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 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!

==Originally written Fall 2011== Equestria Daily Post==
After a long day of ruling Equestria, the Royal Sisters need a chance to unwind. Luna's solution is a few glasses of her once famous Moonshine, a drink distilled from moonlight. Celestia has been sober for a thousand years, but the temptation to have "just one" glass proves too great. Yet, when that one glass turns into several, it's Twilight who will have to deal with the princesses when they’re drunk off their flanks.

This story is a sequel to Drop of Moonshine

Sequel to Drop of Moonshine -

Applejack receives an order from Princess Celestia, for a batch of cider prepared with a very special recipe that involves honey, yeast, and time. She's even invited to taste the special cider when it's ready. But, when Rainbow Dash finds out about the special tasting, the three mares soon have a little too much to drink. What shenanigans will unfold and how will Twilight keep a lid on things this time?

Rainbow Dash told Scootaloo that it doesn't matter if she can fly or not. Then Discord made her put her wings where her mouth is and now she has to live without them for a day. But wings or no, she's still Rainbow Dash, the most awesome pony in Equestria, right?

...Right?

Now has an audio version as well

“Dear Princess, this will be the last day you rule Equestria. But your enlightened leadership entitles you to some explanation…”

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Audiobook at Scribbler Productions.

As the details surrounding the Canterlot Invasion don't add up, Twilight investigates the suspicious disappearance of a guard during the attack.

This story is a sequel to New Life in Equestria

It has now been a month since Joshua's rescue from King Sombra, and now it's Hearts and Hooves Day, and Joshua plans on taking Dinky out for a special night together.

This story is going to go through the process of a rewrite to keep canon with Season 4.

A young human boy of age seven is sent to Equestria by his loving parents in an attempt to save him from the end of the world. He is found by the Royal Pony Sisters and they bring him to Equestria to fulfill his parents' wish.

This takes place after Season 3 and is set in the Past Sins universe.

Edit: Changed a few of character tags.

Cover Art by PonnyGirl

After Twilight became an Alicorn, Twilight, Nyx and the gang gets taken to a new land by an unknown enemy, and Twilight became the ruler of it with the long forgotten Prince of Equestria.

This story use Nyx is from Past Sins by Pen Stroke-"This story is an unofficial sequel/side-story to Past Sins by Pen Stroke"