Twilight Sparkle comes across a small, battered diary detailing a new form of transportation. While the research is sloppy and the notes incomplete, Twilight takes it upon herself to see that the ancient project is completed.

Of course, nopony said it would be easy.

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

It's nearing the summer sun celebration, one year after Twilight arrived, and things are not going according to plan.
Preperation is behind schedule, supplies are still needed,
And to top it off, Twilight has accidently turned her friend's pets into ponies!
Without an easy antidote and time growing short, the mane six decide to let the pets help them in the celebration.
And they'll need all the help they can get.

This story is a sequel to The Skyla Pseudonym

A miscellany of stories from Twilight's accidental kingdom in the Undiscovered West, and possibly elsewhere if the fancy takes me. Not necessarily connected to each other or in chronological order. Marked as complete, but there's a slight chance I may add chapters.

Audio version by VisualPony, HERE!

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

This story is a sequel to The Twilight Enigma

With the queen of Twilight Town present, the Storm King's invasion of Canterlot goes badly for his commander and minions. Not satisfied with a mere victory, Captain Blackmane and her friends go on the hunt. Twilight is determined to find the Storm King and make sure he will never be able to harm anyone ever again. It's obviously a mission of reasonable prevention, not murderous revenge. Obviously... Right?

Book 4 of the Alicorn Adventure series.
Sequel to The Twilight Enigma and prequel to The Skyla Pseudonym.

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.

People will do anything to distract themselves from their problems. In an age where the situation could be both a hundred times worse and a thousand times better, there are still stories floating around. You know the type: a young human gets snatched from his/her homeworld and dropped in a land far from home, and they have to either shape up or ship out before it's too late.

Replace "human" with "Reploid", and you have a good idea what's happened to me. This land of Equestria is as completely alien to me as I am to its residents. If I can't return home then I'll have to figure out how to adapt to its environs, but my time and options are running out quickly. I'm not ashamed to admit that I'm getting desperate.

I am Fairy Leviathan, one of Neo Arcadia's Four Guardians, and I will gladly accept your help if you have any to offer.

There is a Frequently Asked Questions blog on this story. Please read it first before getting into the story. Thank you.

The cover image is Leviathan's official art from Rockman X DiVE. I haven't been able to find a reasonable alternative and circumstances aren't allowing me to commission something, so I'm just going to leave it as is.

Don't know about the 'Human' tag for this one, as it's kind of iffy. Personally I think it's alright, as Reploids are close enough to 'human' for it not to matter, but your mileage may vary.

Has a TV Tropes page here.