Celestia asks Luna to teach Twilight dark magic. Twilight must pass Luna's class in order to graduate. As Luna develops feelings for her student, Twilight questions which princess she really wants to serve and protect.
(Twilight X Luna)

This story is a sequel to Becoming One With the Night

It was supposed to be a good day. Twilight and Luna were sharing the news of their relationship with their closest friends and family. However, Celestia's largest secret yet finally came out. Now, relations are strained between Celestia and everypony else. After all, what's Twilight to do when she finds out her second mother is actually her birth mother?

On top of this massive bombshell, soon Twilight will be sporting a pair of wings of her own. If she thought things were complicated now, just wait until Canterlot gets wind of a new alicorn. Life is about to become one giant nightmare for Twilight. But hey, at least she has Luna, right?

As stated above, this is a sequel. I highly encourage you to read the first story (the writing is extremely rough early on, mind you), but it's not entirely required to understand most everything that will be going on here.

EDIT: Takes place during S3, when it was originally conceived, thus the Alt. Universe tag. There was no redemption of Discord. There was no ascension. Yes, the Crystal Empire is back, and Cadance and Shining Armor are the leaders there. This should cover the more critical aspects of the season in regards to the story.

This story is a sequel to Apotheosis

Celestia leaves Equestria in the hooves of Luna and Twilight.

While she searches among the gods to answer her questions, Luna and Twilight must struggle to fulfill their own duties to ponies and to Equestria.
Now with a Spanish translation by SPANIARD KIWI: https://www.deviantart.com/spaniard-kiwi/art/Apoteosis-3-3-857110357

This story is a sequel to Off The Edge Of The Map

When Twilight is sent with Luna on a diplomatic mission to Draconia, they quickly find themselves somewhere that doesn't appear on any map, and Luna is lost in more than one way...

Thanks to RBDash47 of Pony Fiction Archive for formatting it for submission.
Title image by Valcron

Tremendous thanks to Illya Leonov and Scribbler for the Audiobook version.
Now with a Spanssh translation by SPANIARD KIWI: https://www.deviantart.com/spaniard-kiwi/art/Apoteosis-2-3-857110089

The supernatural: Ghosts, zombies, werewolves, spirits... vampires...

Twilight Sparkle always thought that the supernatural was just a bunch of superstitious nonsense, just some scary stories to tell around a campfire. She couldn't have been more wrong.

After an occult ritual gone horribly right, Twilight finds herself among the ranks of these so called 'myths', whether she likes it or not. Due to the same force that changed her, dark shadows have begun to spread across Equestria, bringing to life these ancient fairy tales. And Twilight might just be the only one that can stop them...

For better or for worse, Twilight has been changed. Will she embrace this dark gift and become the hero Equestria needs, or will she eventually succumb to temptation and become the very thing she fights?

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

Twilight Sparkle wakes up one morning to find she's undergone some changes. She shortly discovers she wasn't the only one. (New cover art by Jamey4 on deviantart http://jamey4.deviantart.com/)

Warning, this work of fiction contains multiple fourth wall breaks, massive silliness, and more than a trace amount of alicorns.
The author may or may not have snapped at times in the writing of this work, and it shows. Bring a towel, you may get wet.

Twilight Sparkle was presumed to be dead. Destroyed without even a body to bury, the young victim of a deadly magical surge that claimed the lives of many others along side her. More than a decade later, reports of a violent murder by a pony bearing her name are brought to Celestia and Luna's attention. A trail of carnage leading directly towards Canterlot's doorstep, brought by a pony who strikes without mercy. As Twilight approaches, in service to an unknown master, the Alicorn Sisters desperately try to uncover what happened all those years ago.

Edited by Zintegy and The Pink Mugsy

Chapter Heading Art by KirillK
All Sketches and Artworks can be found HERE

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.

Training Session
We all knew Twilight Sparkle was a powerful sorceress, but none of us had ever realised just how powerful she truly was. It is no underestimation if somepony said that she’d be able to challenge an immortal to a battle and come out as the victor. The possibility was there, of that there was no doubt, the only thing that was needed for her to actually defeat an immortal, such as myself, was for her to realise her full potential, for her to realise just how much power was stored in that small body of hers