My Little Pony: Pestilence is Magic

by SulMatul

Rating: teen
Tags: Pinkie Pie, Alternate Universe, Twilight Sparkle, Applejack, Drama, My Little Pony: Friendship is Magic, Dark, Thriller
Length: 4763

A very silly crossover between My Little Pony and the 2005 video game Pathologic

Ponyville is a small town on the edge of the map, deep within the Equestrian Steppe - but the town is vulnerable, and a plague will soon ravage it.

Three healers, each with vastly different methods, show up in town on the eve of the outbreak. Will their efforts be enough to stop it? Can they truly save Equestria?

This story will have sporadic updates - the tale will end on the twelfth day. Estimatied 30-40k words by the end, but we'll see what happens!

Published 2023-03-17 02:40:00 UTC
Last updated 2023-03-17 02:40:00 UTC

Chapter 1: Arrival

“Dear Twilight Sparkle,

My faithful student, as much as I admire your work on the study of Magic I regret to inform you of the cessation of funding to your laboratory. I have stalled the Powers That Be long enough to allow you time to pursue another line of magical inquiry. Please consider your research into the nature of death to be henceforth removed from the Canterlot Magical Society’s list of supported studies.

Without concrete results it is difficult to justify the ongoing costs of this laboratory - and, much as you have been my star pupil, I must also remind you that the expense has been disproportionate to what you have been able to bring forth to the Royal Council.

While there are those in Canterlot who view your research as dubious in terms of its ethics, I still have enough influence to protect you - but it is difficult to continue doing so when there is no positive result from your study of pony mortality. You are no doubt aware of the danger this presents you and your researchers if you remain in Canterlot.

I am not unsympathetic to your endeavours. If we are to restore the fabled powers of the Elements of Harmony, I agree that we must understand the nature of death itself. Even Alicorns such as I will age and succumb to mortality without them.

I have therefore arranged for your transfer to Ponyville-upon-Gorkhon. There is a particularly long-lived pony there by the name of Starswirl Kain, who may be able to assist you in your research. If he is as truly immortal as some claim, you may be able to find proof enough to save your laboratory.

I highly encourage you to also make some friends while you’re there.

May you trot ever in the warmth of the sun,

Princess Celestia”

Twilight Nightovna Sparkovsky put the letter down, letting her head rest dejectedly on the train carriage’s window. They were already almost at the strange town, though it had been three solid days of travel. Her diminutive dragon companion, Spike, tried to offer her a reassuring smile - though it hardly seemed to cheer the purple pony up much. She gazed outwards; the apple orchards had long since faded into the distance, and they were deep into the Equestrian Steppe.

“I can’t believe she sent us out to the middle of who-knows-where,” Twilight grumbled. “It’s so deeply unfair. We were so close to greatness!”

“It’ll be okay, Twilight. The Princess even arranged for us to stay in the town’s library! Imagine all the strange research they’ll have there - doesn’t that make you happy?”

“Yes, actually. Yes, it does,” she replied, perking up a little. “I’ve read a good deal about pony history, and a figure resembling Starswirl has come up more than a few times. If he really is this immortal pony, then even if we don’t get to talk to him we’ll still find valuable information about his stories and history. It might be the breakthrough we need. As soon as we arrive I intend to spend as much time as I can setting up a laboratory in this library.”

“Remember, you need to make friends here, too,” Spike cautioned. “We can’t have another Canterlot situation on our hands.”

“Yes, yes, of course,” Twilight said, dismissing his concerns with a wave of her hoof. Spike raised an eyebrow, unconvinced.

“I’m being serious, Twi,” he said, though his juvenile voice lacked the gravitas he longed for. Twilight looked on, out the window, gazing into nothingness. She didn’t take in a single word he said.

Hours passed. Night fell. The pair finally disembarked the train into Ponyville in the early hours of the morning, when all the world was asleep - or, at least, it should have been asleep. The sounds of a scuffle, muffled shouts, and general boisterousness of drunken colts sent a shiver down Twilight’s back. She ushered Spike away from the station quickly, opening her map of Ponyville to get her bearings.

