When Sweetie Belle got zapped during the Zap Apple Harvest, no one thought much of the filly's light electrocution. However, the zapping has given her a most unusual ability... the ability to change the color of objects, temporarily, into the colors of the rainbow. This is surprising to the little filly, as she has yet to achieve mastery of most magical arts beyond a novice.

Naturally, her adventurous streak gives her an idea. Sweetie Belle will become a superhero. She is the vibrant guardian, the watcher of the palette. She is...

Zapfilly.

Twilight copes.

Season 5 Finale-related.
So many realities. So many horrible futures. But in yet another alternate timeline, Twilight finds herself in the Golden Oak Library with the Princess of Friendship: Sunset Shimmer. Rather than the awful futures she's seen before, she now finds herself in a timeline that actually seems nice. But that means she has a tough decision to make...

-Awesome cover art used with permission from the amazingly talented Huussii (Teemu Husso).
-Based on an idea from Silver Quill.
-Featured as of 12/8/15! Thank you to all the readers!
-Editors: GenerousGhibli and E3gner

SF (canon species only; no humans) Ponies were magically and genetically engineered to be the perfect servitor race. They are powerful, adaptable, intelligent and completely under the control of their creators. A laboratory accident frees one such pony from her mental chains, but how can one mare save herself and the rest of her kind if she doesn't even know she's a slave?
This is not the Equestria you know and these are not your little ponies... not yet, anyway.

Tags: Adventure, Diamond Dogs, Gryphons, NO HUMANS (did I mention that already?)
Other tags: historical, mind control, Clarke's 3rd Law, excessive use of high energy physics, before they were famous.
Detailed review by PaulAsaran.
Cover art by endrome , used with permission.
Russian translation (partial -- 'unofficially' completed in the comments)
A Soot-Covered World, book 1.

This story is a sequel to Days of Wasp and Spider

Believed dead by their creators, the ponies that will become Celestia and Luna have broken their mental conditioning and escaped into the wilderness. Here they plan the revolution that will free all ponykind, knowing that it is only a matter of time before their ruse is discovered.

Back in their underground arcologies, the ponies' erstwhile masters deal with the consequences of the escape, all the while unaware that something lurking at the bottom of space-time wants them all dead.

A Soot-Covered World, book 2.
Canon species only/no humans.
This story has nothing to do with the Holocaust.
Art by InLucidReverie, used with permission.

I think that I shall never see
A home as lovely as my tree.
In its trunk I made my nest
With all things that I love best.
Books to read all night and day,
Rooms to learn and space to play;
But no more growing, no more fun;
No more soaking up the sun;
Nevermore to drink sweet rain;
Or to greet the Spring again.
There is no power or decree;
No magic spell to save my tree.

Cover art by The-Paper-Pony. Used with permission.

This story is a sequel to A Stitch in Time

Having discovered the message left for her by Star Swirl the Bearded in the distant past, Twilight once again finds herself caught up in the middle of a struggle against forces far greater than herself. In order to even stand a chance she'll need to travel further and wider than she ever has, and forge some unlikely alliances with old enemies. All to bring down the powers that have manipulated and shaped her entire life, and retake control of her own future.

The conclusion of the Time Loop Trilogy, which began with Hard Reset
Available in Spanish thanks to dgs1993
Series TV Tropes page

To Twilight Sparkle and Princess Celestia, it is a simple surprise visit to Canterlot. To the ponies of the Equestrian Civil Service, it is twenty-four hours of chaos, politics, weaponized dessert, politics, underhooved manipulation of media, politics, and things batrachian and tentacular. Who said bureaucracy isn't exciting?

The star system Omega Centauri was just another oddity on a map to scientists in the not too distant future. However when they found the star was orbiting an earth-sized, earth-like planet instead of a black hole as its motion had suggested, a mission was scrambled to investigate this most unusual of celestial behaviors.

Hamstrung by politics, and nearly crippled before it began, the 'Lone Ranger' mission was reduced to just one crew member and left to his own devices.

These are the logs of Arrow 18 and its lone commander. This information is classified TOP SECRET by the Global Space Agency.

Do NOT tell the princess.

This story is a sequel to It's a Dangerous Business, Going Out Your Door

EDIT: 6,000 unique views! Thank you so much to everyone who has read and enjoyed this story.

TVTropes Page

An ancient evil has awakened. No, really, it has. From the depths of time, a black, noxious threat has risen up after millennia of imprisonment. It washes like oil over Equestria, swallowing up towns and uncovering terrible secrets long buried. Twilight Sparkle, Applejack, Rainbow Dash, Pinkie Pie, Fluttershy and Rarity are prepared to combat this great darkness. However, to do so, they must uncover the truths about the Elements of Harmony, and the truths about the ancient forerunners of Equestrian culture. What they find will challenge their conceptions of their own places in history and ponydom's place in the world. The six Bearers of the Elements must draw upon their friendship and the strength of their hearts to stand firm against the darkness. If they fail, it will mean the end of everything.