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 Cadenza Prophecies

Princess Flurry Heart inherited her mother's beauty and grace as well as her father's strength and bravery. The Empire couldn't hope for a better or more suitable heir to the Crystal Throne. Everypony in Equestria admires her and thinks she will be an ideal ruler.

They're wrong.

Young Flurry Heart has no interest at all in being a prim and proper princess, and would much rather have wild and dangerous adventures like her Aunt Twilight.

Book 5 of the Alicorn Adventure series.

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

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.