Five hundred years after the Discord's first defeat, a lone unicorn scientist makes an interesting discovery. Across Canterlot, over the last few centuries, accident rates have increased in the area around the Royal Palace. His work is ridiculed by his peers, but comes to the attention of the Princesses, who know exactly what is happening: Discord is waking up. With Luna and Celestia, he concocts a plan to stop the Lord of Chaos forever.

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Cover art butchered from UnderwoodART's render of the stained glass in S02E01.
This story is based on S1/S2 (Discord was never released and reformed) and sits within my Soot-Covered World canon, but is stand-alone. No knowledge of the other books is required.

All thanks to ascendant, NoeCarrier, turol, KMCA, Caliaponia and billymorph for their prereading and editing over the life of this story.

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.

First contact. Not just with a new world, but with a world in a whole new universe. Initial negotiations go well, so Princess Celestia makes a visit to this 'Earth' to cement peaceful relations. Unfortunately, even when you are as experienced as the goddess of the sun, it's the little things that can trip you up.

Preread and edited by Noe Carrier. SPOILERS IN COMMENTS!
Russian translation: Все это скоро закончится, принцесса by Smikey

The things we create should stay in our heads.
Sometimes they don't.

The Cutie Mark Crusaders try to follow the example of self-styled survival expert 'Bobcat Griddles' in a new quest to earn their cutie marks. What could possibly go wrong?

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.