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.

This story is a sequel to Past Sins

Side-story to Past Sins - Spike almost lost Twilight to a hangmare's noose, but now Twilight is safe and Nyx is a filly again. Normal life is returning. Still, Spike can't ignore the fact that Nyx just isn't the same as he remembers her. Her temper is more volatile, and, when she gets angry, all he can see is the rage-driven Nightmare Moon of legend.

And thus Spike has to wonder: Is Nyx truly reformed, or is she one bad tantrum away from calling herself Nightmare Moon again?

This story is a sequel to Past Sins

Side-story to Past Sins - Slowly, the wounds inflicted by Nightmare Moon's reign heal. Ponyville is being reconstructed, and the last refugees are leaving the castle. Nyx is with Twilight. Celestia and Luna rule Equestria and guide the sun and moon once more. Everything is as it should be.

But some things are never washed away. These are the things that remain to remind us of the past. They remind us of the good times we've had with friends and family. They never let us forget the mistakes we've made. Everyone has them. Twilight has them. Nyx has them.

And, on occasion, when you share your scars, your photos, and your trinkets with another, they just might share theirs in return.

This story is a sequel to Past Sins

Hearth's Warming is a time for friends and family to come together, celebrate harmony, and welcome the new year. Nyx is looking forward to just this as she rides the train to Canterlot with Spike and Twilight. She's going to meet her extended family for the first time and wants nothing more than to make a good impression. Yet, the sheen of the holidays can't hide the trouble caused by meddling grandparents, relentless reporters, and a paranoid uncle.