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!

Princess Twilight Sparkle discovers a centuries-old mystery hidden in the Royal Archives. Her investigation leads through layer after layer of deception and misdirection, setting her hooves on a path that seems to be leading to a mysterious secret. Along the way, she learns that some friendships can be very, very strange.

Book 1 of the Alicorn Adventure series.

AUDIOBOOK by VisualPony
Featured at the Royal Canterlot Library
TV Tropes Page (Courtesy of Sandtalon)
Goodreads Page (Courtesy of Facedeer)
Equestria Daily Page

WARNING: Major spoilers in the comments. Takes place several months after the end of season four. (Not a Da Vinci Code crossover, BTW!)

Do you see a dark tag? No, you don't. Not dark. Well, okay, there are a couple of dark-ish bits, but that's all. Not enough to warrant a tag. Speaking of tags, there really ought to be "Badass Twilight" and "Friendshipping" ones.

Sequels and side-stories (and more) can be found here Offprint and AO3, and a hardbound two-volume set of all that can be ordered from The Ministry of Image.

My editor for the first edition of this story was Gogito, and I can't thank him enough for all the hard work he did. My editor for the revised version was PresentPerfect, and he did a terrific job of getting the story into excellent shape.

A thousand years ago, Princess Celestia banished her sister to the moon, that much we know. What wasn’t known, and what Celestia kept secret was that before her banishment, Luna had given birth to a foal. Now a thousand years later, as Nightmare returns to Equestria to bring about Eternal Night.

Twilight Sparkle, protege of Princess Celestia, struggles against the tyranny of this ancient foe. But how will she be able to save herself and her friends when the truth of this ancient legend crashes down upon her? Twilight will have to confront herself...and her heritage.

Polaris501

What if Soarin had not been as forgiving as he was when he found out his team had lied to him and tried to replace him for the Equestria games? What would his life be like if he were to up and quit the Wonderbolts, and where could this life-altering choice lead him?

Disclaimer: Story contains subject matter that may hit pretty close to home with some readers, such as pathological depression, borderline personality disorder, and alcoholism.

Harry Dresden, Chicago's only professional wizard, accidentally travels to Equestria after being attacked in the Nevernever. Twilight is none too amused with their newest 'guest', but trouble is brewing. Somepony is planning something sinister and the mane six may need Dresden's help however little some of them want it.

Story Image by: Lynxgriffin
Cover arrangement by: Novel Idea

It was a night that will forever be burned into the memories of everypony. One fateful night in Equestria everything changed. The princesses who had ruled over the world with kindness and heart were gone, and a new ruler had taken their place.
Years have passed since that event. Ponies have grown up, aged, and moved on with their lives. Equestria has become a very different place over the span of these years.
Our story begins when a face resurfaces in Equestria. When a weathered, scarred, but familiar face steps into the light.

This is the fanfic based on Astringe's Bad Future series on DeviantART. He did some great designs of the characters, so make sure you give that gallery a peruse before you read the fic.

Also worth mentioning, he's been nice enough to plop any pics he does based on chapters I've written into this separate gallery, so there will be less spoilers for readers just jumping in to the story.

NOTE: The canon of my story picks up at the start of Season 3, where it begins to diverge away from the canon of the show. I've never read the IDW comics nor have I seen Equestria Girls, so the events of my story aren't canon at all with them.

Now has it's own TVTropes page!
http://tvtropes.org/pmwiki/pmwiki.php/FanFic/BadFutureCrusaders