two diarchs of Equestria. Amidst a lucid dream, an offer is made.

“Hello, Twilight. Would you like to be my student?”

Cover art provided by Lafiir.

This story is a sequel to A Stitch in Time

Having discovered the message left for her by Star Swirl the Bearded in the distant past, Twilight once again finds herself caught up in the middle of a struggle against forces far greater than herself. In order to even stand a chance she'll need to travel further and wider than she ever has, and forge some unlikely alliances with old enemies. All to bring down the powers that have manipulated and shaped her entire life, and retake control of her own future.

The conclusion of the Time Loop Trilogy, which began with Hard Reset
Available in Spanish thanks to dgs1993
Series TV Tropes page

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