After a mysterious and widespread spell causes ponykind to vanish, Fluttershy is left behind to cope with what the future has in store for her and the remains of Equestria.

In a matter of days, the once-prosperous nation begins to descend into a harsh and unforgiving place. While cities crumble around her, Fluttershy finds herself living in a land rife with dangers and heartbreaking reminders. With nopony to turn to, Fluttershy is forced to learn to fend for herself, discover what happened, and, if possible, find a way to reverse it.

Survivor Shy is an illustrated story following Fluttershy in the weeks after a magical cataclysm. While the last pony relives her past, readers are offered a vivid glimpse into Fluttershy's mind and are led on a harrowing journey through the ruins of Equestria and beyond.

Story branches out before Season 3 Finale.

In-progress Reading by Finish Line available
In-progress Russian translation by Papilion_star available.

Reader, in ancient days, the old lords of the world numbered in thousands. Then hundreds. Then even less.
Now, they are found only in tapestries and fanciful ballads.
The creatures are all vanished. All but one.

Rumors say there are more of him, somewhere far away. A young and supposedly gifted mage called Star Swirl, and Heartstrings, a gentle spinster, have joined him on a journey to find the rest.

Featured in The Royal Guard's Fic Spotlight #5
TV Tropes page (that could use more love)

Darrilon has proudly served Princess Celestia for many years, and risen to the rank of Captain of the elite squad known as the Solarian Patrol. But every day is a new challenge when your superior officer (and divine ruler) has no respect for protocol or procedure.

To save her sister and her faithful student, Celestia herself must travel into the ancient tunnels beneath the ruined castle in the Everfree Forest. She, and the guards who accompany her, must face the dark, twisting corridors. Still, what was Luna and Twilight's purpose at the old castle? Why were they unable to return of their own accord?

And what watches Celestia from beyond the light's edge?

Bon Bon's voice is funny, and that's about all that anypony who meets her notices, as her marefriend Lyra soon steals the spotlight with her explosive personality, strange obsessions, and curious beliefs. And why not? Bon Bon is, after all, a perfectly ordinary, boring pony in every way but two: her voice, and the carefully kept secret that she isn't really a pony.

(Edit:) Now with an annotated version, courtesy of the incomparable Shoggoth Lord!

One by one, Twilight and her friends must come to terms with the consequences of being the Elements of Harmony.

These stories take place in the intervening time between Season One and Season Two,
with the exception of Ditzy Doo: Muffins, which takes place early in Season One.

The series continues in the sequel, Secrets and Lies.

Pony Psychology has a TV Tropes Page.

When Twilight receives one of the original journals of Starswirl the Bearded from Princess Luna, she can't wait to try the spells inside it, but the book's magic turns out to be a bit more than Twilight can handle, as her reckless experimentation leads to her accidentally bringing her reflection to life. At first, Twilight decides she quite likes the idea of having a copy around the library. But seeing herself from an outside perspective makes Twilight realize there are some parts of her personality she doesn't care for, forcing her to confront her issues.

Written in the same format as the show, save that it is longer and addresses somewhat sadder themes. No objectionable content or OC characters, focuses heavily on the mane cast.

Special thanks goes out to Pascoite and PavFeira, the two editors who somehow managed to withstand my childish scribbling long enough to make them readable. Couldn't have done it without you!

Poor Spike, all he wanted to do is spend time near the pony he adores. Now, because of one little lie, he's in real trouble. A geography bee, a macabre doppelgänger, and an icebox all play their part as Spike and Rarity once again find themselves on pins and needles...

A letter from Celestia interrupts one of Pinkie's parties with disturbing news. Now friendships will be pushed to the limit as Twilight struggles to uncover which of her friends is not who, or even what, she appears to be.

(While not a romance, this does contain a shipped pair)

in Russian

A heated confrontation with Celestia over her portrayal as Nightmare Moon and her sister's authoritarianism leads Luna to search for answers about the past, unwittingly tangling Twilight and her friends into a cosmic struggle between order and liberty. The tragedy of the past bleeds into the present as the Royal Guard, led by the (in)famous Captain Braveheart, pursues the moon goddess as if the fate of the world depended on it. A tale dedicated to the history and government of Equestria, the psychology and political/moral philosophy of the characters, and especially that amorphous and mysterious force that so many seek yet so few gain: power. What is its nature, what drives us to pursue it and keep it? What does it mean to be a leader, a princess, or a goddess at that matter? These are but a few of the questions the characters must struggle with in order to restore harmony to Equestria. This story tries to bring an edge of realism to the political organization and history of Equestria. If you're seeking utopia or dystopia or extremes of any sort, it's not here. .