Resistance is Magic: Fall of Friendship

by Darkendmind

Rating: teen
Tags: Crossover, Main 6, Gore, My Little Pony: Friendship is Magic, Dark, Doctor Whooves, Spike, Adventure, Derpy Hooves
Length: 7976

A crossover of the Show MLP:FiM, and the Resistance games. It is a continuous story.

On a starry night, a lone meteorite carries what will soon become the fall of the Equestrian denizens. Follow the Mane Six, as well as some fan-favorites, as they combat this new enemy which so easily is wresting control of the planet away from the peaceful inhabitants and throwing it into a violent war over not just friendship, but the pony species as a whole.

Published 2012-02-25 07:24:01 UTC
Last updated 2012-02-25 07:24:01 UTC

Resistance is Magic: Part 1

MY LITTLE PONY: RESISTANCE IS MAGIC

PART I: FALL OF FRIENDSHIP

Written and edited by:

Darkendmind

and

Littlemanneb

(ben.f.daley)

Artwork by:

Darkendmind

All content below is a fanfiction, all copyrights belongs to Hasbro or Insomniac games

PROLOGUE

Twilight took another look in to her telescope that she had received in the mail only a week ago as a gift from the Princess. Within that time she had already gotten multiple notebooks filled with observations and notes on patterns of Planets and distant galaxies. She looked into her telescope and saw a small distant planet but before she took her eye away to continue her notes, an enormous object blocked her view. She immediately grabbed the telescope with her hooves and turned it to track it, while also adjusting the zoom and focus to bring the object to size. In her view was a flaming meteor approaching in her direction, slightly angled to the side.

“Spike! I found something!” she yelled loudly, waking her assistant with a startle.

“What is it now?” he dully asked.

“A meteor, its very close to us, so we only have tonight to write everything we can about it before it travels to the other side of the planet and wont be able to see it!” Twilight said in an exited tone, “Now hurry!” Spike grabbed a ink quill and a sheet of paper. “it seems to be traveling in a direction that will cause it to either enter Earth’s or the moon’s gravitational pull, in either case, it will be destroyed on impact with the moon, or in the atmosphere. If it doesn’t get pulled in, it will be drawn in by the sun and then burn up.”

“Sad day for that meteor...” Spike added.

“Actually Spike, it could take months for the meteor to travel all the way to the sun.” Twilight added. Spike simply stood silently and starred at Twilight.

Twilight turned back around and continued to observe the meteor for the rest of the night as Spike walked off to bed, and back to his imaginary sheep.

The Meteorite flew across the sky, bits of ancient space rock burning off in the upper atmosphere in a brilliant display of both sparkles and flashes. Below it, no living thing suspected the meteorite of anything, or any kind of purpose other than that of burning up. Stars behind it were blotted out by the vibrant display created by the friction. To everyone below, it looked just like a shooting star, like the usual ones that passed by all the time. This was no star however, and soon everyone would remember what it signaled in the years to come

The heat began to build with every passing moment in the upper atmosphere, climaxing in a burst of flames that lasted all the way to the soft, loamy earth under it. Trees shook with the concussive force of impact like a choir of ruffling leaves. Then, as soon as it had started, it became silent again. Crickets resumed their usual musical performance, barely taking note of the new rock formation. They only stopped at the occasional dropping of an apple.

Across the orchard, a light came on. Voices began to rise, arguing over the origin of the noise off in the distance. A few shadows moved about in the window. The door crashed open, and two ponies made their way to the center to the trees.

“Nothin’ good ever happens when you hear a crash,” Argued to first one, “ Now what the hay coulda made such a rukkus!"

The second just calmly looked to his sister, his eyes lazily moved to the trees.

“Applejack, the trees look fine.” Big Macintosh stepped back, ready to return inside to his warm and cozy bed. A sharp pain stretched across the side of his cheek. Another flick of her tail and Applejack smacked the other side as well.

“You ain’t leavin’ so easily, Big Mac. We have to check the crop. There ain’t no way I’m lettin’ some noise ruin my apples.”

It was a battle he couldn’t win. Big Macintosh sighed and followed after his sister into the thicker parts of their farm. they walked for what felt like an hour before they found the rock, still glowing in the faint residual light from the burn-in. They stood in silent awe at the sheer size of the object, which easily towered over their farmhouse. Every few seconds, a chuck the size of a melon would break away and crash to the ground. One landed a few feet from Applejack's hooves, causing her to jump up a good foot, right into Macintosh.

