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!

This story is a sequel to Twilight Sparkle And the Very Confusing Day

There were a few loose ends after Discord, who had turned into Eris, had gone into season and turned the entire world upside down in order to create enough chaos for favourable draconequus breeding conditions. Celestia had released the Flutterbeast upon Eris, restoring order and gender normality all over the globe.

Except not everypony and everybody changed back. Males who became mares and became pregnant, stayed mares, Eris' final parting gift of confusion and chaos in the world.

Both of the sexes are now so much more aware of each other's needs following the events of the Great Swap, and Eris' chaos had the unintentional side effect of creating a new level of harmony in the world, as suddenly everypony and everybody now had first hoof (or firsthand) experience in being the opposite sex.

Eris going into season also created the ideal conditions for the apocalypse.

Edit: Featured on Sunday, April 20th, 2014! Oh my gosh oh my gosh oh my gosh!

Now with 23% more sequel!

Twilight and her friends all get together for a sleepover, looking forward to some well deserved downtime. Discord arrives, standing outside in the rain, pleading for entrance and to come in out of the weather. Twilight Sparkle insists that this is a mares only sleepover, so Discord does the only thing he can do, doing the unthinkable to gain entry.

Once inside, Discord, now Eris, tries to bond with the mane six and learn the magic of friendship.

The mane six fail to take into account the magic of Discord.

Now featured on April 16th, 2014. Thank you all so very much!

New cover image commissioned from rainbowfaux

While spending the day at a fair in Ponyville, Soarin' is injured and stays at the farm for a while. He develops feelings for AJ, but can't act on them. When unexpected circumstances turn AJ's world upside down, will Soarin' stay to help her through? Will he ever be able to tell her he loves her?
Please comment and critique.
My little pony is property of Hasbro.

A famous unicorn artist, now in midlife, shocks her doctor by revealing that the father of her unborn youngster is a teenager. But that's only the beginning: Can there truly be such a thing as trans-species pregnancy?

Anonymous, a twenty-two years old musician, is somehow transported to Equestria. He must learn to adapt to this new world. Communication with the ponies will be hard, he doesn't speak the same language as they do.

The story will be centered around Anonymous' interactions with the Mane 6 and a few of the background ponies, notably Lyra and BonBon.

The royal court of Canterlot welcomes its newest member with open forelegs: the human philosopher Voltaire, from Earth.

On Earth, Voltaire is known as the greatest enemy of tyranny in the history of literature, and a legend in his own mind.

On Equestria, the court betting pool is giving him a week before the Princess banishes him to the Moon.

Note: This story doesn't have sequels per se, but there are a couple of short follow-ups set in the present day ("Parade Coverage" and "Secret Histories"), and a prequel of sorts in "At the Inn of the Prancing Pony".

TV Tropes page.

You know what they say once you hit rock bottom...

Apple Bloom and Rumble are bored out of their minds. Their friends are away and most of the other foals in Ponyville are too busy to play with them regularly. All they have is each other for one week. On the second day, they decide to go and explore a cave in the mountains near the little hamlet. They will not return the same.

“But there is something you should know, Queen of the Changelings. You haven’t hurt me or my people half as much as you’ve hurt your own.”

"So the question you must ask yourself now," The princess concluded, "Is what you intend to do about it?"

Cover made by the very awesome Conicer. Go thank him!