The town’s library was built within the confines of a great oak tree; a suitable place for a pony researcher to build a makeshift home. It even had an observatory at the top, though Twilight ignored it in favour of the plethora of books stacked around the walls.

“Excellent,” she muttered to herself, setting up a microscope, a series of slides, blood samplers, and a large set of medical equipment near the hay cot. Spike had already fallen asleep in a small nook, beneath a pile of old books. She sighed, placing Spike in a slightly more appropriate cot - though it was still spartan and somewhat uncomfortable.

“It’s too late to go see Starswirl now,” Twilight hummed to herself. She glanced at the clock; a few hours longer and the town would see the dawn of Celestia’s sun. Too few to get a full night’s rest, but too many to pull an all-nighter again. “First thing in the morning, then,” she muttered, reluctantly trying to settle herself down to sleep.

“My dearest daughter Applejack,

I’m writing to you after so many years apart ‘cause I’m hoping you’ll find a way to return quickly to us.

Something has set Night-mareish Fear in my bones. A difficult trial is coming, and I ain’t got no idea if we can face it. I really do hope your studies have borne fruit, and that you’re a skilled surgeon. Such a skill will come of use soon, much as I don’t want it to.

I’m the only physician in Ponyville. But I’m growing old. In my bones I feel more aged than even Granny Smith, though I’m a might younger than her. Something ain’t right.

I don’t fear death. And neither should you. Death is, to a healer, just a partner in a barn dance. The other half of a conversation. The constant witness to our work - even when we succeed. It ain’t old age, or what comes after it, that worries me.

Instead, I’m beset by the thought that I might fail to pass on my role.

Make haste, my daughter. I truly need you.

Your loving mother,
Pear Butterakh”

The last train into Ponyville. It had been a long time since Applejack had set hoof in her hometown. A place she had once known so well now frightened her; she was an alien amongst her own people.

Training to be a healer had seemed only right - after all, every mare in the family line before her was a healer, too. But they were Menkhu. Butchers, in a way. Old holy ponies. Blessed with the knowledge and the skill to heal, but a far different knowledge to what she’d learned in long distant university halls.

Still, she was a deft hoof with a scalpel. And she hadn’t forgotten how to buck apples. She was still her mother’s daughter.

“Best turn yer mind to the here an’ now, Applejack,” she said under her breath, hugging herself for warmth. She walked down the train carriage to find her second class seat; a cheap ticket was all she had the bits to afford, even with all her fancy education. She’d never quite blended in with the other ponies studying medicine, always feeling a little too big, a little too burly, a little too low-class when placed alongside unicorn nobility.

She’d showed them all up, though. She was the only pony actually willing to get her hooves dirty. She was real good with a scalpel and bonesaw.

Somewhere in the first-class carriages a purple-maned pony and a strange little creature were talking in hushed tones, but Applejack paid them little mind. The mare seemed a pretentious sort, and her companion seemed a touch too incompetent for his niceness to mean much.

She was in no mood for making new friends anyway.

Setting her cap down over her eyes, she tried to let the jostling of the train carry her off to sleep. It wasn’t much, but an hour or two of rest was better than nothing.

“So strange seeing one such as you here,” a raspy voice said. She snapped around, looking over her shoulder. There was no one there. “I haven’t seen you around these parts for years.”

There was no one anywhere.

She was in the pitch black. Floating aloft on nothing.

Her stomach lurched. But she didn’t fall.

She paused, taking a few gasping short breaths of air in as she convinced her body she wasn’t in danger.

“Ah, I’m dreamin’ ain’t I?”

“Why, of course you are, dear Applejack. But that doesn’t make it any less real, does it?”

“Uh, beggin’ yer pardon?”

“It doesn’t matter. Don’t worry about it. Just think of me as a… fellow traveller, of sorts.”

“A fellow traveller, huh? Well, then would you mind showin’ yer face?”

“Ah, a brave little pony, I see,” the voice rasped, a smirk dripping from every word. A small candlelight illuminated itself in the distance. Applejack stared at it, trying to make out the visage of the pony behind it - though it was almost impossible to make him out.

“I ain’t afraid of nightmares.”

