This story is a sequel to Upheaval: Breaking Point

Following the events of Breaking Point, Twilight Sparkle and her friends discover that Equestria's demise may not come from an enemy invasion, but from within. The Barrier Lands and the Heartland begin the slow and uneasy process of reuniting into a single Equestria, but this long-delayed joining is already in danger at its conception.

With Celestia's power in her grasp and her agents by her side, the wheels of Black Rose's plans for Equestria's future continue to turn. However, her brazen gamble has done more than just bring down a centuries-old barrier. Ancient powers begin to stir: the remnants of a dark period in Equestria's history, the immortal inhabitants of Celestia's homeworld, and a rising tide of darkness coming ever closer.

Equestria is a land of magic and harmony, a peaceful realm ruled by immortal and benevolent monarchs. At what cost is this possible?

Following the discovery of a strange and powerful device, Twilight Sparkle is whisked away to the edges of a land she thought she knew so well. Here, surrounded by ponies whose very existences have been kept secret, she must contend with vicious enemies, hostile allies, and the truth.

Chapters 1-16 edited by KiltedKey

This story is a sequel to Upheaval: Reckoning

Equestria's fragments have reunited, and the power of sunlight shines once more within Celestia. With the remnants of the Old Kingdom destroyed, the Abyssal Throne sent away, the threat of Gravitas defeated, and Black Rose no more, Equestria now faces the encroaching darkness of Oceanus and his rebels.

But the stage is not yet fully set. Twilight Sparkle and her friends must gather what means they may before the battle is joined.

Cover art provided by Captain Nibbles

This story is a sequel to TD the Alicorn Princess

Prince Antares, formerly the human TD Powell, has ascended to rule Equestria alongside Celestia and Luna to form the Equestrian Triumvirate. Taking his residency in Baltimare, Antares comes into his role as smoothly as he can, given the circumstances.

But not all is right with the world.

A warmongering king in the newly formed minotaur nation has just allied with the griffin empire, a country that recently gained a leader unfriendly to Equestria. Now Antares will face his first true test as an alicorn prince of Equestria. He must lead his peace loving ponies into the hells of war, and face an Equestria that will never be the same.

Edited wonderfully by Strike89

Buy a print copy of the original here!

This story is a sequel to The Prince

Five years have passed since the Equestrian victory against the invading minotaur army, and peace has returned to the land. The first annual memorial celebration has arrived in Canterlot, led by Prince Antares. However, in the midst of the celebration, Equestria is invaded by an army from far away, led by the powerful unicorn Tempest Shadow in the name of The Storm King.

Now on the run, Antares must reclaim his conquered nation, no matter the cost.

Buy a print copy of the original here!
Just as a brief point of interest: I loved the movie. This is not a fix fic any more than the first TD Alicorn story was a fix fic of the Season 3 finale. This is just an interesting idea I had.

Edited by Strike89 and roker12

TD, the human first seen in No, I am NOT a Brony, GET ME OUTTA EQUESTRIA!!! has been in Equestria for a little over a year now and he's just beginning to fully adjust to his life there. However, when he wakes up one morning to discover that five of the Mane Six have switched cutie marks, he endures a significant change when he helps them out.

He is less than pleased.

Edited wonderfully by Strike89

Buy a print copy here!

It has been two years since the human TD ascended to become Princess Antares, and he is settling into his role as one of the rulers of Equestria quite nicely. His loyal guard is strong, his palace is awe-inspiring, and he is beloved and worshiped by ponies everywhere. However, when the Element of Magic is stolen by an old student of Celestia's and taken through a magic mirror while he is visiting the Crystal Empire with the Mane Six, he discovers that another world has been very close by during his whole reign. A rather familiar world at that. Deciding that he is the best pony for the job, he takes his two best soldiers through the portal with him to get the Element back. So, pretending to be a foreign exchange student from Canada, he infiltrates of all things... a high school.

He is less than pleased.

Buy a print copy of the original here!

Edited by the magnificent Strike89

Cover art by the perpetually awesome SoaringSketches

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.

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.