A Knock at the Door
by InfinityXanadu
The year was 1126. One thousand, one hundred and twenty-six years after Princess Luna's original banishment. Twilight Sparkle, the first Enhanced--ponies who submitted to extensive genetic and biomechanical modification--was still alive, mostly due to her implants, which took over the functions of her heart, lungs, and almost every other body function. Save one: her brain.
The Enhanced had been scorned, at first, viewed as monstrosities and abominations. Even Princess Celestia, perhaps Twilight's closest confidant--besides her friends, of course--had viewed Twilight as... a mistake. Twilight could still remember that day, when she confessed to performing the Enhancement upon herself: magically mixing the necessary reagents, crafting the surgical equipment to irreversibly... change... herself.
First, as expected, had come the gasps of shock. Celestia and the others had certainly known about the Enhancement process--Twilight had developed it in seventeen grueling months, after coming across an ancient text written by none other than Starswirl the Bearded--but they'd never expected that Twilight would test it on herself. It had been instantly condemned as unnatural and antithetical to the Princesses' morals--deemed "black magic," the worst of unicorn-exclusive offences. For Twilight Sparkle, the Princess' sole protégé, to commit such a dreadful crime was not only unthinkable--it was impossible.
But the impossible had come true, and Celestia had summarily--with tears in her eyes, but summarily nevertheless--been forced to strip Twilight of her powers, banish her forever, and scratch the name "Twilight Sparkle" from the annals of history in the hope that no other pony would attempt to alter themselves in such a manner.
For all the Princess' efforts, however, others inevitably learned of the process. Soon, there was an exodus--a small exodus, but to lose even one pony brought great sadness to Celestia--to the Wastelands, to the banished-lands where the now-infamous Twilight Sparkle now lived.
Then, something far worse happened. Strange rumors began trickling from border towns near the Wastelands: Villagers had found dragon skeletons skewed in such a manner that could only suggest the most thorough, methodical evisceration; pets and predators alike had been vanishing; and there was that one heart-stopping report from Appaloosa... Celestia did not like to even think about the report from Appaloosa.
Inevitably, panic struck. Frontier towns were abandoned in droves, becoming nothing more than "ghost towns," there were protests and riots in major cities, and it was all Celestia could do to keep her citizenry in check enough to not impose martial law.
Shining Armor had begged to lead an expedition to investigate--and Celestia knew he dreadfully wished to at least attempt to reclaim his sister, however impossible the chances--and Celestia, seeing a chance to both ascertain the status of Twilight and her supposed Enhanced compatriots, as well as placate her populace, had sent him off with five thousand of the Royal Guard's best. Two years had passed before she, alongside a grief-stricken Princess Mi Amore Cadenza, had given the expedition up for lost. The foray would stand as a reminder of the power of Enhancement--the terrifying, abominable skills that permanent alteration enabled.
Finally, with the confidence of Equestrians crumbling, and at her own wit's end after losing Cadance--who committed suicide three weeks later--Celestia had ventured herself, along with the entire remaining Royal Guards, in a desperate attempt to utterly destroy the Enhanced outcasts.
Twilight remembered the day she saw her former brother, clad in his immaculate regalia, howl with the fury of loss as his army was decimated. The Enhancements she had provided to her troops not only improved their physical capabilities far beyond the bounds that a normal pony's physiology would allow, but also twisted their mind into slavering wrecks. Thus, they had attacked in waves, in droves, and in brutal charges, slamming into their enemies and allies indiscriminately as they used their sheer mass and staggering force to overpower their foes.
The result had been an utter victory, inevitable and pyrrhic. Twilight's army lay in ruins, with staggering clumps of shambling ponies wandering aimlessly throughout the battlefield before finding, ravaging, and finishing off the wounded Guards they found. Shining's redoubt lay in ruins, as well, and only his honor guard remained--shattered and weary.
Twilight had enjoyed leading her best troops into the final slaughter, and the vile burble that had replaced her former laughter sounded as she recalled driving the spear into her brother's neck, and seeing the glimmer of life fade from his eyes.
After the battle, Twilight had rolled into action her next plot--she unveiled a new, somehow even more dreadful Enhancement process, that could reanimate a pony's body into what resembled the original owner, but was merely rotting skin stretched over a modified skeleton frame.
Celestia's troops had fared no better, and had been similarly dispatched. The last battle of the Enhancement War had pitted Twilight's mass of Enhanced minions against Celestia herself, and had cost nearly everything. But the sheer amount of her equine weaponry had proven inexorable--for all of Celestia's godly might, it had taken only one charge to reduce her to dust, dust that was soon ground into the blood-soaked earth that had been Ponyville by none other than Twilight herself.
That had left the slaughter. Nopony truly knew why Twilight had decided to change herself so, but they all agreed on one thing now--she was indisputably and irrefutably an abomination. Her masses of Enhanced prowled the streets, now having been given yet another modification that granted enhanced sentience. The last survivors, fleeing hopelessly from the shattered remnants of once-proud cities, had been hunted down and destroyed mercilessly.
Even the Elements of Harmony, Twilight's greatest friends, had been cruelly and unemotionally murdered--Rainbow in the First Foray, Fluttershy as she fled Ponyville, Applejack in Celestia's Last Stand, Pinkie Pie in the Second Massacre of Ponyville, and Rarity as she had tried to rescue those insufferable three little filles, who had in turn been cast to the Enhanced as prey.
Eventually, however, Twilight realized her final, grave mistake. The Enhancements steadily destroyed neurons, for all their wonderful properties, they twisted minds. She had not known the depths of her animality as she had wrought such carnage, but the day before, Twilight had finally, in the lucid depths of her chemical hallucinations, finally realized her failure.
And that was why she sat, in the ruins of what had once been her Library, in what had once been Ponyville, Equestria, and wept. All of her Enhanced monstrosities had perished not long ago, as their brains--inferior to her's in the end--became irreparably and entirely degraded. Twilight was the last pony, the last--and first--Enhanced, and so she wept. Once she was gone, only ashes would remain--only the ashes of what had once been Equestria, of what had once been life.
There was a knock at the door.