Twilight's relentless study of Pinkie's strange abilities leads to a horrifying revelation.

This site really needs an existential horror tag.

Eighty years after the events of The Dread Chitin, Equestria is a radically different place. The arcane science of the late Duran Thirk and the information found on the Star League library core have combined to catapult the nation's science ahead by hundreds of years.

Now, facing the possible aggression of a completely unknown alien power, Twilight Sparkle and her friends have to gather together once more, leading a crew of the best ponies they could assemble in a voyage outside their own star system. They seek to learn about their potential foe, to explore the galaxy around them, and possibly find allies and friends to stand alongside them. Who knows what they will actually find?

Stranded on a hostile, alien world, Twilight Sparkle and Rainbow Dash must depend on one another and a fellow alien castaway if they want to return home to Equestria.(originally published on FFN)

When facing Twilight Sparkle, Nightmare Moon was given a choice: redemption or revenge. What if she had chosen the latter? A grim fate awaits Equestria, but in a time of greater strife and conflict, Discord's return is accelerated. While he expected to bring chaos, he did not anticipate that he would end the Longest Night and bring hope and joy back to the land.

Discord struggles to reconcile his nature with his desire for admiration. While Twilight's friends strive to carve a new life in the ever-shifting Equestria, she searches for Celestia, the only one who can bring harmony back to her lands. But Nightmare Moon also seeks her sister in a desperate attempt to find her place in the world. New dangers lurk in the wild and more threaten to fall over Equestria. Nightmare Moon's decision broke the balance of the world. Will Equestria ever turn to peace, or will the spiral of chaos and destruction be the end of everything?

(An alternate history, this story takes the universe established by the canon and explores one possible outcome if Princess Luna had not been redeemed.)

Comments contain huge spoilers. Walk softly.

Special thanks to my pre-readers, MmmandarinOrange and DarkmatterButterflies for keeping my head on, taking the journey of the story, and making it so much better than it would have been if I wrote it alone.

Luna likes to conduct her own research.

In fact, she has only ever had to ask one question for it.

Early one morning, Twilight Sparkle gets up to make some tea.

Sometimes, a cup of tea is just a cup of tea. This is not one of those times.

One beautiful morning, Twilight Sparkle decides she wants a free salad. After a small amount of theft, assault, battery, and arson, she sits down to enjoy what is sure to be the best tasting salad ever.

...Or she would have, if it weren’t for the Equestrian Intelligence Service locking her up as a potential threat to national security. Now, Twilight must escape a maximum security holding facility hidden deep underneath Canterlot. And to do it, she’ll need a paperclip, a spymare catsuit, an escape plan, and an alliance with the dastardly Drakbog, King of Frogs.

Over the course of several years, Rarity has achieved a fabulous career, contributing to both Equestrian fashion and the Ponyville community. She is admired by her clients, envied by her peers, and cherished by her dear friends, proving that she's a dependable shoulder to lean on.

Then one day, a mysterious pony visits from out of town. She wishes to meet Rarity, but not to thank her.

The Shaper is a smith of unparalleled skill, her creations the most sought after in the fallen world. When a pony named Lyra comes to her with a unique commission she has to put all her skill to the test to craft a weapon of great power. For Lyra's goal is not an easy one, and it is not just any weapon that can kill a Dragon.

A story inspired by this and this image, as well as this challenge by CDRW (whose fic A Still More Glorious Dawn Awaits is quite good).

"It has been the pivotal teaching of the great Fountainhead, personal mentor and Celestia's most esteemed archivist, that the grand unified theory of magic, if discovered, is to be found within the mage's affectivity –that is; of the polarizing impetus of love, for unicorn magic, and hate, for Black Magic. It is claimed, further, that reality itself, too, is subject to this principle; and to deny so was self-contradictory. The dogma, however was not uncontested. Unicorns, Mages and Archmages from all over Equestria of all emotional preconditions would challenge and confute the thesis with ease. It was here that the great Fountainhead replied that the grand unified principle was too profound to be felt and too minute to be perceivable. He posits that, though invisible, this maxim holds together the fabric of the universe: matter with magic; existence with consciousness; dreams with reality; and–most significant of all–ourselves with one another."

-Starswirl the Bearded, "Hermeneutical Phenomenology of Pre-Classical Metaphysics", Royal Canterlot Archives (323 L.B.), p. iii-iv

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EDIT 04/16/13: Remastered version coming soon! Grammatically sound, split into several chapters and improvised.