After the defeat of Tirek, Equestria is safe once more, but Luna can sense that her sister is troubled. When Celestia retreats to the starry realm of ascension in order to look upon the past, Luna joins her to discover what is bothering her.

There is now a Spanish translation of this story, courtesy of Spaniard Kiwi

PRINCESS TWILIGHT SPARKLE: DEAD AT 18

TELEPORTATION INVARIABLY FATAL, WARNS LEADING SCHOLAR

One look at the headline of the Canterlot Times and Twilight knew that she should have slept in today. But at least none of her friends would be silly enough to believe she was killing herself every time she teleported, right?

There is now a Spanish translation of this story, courtesy of Spaniard Kiwi

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.

Twilight Sparkle has always loved Celestia—as a friend, and a mentor, and something else as well. And she finally, finally found the courage to admit those feelings.

Celestia turned her down as gently as she could. That's what she thought, anyway.

But the night is still young—and it's a night for being wrong.

[Rated T for suggestive sexual content. This story takes place between the Season 2 and 3 finales. Additionally, I wasn't able to find the artist who did the cover art, if anyone knows please drop me a line so I can credit them.]