[Complete! With TVTropes apparently!]
Also, apparently, an animated trailer.

In a world of brass and steam, Twilight Sparkle had thought she had made a life-changing discovery with the invention of the telescope. For better or worse, she was correct.

Now her discovery has not only changed her life, but the lives of those she seeks out in her desperate attempt to contact the only other creature as lonely as Twilight herself.

It all would have been much simpler, but it had to be the one Twilight could only call The Mare on the Moon.

Decidedly not within walking distance, then.

[Featured on EQD before story was meant to be submitted. 4/03/2015]

[Editing team: Southpaw, Wolfvenom, Maskedferret, SwanSong and BluePaladin42, without whom this story would be a fraction of its current state.]
[Special thanks to Novel-Idea for the updated cover]

After the Changeling invasion, Celestia and Luna make the decision to have Twilight investigate the Elements of Harmony and solve the mystery of their power.

A thousand years later, Rainbow Dash awakens in a world she does not recognize. She has no idea how or why she came to be there. She does not know the language, the geography or any of the rules of this new time. She soon finds allies in Star Fall, a scholarly pegasus whose Talent is Magic, and Astrid, Star Fall's Griffin guardian. Together they set out to discover why Dash has been sent to the future, and how she might return to when she belongs.

War threatens the nations, a Nightmare stalks the shadows, and Rainbow Dash's arrival has turned her into a wild card in a deadly game that pits the law on both sides of a broken Equestria against a mysterious criminal figure, Max Cash. Yet the stakes are higher than anyone knows, for in her research Twilight Sparkle discovered a dark secret about the Elements, something that will shake the foundations of the world.

Cover image by SierraEx
Has a TvTropes page

A diplomatic crisis arises between Equestria and the small, poor kingdom of Tarandroland, ancestral home of the reindeer. Celestia and Luna agree that it is time Luna takes a more active hand in foreign relations again, and Luna brings Twilight with her as someone she actually trusts and can talk to. But the mission turns out to be much more than political discussions - if scheming unicorn courtiers, unfriendly surly reindeer, bloodthirsty pirates, ancient sorcery and dangerous monsters weren't enough, our heroines must deal with something old - older than Luna. And is Luna really ready for diplomatic action, will Twilight learn to use a fan properly, and exactly how wrong are Spike's superhero comics about reindeer mythology?

Now has a TV tropes page

Twilight Sparkle has too much magic, and it will take her decades to learn to control it. Her spectacular loss of control during her entrance exam only proves that fact. She is a danger to herself and others.

After Sunset Shimmer’s disappearance, Princess Celestia needs a new student to bear The Element of Magic to defeat Nightmare Moon. With all of Equestria at stake, Twilight Sparkle…is not the pony she needs.

Princess Celestia seals Twilight Sparkle’s magic with the distant promise of one day teaching her.

But there are two diarchs of Equestria. Amidst a lucid dream, an offer is made.

“Hello, Twilight. Would you like to be my student?”

Cover art provided by Lafiir.

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

When Celestia went on sabbatical into the west, she promised Twilight it would be only a couple of months. A year and a half later, the sun resists control, the country is in ruins, and her teacher is lost in the wilds. Twilight has become the apostate, her faith in her teacher and her teachings waning. In the wake of tragedy, her resentment blossoms into fury and she vows that something must be done. Shadows gather around Canterlot, and old things that should not have been awakened are on the move. The Student goes west, her hope restored by friendship and righteous fury.

The night, at long last, is passing.

April, YOH 1505 (almost 5 years after Luna's Return): Twilight Sparkle and her Companions defeated Starlight Glimmer at Our Town, and return to Ponyville. But though they are victorious, they bear battle-scars on their souls -- and they know that the mad mage is still out there, doubtless lusting for revenge. Sometimes, mere victory is not enough.

Takes place between S501-02 The Cutie Map and S5E03 "Castle, Sweet Castle."

North of Canterlot, in the far marches of Equestria near the border with the Griffon tribes, there is a mountain that flies.

West of Canterlot, beyond the Galloping Mountains and a desert painted in the pastel hues of a faded rainbow, a tower sits at the edge of the world.

South of Canterlot, past the Everfree forest and the desolate badlands, a city of gardens waits to be born.

The Lost Cities Challenge! Awesome authors who have taken it upon themselves to explore other abandoned places:

- The Land of Glass and Stone, by RazgrizS57
- The City that Breathes, by Pearple Prose
- Aletheia, by Foehn
- Far Kobresia, by Baal Bunny
- Keskiyönnon, by Bradel
- Unknown Architecture, by Not_A_Hat
- The Gentle People, by Bad Horse
- The Seal of Wax and Glass, by DuncanR

Dramatic Reading by Illya Leonov: Chapter 1, Chapter 2, Chapter 3, Chapter 4.

Royal Canterlot Library interview for Lost Cities.

Twilight Sparkle, Celestia and Luna are transported into a strange alternate Equestria, the Land of Always Summer, where the day lasts forever and a terrible queen rules with an iron hoof.

Feel free to check out or add to the story's TV Tropes page.

Celestia sends Twilight her last, greatest assignment. The lost masterpiece of Star Swirl the Bearded!

The spell that the greatest mage of all time couldn't figure out.

The spell given to her by the mare who thought releasing Discord was a good idea.

The spell that, upon closer inspection, seems about as stable as Rarity's emotional state and as safe as Rainbow Dash's usual workout.

... Maybe Twilight should double check with the princess first.

Winner of the Rage Reviews F*CK THIS PROMPT 6 contest. Prompt: "Equestria is getting a new Alicorn Princess."