Nopony expected the attack on the Crystal Empire. Nopony expected monsters to come pouring in from the frozen wastes, invading the city, killing and destroying indiscriminately. With the Pillars of Equestria scattered to the corners of the world, it seemed only the Elements of Harmony and the Princesses could fight this new threat. The Crystal Empire was evacuated, leaving only those who were fit to fight.

After months of fighting, only five of the Elements came home.

The Princesses had fallen in battle, one by one, until Twilight was all that was left. Knowing that there was no way for them to defeat the scourge that had invaded the Crystal Empire, she had one last plan. Her friends didn’t know they were taking her on a suicide mission when she began channeling the raw power of the Crystal Heart. She teleported her friends out of the city, and unleashed a massive spell on the Empire, destroying everything inside, and undoing the magic that kept the Empire from being buried in snow. The fought had been won, for a certain definition of winning.

In the following months, however, Anarchy rose. The closest living heir to the throne was Princess Flurry Heart, and she was too young to be a princess. Nobility bickered about the idea of a regency who would reign while Flurry Heart grew, with many supporting the idea, and yet others against it, opting instead to give the throne to Prince Blueblood. Yet others saw their opportunity and demanded the throne for themselves, opting things such as military experience and wealth as the reason they should be given the throne, and yet others declared that a new government should be formed entirely.

Half a year after the fall of the princesses, Equestria found itself with Flurry Heart as the new Princess, and a regency overseeing Equestria. Small towns chafe under high taxes, guards begin arresting ponies more frequently, and punishments for crimes become more severe as statues are erected in the Regent’s honor, with Flurry Heart being little more than a footnote of his glory. In another half a year, Equestria is embroiled in a civil war – one side supporting the Regency, the other wishing to depose him and give Blueblood the throne.

Meanwhile, in the heart of the Crystal Empire, sompony was sending a call.

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Years pass. Equestria has fractured into many splinter groups, each fighting to gain control of Equesria. None of them expected a new challenger to approach from the frozen wastes.

It started with Windigos flying over settlements and causing small, localized storms. Then, from the wind came skeleton ponies, who would march into the streets of the town. A single stallion, coat grey and decaying, eyes glowing green, moving with strange, forced motions, would march to the mayors, and speak in a familiar voice.

“This Town is now under the protection of Wraith Tower. You have twenty four hours to swear your loyalty to the Sorceress Queen.”

The pony before them was not speaking - it was clearly dead. No, the Queen spoke through it. Covered in a cloak that hid most of her being, standing outside of the town on a hillside with an army of monsters behind her, Twilight Sparkle watched the town, now covered in snow and ice.

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Wraith Tower is what remains of the Crystal Empire, converted into a research facility. While much of the Crystal Empire is destroyed and/or buried in snow, Twilight managed to create a number of magical wards that protected what remained of the Empire from the snowstorms. For years Twilight remained in isolation from the rest of the world. During the years, she would recruit old friends Starlight Glimmer and Sunburst, as well as others, to hide away in Wraith Tower, doing research.

At first, Twilight wanted nothing to do with Equestria. Embittered by the growing war, and the fact nopony ever came to search for her, she grew to loathe her former home. Eventually however, she began to have a change of heart, and realized that Equestria itself was crumbling. And so, having learned that an army of monsters was much more powerful than an army of ponies, she began to create an army. Twilight aims to claim the throne, but she knows the Regent and Blueblood will not give up without a fight, and she intends to give them one.

Wraith Tower is a faction manned by scholars, sorcerers, and scientists, while the bulk of their forces are constructs, undead, and savage monsters. Their ponies tend to act as leaders of the armies, though they like to avoid sending a living pony to a fight if they can.

Twilight the Spellbinder:
Nopony is sure how Twilight survived the destruction of the Crystal Heart, but what is known is that in her isolation, she has grown dark and somewhat cynical. Having grown pragmatic, Twilight has turned to using darker magic to achieve her goals, animating the dead and draining the life force of her enemies. Her motives beyond that are hard to pin, and many worry she has become an enemy of Equestria not unlike Nightmare Moon once was.

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This is an idea inspired by many things, such as Equestria Divided, Shadow of War, Game of Thrones, and Fallout: New Vegas. I wanted Twilight’s particular faction to feel like the sort of faction that would employ intelligence primarily, so rather than having an army of ponies, they use their smarts to create an army of monsters (though some of said monsters were ponies at one point or another I am sure).