“Night-mares? Oh, my little pony, if you think I’m some mere tantabus you’d be sorely mistaken. I’m just an… interested observer.”

“Then observe away. But leave me be.”

“Ah, perhaps I will. Perhaps you and I shall never speak again. But I thought it only fitting that after visiting the mother, I should at least exchange pleasantries with the daughter.”

“You - what did you say?”

“Take heed, dear chosen child of the Apples; your mother was right to be cautious. Perhaps you may outwit that which hunts you. A gentle suggestion; without friends, you are all sure to lose. Good evening.”

The speaker vanished in an instant - but just for a moment Applejack could have sworn she saw an enormous beak, and the glittering eyes of carrion fowl.

The rest of her dreams were no more restful than the first, but the memories of them slipped away like water through her hooves. She awoke in full when the train finally blew its whistle.

She had, at last, arrived home. Back in Ponyville-upon-Gorkhon.

She stepped off the train, hauling her few meagre possessions into her saddlebags. She hadn’t made it more than ten steps into the trainyard before she heard hoofsteps approach behind her.

“Well, well, if it ain’t the prodigal Apple, returning to the scene of her crime,” said the voice of a colt behind her. She didn’t recognise it.

“What in tarnation? You mean me?”

“O’course we mean you, murderer,” another voice said - this time a mare’s, approaching from the front. She was masked. Her cutie mark was covered. Two more colts stepped from the shadows of the trainyard, surrounding her.

“What the hay is this? I’m Applejack, y’all know me!”

“I don’t think any of us know you any more,” the mare replied, revealing the glitter of a knife in her hooves. “You killed Pear, you pay the price. Matricide ain’t somethin’ we tolerate here in Ponyville. Buckin’ traitor - get her!”

The next moments passed in a blurred rush. Applejack wanted to ask what the hell was going on, to know what they were talking about, to process the fact that they thought her mother was dead, to understand that they thought she had killed her own mother, how the hell any of it made any sense -

But those questions didn’t matter.

Acting on muscle memory, she ducked.

She kicked out.

Her hooves made contact with another pony’s chest.

A blade slashed her side. Her leg was bleeding.

She flailed. A pony’s face hit the side of the traincar.

Another cut.

Another hoof in somepony’s jaw.

A knife, skittering across train tracks.

Three dead ponies, and another one injured, gasping weakly on the side of the tracks.

“Oh. Oh horseapples,” Applejack muttered, her flank openly bleeding. She staggered forward, collapsing from the headrush. “This ain’t good…”

Pulling herself to her hooves, the mare crawled into the outskirts of Ponyville. Amidst the industrial warehouses were still a few trees. In one of those trees was a treehouse.

It would do for now. A brief place to breathe and to patch up her wounds.

She stumbled up the ramp and pulled a makeshift draw-switch beside her.

The house wasn’t empty.

“What?! Who are you?! This is a house only for blank flanks!”

“Ah, I uh… Oh, fillysticks,” Applejack muttered as her vision swam. The blood left her brain.

She passed out. The orange-coated filly before her looked on in horror.

Pinkie Pie woke up in a shallow grave.

It was kinda bad, kinda dirty, kinda muddy, kinda dusty, but still kinda fun because if you looked really really hard sometimes you could see little earthworms and bugs and other cool things and gemstones and like isn’t this so exciting like seriously we get to even star as one of the main characters in a cool new fiction and we get to have like such a melodramatic start to it all plus also like it’s the one about the plague game that got kinda popular a while ago and that’s really really cool right isn’t it????

Pinkie Pie turned to the audience, grinning a little too widely. She was just really happy to be a part of the production.

“Wait, sorry, is this the wrong tone? Is this too enthusiastic? Do I need to, like, put on my serious growly grouchy oopsie doopsie meanie weanie Pinkie face for this? I could just do the whole thing as Pinkamina instead would that be better because I can do that instead and that wouldn’t even be hard for me I could be all like GRR and Scary and like even do the Cupcakes thing because y’all loved it when I was being scary an-”

“No, no, Pinkie,” a purple-maned alicorn replied, cutting off her incessant stream-of-consciousness. She spoke from off-stage. It was difficult to fully see her face; any time Pinkie tried to squint too long at her, all she could see was an expressionless mask. Spindly, black-clad limbs. The garb of a stagehand. Or a director.

