Cheer up, Twilight. It's not every day somepony changes species. In fact, no pony has ever changed species. It's something new and you like discovering new things. Granted, Equestrians don't like new things, especially things that fundamentally alter their government. So maybe there is reason not to be happy after all.

Ponyville, by all means, has never been a town without incident. Somewhere within it, something was always going wrong somehow. However, for so many different things to go wrong so close together...it means things are more wrong than usual. And Twilight has more to do with it than even she realizes...

Some things are best left forgotten. The truth is not always sweet.

But, do not think things will be completely dark and grim! There will be plenty of strange things, and Pinkie Pie being Pinkie Pie! Because Equestria is not Equestria without its share of strange things.

(joint effort between a friend and I)

Twilight has spent the last two decades fighting against the dark forces which threaten the peaceful kingdom of Equestria. As a Royal Alicorn Princess, she has no choice in the matter. She is the greatest magician Equestria has ever known, but it has all come at a cost, both physically and mentally. She resents her friends for the happy, carefree lives they've been able to lead. Somepony will have to breach her walls of isolation and sorrow before she does something foolish.

The princess's fanatical student. A startlingly honest bootlegger. A prissy high-class escort. A traitor caught between two loyalties. A hyperactive pyromaniac. A quiet assassin who can kill with a word.

The night that has covered Equestria for a thousand years might just be coming to an end. And all of these familiar faces will be engulfed in the war between a victorious Nightmare Moon and her sister, returned from a millennium of exile.

Even as the sun rises, the situation has never seemed so dark.

This story was edited, preread, and otherwise improved by Einhander, Comrade Sparkle, CartsBeforeHorses, Spigo, and IR Pony.

Luna discovers something hidden from Celestia for twenty years, now, with emotions running high, she enlists the help of the Mane 6... but what seemed to be a single mystery, soon reveals a darker and much more complicated plot that will soon decide the fate of Equestria.

Check out the Empty Room TV Tropes Page (Warning: Spoilers!)

Revised chapters edits and proofing (with many thanks) by: lammy, Trevor, Nick Nack, Fifth Alicorn

As the newest Princess of Equestria, Twilight Sparkle will have to face many changes and challenges in her new life. However little does she realise that one of the major changes was set in motion a long time ago, as nopony can come out unscathed from a fight with a demigoddess. Now however, days after her coronation Twilight will have to face the consequences. And the decisions she will have to make in the nearest future may very well change Equestria forever.

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AN: Tags may be added. The cover art was made by I-am-knot

Changelings are not what they seem to be, as Twilight and Celestia find out so soon after the invasion. In fact, Twilight becomes intimately aware of said fact. The problem is, though, she doesn't know it.
Funny what an expedition into the woods, amnesia and a queen that only wants to help can do to change a girl's life.

Years have past since the changelings were driven away from Equestria, giving room for peace and love. Suddenly, Twilight is captured in the middle of the night, and is brought to the hooves of Queen Chrysalis. Seeing that she has captured the element of magic, she is determined to gain her revenge against both Twilight and anyone that has ever wronged her.

Using her dark magic, the queen transforms the unicorn into a horrifying creature. Will Twilight hold on to her sanity, and more importantly, her devotion to friends?

Or will she slip into the darkness, and lose all hope.

Props to chaos2012 for bringing me this idea. The story is mine though

Evilpresident is also onboard as a Pre-reader.

Okay, new cover art! This time it was actually made for the fic, so credit goes to BronyInvestigator
I cannot thank him enough.

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!

Some ponies just don't have any luck.

Twilight Sparkle is one of them.

Sure, other ponies might say she's the luckiest pony ever, being the personal protégé of Celestia, a well known pony in all of Equestria.

What they don't know, Twilight Sparkle isn't Twilight Sparkle.

Everything was perfect, her cover has never been blown. Until that one fateful day, the day Shining Armor, Twilight's brother, should have been married, the day of the changeling invasion.

The cleansing wave of love that send every changeling away...

There are only three ponies who know the truth, Twilight Velvet, Night Light and Twilight herself.

Edited by Jphyper, thanks for that.