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.

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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!

Twilight becomes alicorn of the stars. This is sort of a problem, because Luna kind of already was alicorn of the stars. Oops!

TV Tropes

There is a secret in Equestria. A secret the newly crowned Princess Twilight Sparkle doesn’t dare to believe. Like puppeteers pulling on marionettes, they have influenced Equestria for better and worse since the fall of Discord. So far they have been benevolent, but their potential for evil is vast. What’s worse, she doesn’t know their name. She doesn’t know their mission. All she knows for certain is one thing.

That they all seem to be zebra.

Princess Luna is slipping back into her Pre-banishment ways due to boredom, when she suddenly stumbles on an idea that will change her life forever.
I don't know where this story will take me. It is only my first fic, so if anyone would like to comment on the writing style, or indeed things you want to happen, please go ahead. Anything you guys can add to this will be appreciated.
I do reserve the right not to use bad ideas. This is not a clopfic, but I do intend for there to be drunken partying somewhere down the road. There will be ramifications.

*If you'd like to purchase a physical copy of this story, click here*

One of Equestria's greatest traits is tolerance. Every pony, whether Unicorn, Pegasus, or Earth, is accepted for who they are, and have their own parts to play in keeping Equestria running.

But what if an Earth pony decided he didn't want to play his assigned part? What if he wanted to rise above everyone else and become an Alicorn? Such a thing is possible... but the path to fulfilling one's dreams is never simple. Risks must be taken. Sacrifices must be made. And the question is always asked: How far would you go to get what you wanted? And would you be willing to pay a terrible price to get it?

It has been ten years since the defeat of the Changling Queen, and Equestria is again at peace. Twilight Sparkle and the Elements of Harmony have reached their prime, and have begun to settle down. Love and life abound in Ponyville, especially for Twilight's friends, but she has nopony to call her own.

There is a reason.

A series of events lead to a horrible revelation, and Twilight is thrust deep into a terrifying web of secrets and lies. Her peace is over.

This time, however, she won't be fighting monsters or madponies. What she faces will be much, much worse.

Act One of Two.

Act Two is here.

Currently undergoing editing by the wonderful Mstar!