“I know you’re enthusiastic to play the part well, but just relax. The first play was a flop. This time we’re going to do it a little better.”

“Okay! Gotcha! And scene!”

The world went dark.

Pinkamina woke up in a shallow grave.

She had no memory of how she got there. She had no memory of who she was. Nothing really seemed to make much sense.

She supposed it should be scary, yet no fear entered her heart.

“Remember,” the stagehand spoke, “you’re basically a criminal. You’ve got to have the mindset of a thief.”

Pinkamina, her mane flowing deceptively straight, turned to the stagehand. Her face was expressionless, but there was a dangerous fire in her eyes.

“Why would they call me a thief, pray tell? What did I steal? Why does the Law detest me so?”

“Ah, fantastic!” The Stagehand said, gesturing to the camerapony; Pinkie was her favourite method actor, and at last she had a chance to capture her brilliance on the stage. “Yes, good, keep going!”

“The only thing I remember is that I am an outlaw, and will forever be persecuted… Was I really that good a thief, I wonder? I have nothing of value, just myself and these rags I am wearing. My crime is horrendous, still.”

Pinkamina climbed out of her grave. Rats scurried before her. Dogs howled, and bulls moaned their guttural cries in the steppe beyond.

By Celestia, playing both good and evil roles at once was just so fun!

“I am beyond redemption. Back in the day, every heart was open before me. Now, whatever door I approach is slammed in my face. Where should I run? With whom shall I seek shelter? Shall I find what I stole and give it back? Who will agree to take it off my hands?”

She turned, staring directly at the camera; a Brechtian to the bitter end, she had no love of the fourth wall nor its needless restrictions.

The audience in her eyes, she begged for the response she would never receive;

“Who will answer my questions, if not you?”

Chapter 2: The First Day (Twilight; 06:00)

“Twilight, I think there’s somepony out there,” Spike whimpered, glancing nervously out the window. “I heard them creeping around behind the library!”

Twilight groaned as the first light of Celestia’s morning sun hit her eyes. She groggily got to her hooves and pulled the curtains back a little, revealing that Spike was, indeed, right; a strange-looking pegasus seemed to be lounging in the library’s backyard, alongside a strange earth pony that seemed to be drowning in a set of brown robes that were markedly too big for it.

In fact, was that even a pony? It was hard to tell.

“Oh gosh I hope they’re friendly… Things sounded all tense out there last night at the trainyard.”

“It was probably nothing, Spike. There’s no sense in being paranoid.” She tossed her mane, her tone disinterested.

“Are you going to talk to those ponies out there?”

“I don’t intend to make friends with them, if that’s what you’re meaning,” Twilight said, donning her coat. It was long, and black, and dotted with snakeskin patterns; while some in Canterlot seemed convinced it made her an unfriendly goth, to her it was a necessary part of her personal pony protective equipment - her P.P.P.E.

She tied her red cravat beneath her neck as she prepared her medical bag, levitating various medical items and trinkets inside it; a stethoscope; a set of needles; syringes; catgut sutures; a scalpel.

She paused before putting it in her bag, instead opting to carry the blade in her pocket. In a strange town, it couldn’t hurt to have a little extra defence if she needed it.

She blinked, suddenly noticing that Spike had been talking all this time. She had been too caught up in her checklists to notice. She felt a twinge of guilt in her stomach; she didn’t mean to be rude or inattentive, she just had a goal to achieve. Sometimes it was hard to focus on anything else; that goal was too important.

“... and the map says that Starswirl Kain lives here, just on the side of the riverbank. Hey, Twilight, that’s not far from here! It’s just opposite the Cathedral.”

“Cathedral? I didn’t know Ponyville had a Cathedral. I feel like I shouldn’t have missed that.”

Twilight levitated the map towards her, glancing over its contents. Spike was correct; a cathedral was, indeed, present. Barely a five minute hooftrot away, too. Still, it seemed strange. There were no Cathedrals dedicated to the Princesses since the original banishment of Princess Luna. Ponyville was a new town - any cathedral built in it would have had to be constructed within the last decade.

