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

This story is a sequel to Upheaval: Breaking Point

Following the events of Breaking Point, Twilight Sparkle and her friends discover that Equestria's demise may not come from an enemy invasion, but from within. The Barrier Lands and the Heartland begin the slow and uneasy process of reuniting into a single Equestria, but this long-delayed joining is already in danger at its conception.

With Celestia's power in her grasp and her agents by her side, the wheels of Black Rose's plans for Equestria's future continue to turn. However, her brazen gamble has done more than just bring down a centuries-old barrier. Ancient powers begin to stir: the remnants of a dark period in Equestria's history, the immortal inhabitants of Celestia's homeworld, and a rising tide of darkness coming ever closer.

Equestria is a land of magic and harmony, a peaceful realm ruled by immortal and benevolent monarchs. At what cost is this possible?

Following the discovery of a strange and powerful device, Twilight Sparkle is whisked away to the edges of a land she thought she knew so well. Here, surrounded by ponies whose very existences have been kept secret, she must contend with vicious enemies, hostile allies, and the truth.

Chapters 1-16 edited by KiltedKey

It all started with a simple question: What if? What if Luna had ponies who noticed the beautiful nights she created. Would she have turned into Nightmare Moon? Would she and Celestia rule together for a thousand years? Would Twilight meet the rest of the bearers of the elements and become friends with them? Now, with the help of a new magic spell that she created, Twilight is going to find out!

Welcome to the Lunar Republic!

Featured 4/9/15

This story is a sequel to Stories in Stone, Luna's Royal Guard.

The Canterlot Royal Gardens: a complex prison housing some of the greatest threats Equestria has ever known, sealed in stone. But what happens when something goes wrong, and some of these threats are freed?
Twilight Sparkle and her friends are again called to defend Equestria from an attack that the Royal Sisters are unable, or too afraid, to deal with. But can six ponies raised in a time of peace be any match for creatures who knew nothing but war and conflict?
Perhaps the only hope Equestria may have lies in another set of the gardens residents: the Five Beasts of the Moon, Nightmare Moon's generals, the very ponies who helped her nearly destroy Equestria a thousand years ago.

[This is a direct sequel. Please read,
[ http://www.fimfiction.net/story/1918/stories-in-stone-lunas-royal-guard ]
before starting on this fic or you will be quite lost.]
Season 3 is not accounted for in this fic.
Tags: Action, Sad, Humor, Roller Coaster, Violence, Singing, Some Romance, 80's HBO late night sex scenes... also, nearly every pony is naked... like normal.

Twilight isn't having a very good day. An experimental spell blew up in her face, an army of changelings is attacking Canterlot, and she just died. Yet somehow, it looks like it's going to keep going downhill from here.

Given the chance to correct what's gone wrong, Twilight swears she's going to fix all this even if it kills her. Which it will. Frequently.

Cover art by Pixel Prism
Spanish Translation
Series TV Tropes page

When Rainbow Dash's newest trick backfires spectacularly, she and Fluttershy find themselves stranded in the middle of nowhere. Together, they'll have to survive and find their way back to Equestria and Ponyville...no matter how far the journey.

Now with a Spanish translation by SPANIARD KIWI: https://www.deviantart.com/spaniard-kiwi/art/Apoteosis-1-3-857109863

(Originally submitted to Equestria Daily)
Art by katwalk.

It has been ten years since the defeat of the Changling Queen, and Equestria is again at peace. Twilight Sparkle and the Elements of Harmony have reached their prime, and have begun to settle down. Love and life abound in Ponyville, especially for Twilight's friends, but she has nopony to call her own.

There is a reason.

A series of events lead to a horrible revelation, and Twilight is thrust deep into a terrifying web of secrets and lies. Her peace is over.

This time, however, she won't be fighting monsters or madponies. What she faces will be much, much worse.

Act One of Two.

Act Two is here.

Currently undergoing editing by the wonderful Mstar!