My name is Twilight Sparkle, and 350 years ago, Sweetie Belle and I vanished without a trace.
Now here we are, in the future.
Equestria has become a utopia, with everypony living in peace and harmony.
Everything is perfect. All a pony could ever want, and more.
My name is Twilight Sparkle, and I want to go home.

Editing provided by Stereo_Sub and JustAnotherTimeLord.

Cover art courtesy of Geomancing.

Reading by lieilengi

Spanish translation by Spaniard Kiwi

After miscasting a spell Twilight's friends begin to feel differently about her. When Luna and Trixie show up in town things really start to get crazy. It seems a new competition has begun on who can win the purple unicorn's heart. Meanwhile Twilight struggles to understand why everypony seems to be falling head over hooves for her. Well not literally everypony, but you know what I mean.

WARNING: This pretty much ignores Season 3 entirely. Well Trixie's part anyways.

Harry Potter was a lonely boy who one day wished for a friend. Luna, trapped on the moon, wished for the same. And so their wishes are granted. How will the two deal with each other? And what about Nightmare Moon? Needless to say, their lives are going to change in both expected and unexpected ways...

Other stories in the Lonelyverse:
Hooves, Plush, and Magic: The Untold Tales
The Wizard and the Lonely Princess: Hallowe'en Special
A Nightmare Christmas

Chapters 9-11 now re-written.

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

This site really needs an existential horror tag.

Some Canterlot entertainers aren't just musicians... and some ponies fall in love with them anyways.

When one of Equestria's most popular cellists appears at Twilight's birthday party, it's just another gig for Octavia, but a shock for Twilight and the rest of the party-goers. She arrives, wishes Twilight a happy birthday, wows them with her beautiful music, wows them with her musical beauty, and doesn't leave until after everypony else has left. So when a few ponies suggest that this 'entertainer' might be more than just a musician... some eyebrows are raised, but nothing more. Twilight is beyond reproach, after all, and Octavia can earn her living however she wants. When she sticks around Ponyville, however, it becomes a slightly different story - Twilight is romantically-naive, after all, and Octavia is... most certainly not.

The romance of Twilight Sparkle, Celestia's protege, and Octavia van Clef, Canterlot's most famous entertainer.

Rated 'Teen'. Per FimFiction's rating guidelines, this story contains some 'more adult themes', but has no 'graphically adult content'. Rated primarily for sexually suggestive material, but also (in later chapters) alcohol use and adult language.

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.

Rarity has risen to the highest stretches of the fashion business and high society, but she's found that not all is as it seems. In the corners of cocktail parties all over Equestria, dark conversations are found. Eventually, Rarity can take no more of this, and begins reporting back to Celestia in secret while delving deep into a world she had no idea was so intertwined with her life's goal.

How much of herself is she willing to give up to protect the throne and, more importantly, Twilight Sparkle? The life of a spy is a dangerous one indeed.

A canon story in the Rites of Ascension Expanded Universe! Artwork by Violet Squiggles. Author's Notes, including proofing credits, can be found here.

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

Canterlot... For centuries, Canterlot was the shining gem of Equestria, the pinnacle of pony society. Now, it’s a reminder, a bleak and monolithic warning to the world. 

Changed by the chemical and technological poisons that plague the mountain, an abomination of nature, I wander the greatest disaster Equestria has ever seen. 

... I will escape eventually, and when I do, I hope my friends still see me as Twilight Sparkle, and not the monster that hides among the ruins. 

Twilight reads about a way to view a pony's soul, to see everything about them laid bare. When she tries it on her friends, will she be able to look at them the same way again? Or will the secrets hidden in their hearts drive her away?

(Yes, I borrowed the idea of a "soulgaze" from The Dresden Files, because it's something that really fascinates me. It's not a crossover, just an idea.)

Now has a sequel!