Who would build such a thing? And Why?

Twilight put it to the back of her mind; it wasn’t important right now. What was important was finding Starswirl Kain. Spike continued talking, but Twilight barely took in any of what he was saying.

“... looks like the architects were a pair of ponies, one of them from Canterlot. You ever heard of a Sunset Shimmer before? I wanna say I’ve heard the name, but…”

“Spike, you know we don’t have time for that right now. Point me in the direction of Starswirl, and you stay here and keep going through the library. There has to be something here worthy of inquiry. Both our livelihoods depend on it.”

Spike huffed and grumbled, but nevertheless obeyed; he was a good kid, even if he was unfocused. An inquisitive mind, but too easily distracted by frivolity. In a better era, she would have encouraged his curiosity. In their current situation, she had to keep him on-task.

She stepped out into the autumnal Ponyville air. It was humid, and dense, and tasted like the faint sweet decay of old apples. She grimaced a little; was she too harsh on him? He was only a baby dragon, after all.

“Ah! Miss Sparkle! A word, if you will!”

Twilight jumped, her attention suddenly snapping to her surroundings. Who had spoken to her?

“Over here! Come, come now! No time to delay!” A strange pony said. She seemed tall, spindly, even Alicorn-shaped in her form - yet her wings, her horn, were hardly perceptible beneath a vantablack skinsuit. She wore a mask, expressionless and empty. Beside her a second pony stood, garbed in a giant robe. She, too, was masked, though hers resembled an enormous carrion-bird.

Twilight approached the strange pair - a different pair to the ones Spike had gestured towards when she had woken up. They seemed strange, like they weren’t entirely perceptible to her eyes. The little bits of motion she could see beneath the masks were off. Like they were operating in a different plane, an imperceptible dimension, and were only appearing in the briefest of moments.

“Miss Sparkle! It is an honour to make your acquaintance!”

“That’s Doctor Sparkle to you,” Twilight said, her voice cold. There was something deeply wrong about these ponies - she couldn’t bring herself to be friendly with them. “What is it you so deeply want to tell me?”

“Ah! Well - of course! I’m only an understudy in this theatre, but one day I hope to become an actress in my own right! Maybe even the star of a show! My name is Sunny -”

The spindly pony was interrupted by her bird-masked compatriot, who coughed loudly enough to destroy all sense of subtlety. Twilight regarded them both coolly.

“What my friend is trying to say -”

“Izzy! Stop! I wanted to tell her the rules!”

“You’re fangirling! And you’re doing it all wrong!”

“Shut up! Just let me tell her -”

Twilight, her patience rapidly waning, turned to leave. The spindly pony trotted up, bidding her stop. “Wait wait wait - please just listen? We shan’t take up too much of your time! In fact, when you speak to us, time will stop. We just wanted to take this opportunity to tell you that the, uhm, rules of Ponyville don’t operate quite the same.”

“Explain yourself quickly, or get out of my way.”

“There are… walls. You know. Barriers. And here in Ponyville, they get thin. Time doesn’t operate the same. Things get hazy. The Magic of Friendship is strained here and doesn’t always work how you think it will. You’ll die. And awaken again, and live the same life, maybe ten, twenty, a hundred times over.”

“What? Are you trying to tell me Ponyville is some form of hell? Honestly, I think I could tell that already from the, uh, rural surrounds -”

“Stop being a fool and just listen,” the one in the bird-mask, Izzy, interrupted. There seemed to be a hint of a unicorn horn within her birdmask. “The closer you play the role, the more likely you’ll be to get out of this alive. Do you understand?”

“What? What role? You’re not making any sense -”

Twilight blinked. She found her mouth forming different sounds. She was already halfway through saying a totally different sentence. She didn’t remember doing so. “I always play my role admirably,” she replied, curtly. It didn’t entirely feel like herself saying the words.

For a brief moment, she felt alien inside her body. Or was it that her body felt alien inside her?

Everything shifted, imperceptible to most. But she could feel it.

“Ah! Bravo! Then we have an understanding,” the spindly Sunny said. “Well, if you find yourself trapped or unsure what to do, we’ll be sure to show up eventually.”

