Twilight is sentenced to life in prison. This prison, unofficially named 'Lunar Prison', has Celestia as its head warden though. Another thing is the fact that it practices Caped Panzer Games, which are death games in which certain inmate participate in various types of deathmatches and objective based combat in large mechanized tanks for various rewards. One thing, though, if you lose you die.
tags and such updated as story progresses
cover image source linked

Twilight didn't know what came over her. At one point, she was having a wonderful tea party with her friends, and the next thing she knew, she was trying to kill the princesses.
This could have something to do with the fact that nopony would listen to her at her brother's wedding, everypony thinking she is crazy, or even the fact that Discord was set free without anypony noticing.
She finds herself at Celestia's court, facing crimes she didn't commit.
"Twilight Sparkle, for stealing the Elements of Harmony, attempting to kill me and Princess Luna, and Betraying everything you were supposed to protect, you are hereby banished from Equestria, never to return!"
Celestia's words continued to ring in her ears as she followed the road out of Equestria. She would never see her friends again.

My entry to The Exiled Competition

Cover art can be found here. It was made by StarlightSpark on DeviantArt.

The Witch of the Everfree... a tale that has spread among all who live by the ever illustrious forest, to whom the witch truly is, no one knows apart from the one herself... until now. Twilight Sparkle had lived in the Everfree throughout most of her long life, since the corruption she was alone until not long ago when she met few companions. Trained along side her sisters through bond in arcane magic, given true immortality, she continued her studies alone only every now and again seeing how her race fared. Now, forty years after she was dubbed a witch by her race, three little girls stumble through her woods in search of the ever mysterious "witch", what could really happen? read to find out.

FEATURED: 16/03/14

Clarifications:
Many have wondered what Twilight looks like and such so to clarify, she does not look like a human female, she retains her fur coat, she is of human height and has hands. The facial structure is more detailed such as where the eyebrows should be there is a darker patch of coat much in the color of her mane.

The story starts a few episodes in, around halfway through season one I would say, some shall stay canon whilst some with alter, I am sorry for this inconvenience.

Twilight is still Twilight in every way, though she has been with little to no contact throughout her life apart from when the Everfree retained people, in such her words would become haggard sometimes so that's why you will probably go "huh" when you first see her talk to the CMC.

That is all for now.

This story is a sequel to Can't Stand To Be Apart

After The Cutiemark Crusaders died mysteriously after getting their cutiemarks, Twilight finds a book that might explain it all.

After getting their cutiemarks, the Cutie Mark Crusaders realize that the symbols on their flanks means something. That they are bound together forever, and the markings will not let them separate for even a moment.

Only death will do them part they think. But even then, will it?

This story is a sequel to Chrysalis's Revenge

The following story contains heavily sensitive content that may disturb some readers! Proceed at your own risk! THE SUICIDE TAG IS NOT THERE JUST FOR SHOW!

Three weeks after being forced into a sinister game of revenge, arranged by Queen Chrysalis, Twilight returns to confront Chrysalis one last time, only to learn that her along with her friends were not the first round of victims.

The game was never over.

Before anybody asks, yes, this is very heavily inspired by the "Saw" movie franchise. I just felt that the original story needed more of a story, so here's my attempt at adding more to the story. This takes place after the events of season 6!
Dramatic reading: Chrysalis's Revenge: End Game [MLP Grimdark Reading]

Celestia discovers a lingering trace of Nightmare Moon's soul still lodged in Twilight's mind—a survivor of the lingering effects of the Element's magic.

Faced with the threat of gradually losing her friend to Nightmare Moon's evil influence, Celestia realizes the only way to save Twilight is to let the storm of dark magic take its course all at once.

And yet, as Nightmare Moon's corrupting magic tears away at Twilight's forgiveness and understanding, and Twilight begins dredging up unexpressed doubts once kept controlled, Celestia must face a lifetime of confrontation her student has kept covered.

It is going to be a long night for both alicorns.

This story was written for the Tenth Bimonthly Twilestia Contest. It placed somewhere.

After an accident reveals that Sweetie Belle is a robot, she is abducted by the government and forced to defend her right to exist. She endures trial after trial in hopes to earn her freedom.

During this ordeal, she discovers dark secrets about her past.

This story is a sequel to Rainbow Factory

Cloudsdale Weather Corporation has been running without incident for over twenty years. That is, until two foals manage to avoid being processed and find themselves in the haunted bowels of the massive facility. Can they make it out of the abandoned factory with their sanity intact? Will they uncover the secrets even a company as dark as the CWC is ashamed to keep? And what of the workers who help ensure that, in the end, not a single soul gets through...

Love the series? Buy the book!

—[TVTropes Article]—[Plagen Shiki's Reading]—[The Song Inspired by the Story]—

It has been several months since the disappearance of Twilight Sparkle..

One night, after watching her sister raise the Moon and set the heavens alight, Princess Celestia begins to bed down for the night, only to be interrupted by portal forming in her room. From out of the portal comes none other than Twilight Sparkle, garbed in strange armor.

Princess Celestia, along with Luna, Cadence, and Shining Armor, are overjoyed by the Element of Magic's return, but are justifiably curious as to where she had been and what she had been doing. And so, Twilight begins her tale. A tale of survival against impossible odds. A tale of a people fighting for the most basic right of all sentient beings. The right to exist.