“It is probably best if you don’t meet us too much,” Izzy added. “It unweaves the fabric of the narrative if we appear too often.”

“Very well. I shall bear your advice in mind and continue to ignore your presence from this moment on - unless you have something of desperate importance to tell me,” Twilight said. The longer she talked to these two, the more she felt unmade. Like she was breaking down to component parts.

An echo haunted the back of her mind. A voice, her voice, yet somehow not her. A woman named Tara. Who was she?

What in the name of Celestia was going on?

Her mind hurt to think about it, something was putting pressure on her self, fracturing her soul -

“Well, good day, and good luck, Doctor Sparkle,” Sunny said, exaggeratedly bowing to the ground, her snout touching the grass beneath her. “Let us hope you have no need to meet us again.”

The pair vanished.

Twilight stood for a moment, her hooves refusing to move.

What

Was

Happening?

This

Isn’t

Right?

She shook her mane. She took a deep breath of that apple-scented air. She had no time for the distractions of whimsical, weird ponies - she had to focus.

She trotted around the corner, to the small pond near the library. A strange pair, dishevelled and unkept, seemed to be hanging around beside a small makeshift fire. The pegasus, now she could see them more clearly, was grey-coated and blonde-maned. Her eyes seemed mismatched, her pupils pointing in opposite directions. The creature beside her stood on all fours, but now she had a closer look she could tell it was no pony.

It had a snout, yes, and walked on four legs - but its form seemed misshapen and off somehow. Its teeth were longer, and its back and shoulderblades arched in ways that seemed incorrect. It seemed almost canid in nature.

“You there, you two,” Twilight said, trotting up with false bravado. “What are you doing here?”

“Oh uh, uhm, uh,” the pegasus stammered, looking to her misshapen friend. The dog-like thing grumbled something guttural and heavily accented that was difficult to fully make out.

“We cause no trouble for you,” it said. Twilight raised an eyebrow at it as it shied away from her, seeming fearful of her horn. “We are no problem, no problem. You leave us alone.”

“Who are you? This Library is official Celestial property - what are you doing here?”

“Umm, uh, we don’t wanna hurt anypony,” the pegasus mumbled. “I’m Ditzy… please don’t tell anypony we were here!”

“You should go back way you came,” the misshapen creature said. “You should forget you saw.” It pulled back its robes, revealing menacing claws on its paws - distinctly not hooves, and distinctly dangerous and predatory.

Twilight felt her heart throb in her chest, the adrenaline start to pump.

“A likely story,” Twilight began to say -

But there was a flash. A moment. She blinked. She had wanted to say “but I don’t believe you” - but there was a moment.

A flash of violence.

After-images of screams and shouting, of the creature’s claws meeting her throat as her scalpel slashed and slashed at its face. Her hot blood spilling into the earth.

An echo of the spindly, masked Sunny, a faint memory of her saying “Oh dear, not so soon, Doctor Sparkle. You really ought to be more careful. Come come now, that’s not how the script goes -”

“Ah, yes,” Twilight heard herself saying agreeably. Her tone was warm, and friendly - far more friendly than she felt she ought to be. “Well, I can see you’re not harming anypony. But, still, it might be a good idea for you to be on your way. I wouldn’t want to see you in trouble.”

“Y-yes of course!” Ditzy mumbled. “Just let us stay warm by the fire a little longer?”

“You have anything to eat?” The larger robed creature asked. Twilight hesitated, then fished in her saddlebags for some crackers - it wasn’t much, but she wasn’t hungry anyway.

“Take it,” she said, gingerly offering the canid a snack. It took it from her, wolfing down one and offering another to the pegasus. They both looked malnourished.

“Th-thanks!” Ditzy said, huddling closer to the fire. “W-we’ll go soon, I promise.”

“Very well,” Twilight said. “Pray tell, do you know the quickest way to Starswirl Kain?”

“That way,” the creature mumbled, pointing the way down the street.

Wordlessly, Twilight nodded and left the pair.

She had the odd, deeply sinking feeling that some part of her had died, somehow. That she wasn’t the same as she was before.

There was something deeply wrong about Ponyville.