“What the hay is this supposed to be?,“ she said after pulling away from her brother. She moved to the edge of the crater and tapped the edge of the charred space material with the edge of her hoof. The air was still thick with the dust from the objects impact. Applejack sneezed a few times before she finally figured out what the rock really was.

“Mac, I think this is one of those meteors that Twilight Sparkle is always talkin’ about!”

“Eeeyup.” Macintosh was already backing up. His bed was calling his name, and he was getting ready to make a beeline for the house. Once again, however, Applejack stopped his journey before it began.

Her right leg thrust out, pointing to the now barren trees in the immediate area. Macintosh slowly craned his head around, trying to see what it was that Applejack seemed so determined about. In response, Applejack pointed even lower, this time to the piles of apples that littered the ground.

“We’re havin’ the big apple sale tomorrow, and look at all the apples that just went bad, Mac. Now we have to change all the market signs by the mornin’ light!”

Big Macintosh blinked and shook his head. He walked to one of the piles and casually lifted one of the apples up. Besides an unusual coating of some glittery golden dust, the red fruit was completely unharmed. A quick blow on the top and the dust seemed to flutter away with the wind. Applejack still seemed unimpressed, however, and kept circling herself, mumbling about how many apples they lost.

Macintosh looked back to his apple. He shrugged and popped it clean into his mouth, savoring the juicy taste of the glamorous fruit.

“See, just fine.” He wiped his mouth on his arm to get the last bits of the apple off his lips.

Out of nowhere, Macintosh began to cough. Applejack moved closer and tried to pat his back, but he just shook his head. He felt something forming in the edge of his eye, but was able to blink it away. He grinned at Applejack.

“Happy now?”

“Fine, you win this round, buster. C’mon, lets go. We’re pickin’ all these up tomorrow morning, so you’re gonna have to be bright eyed and bushy-tailed.” Applejack nudged Macintosh towards the house. He turned over his shoulder and looked back to the meteor. Applejack bumped him forward, snapping his attention away.

“No don’t ya’ll worry, Twilight can deal with that later. We just gotta worry about the apples. No back to bed you go.” He snuck one last look back, then shrugged and walked away, to the calming lights in the distance.

“So then Spike and I took some notes on the trajectory-”

“Actually, you took notes Twilight. I went to sleep.” Spike scratched the back of his neck and let out a huge yawn. Around them, the grand apple market sale was already in full swing. Hundreds of ponies were busying tasting apples and asking questions about what kind of pies will be available for them to sample.

In the center of the event stood Twilight Sparkle, Fluttershy, Rainbow Dash, and Applejack, all discussing the solar event that had occurred the previous night.

Twilight seemed really excited when Applejack told her about the meteorite crashing into her orchard, and promised to be right over as soon as she could bring one of Equestria’s foremost scientists, Doctor Whooves, who had quickly hidden himself away from the main crowd upon seeing Apple Blossom.

“So what’s the point of taking the rock anyways? It’s pointless.” Rainbow Dash ruffled her wings. Her mane’s colors had quite the sheen in the bright sunlight, and even began to cast its vibrant hues across the lawn.

“Well that’s simple, Rainbow.” Twilight flicked her tail in excitement, “It so we can understand more about the composition, and origins of them, we can even tell how old it is, which we can connect to...”

“Yea, yea, enough sciency talk, you’re going to turn me into an egg head Twilight!” Rainbow Dash cut her off. She grabbed an apple off from a near by market stand and took a big bite it. For a moment, Rainbow just relaxed to enjoy the taste.

“Mmmmmmmm...”

“Where’s Big Mac?” Twilight asked Applejack after noticing her brother wasn’t around to help her with the market. Applejack turned her head to face her friend, a small look of sadness in her deep green eyes.

“He’s at home restin’, he woke up this mornin’ with a stomach ache and a fever.” Applejack replied. She faked a smile and tried to pass it off to the group.

“Is he alright?” Fluttershy immediately asked. “Oh, I hope he’s alright.”

“He’s fine Fluttershy, he just needs to get some rest.” Applejack turned her attention away from her friends and back on the customers craving more delicious apples. The others continued their conversation until Doctor Whooves finally managed to pop out from one of the bushes nearby.

"Where have you been?" Twilight impatiently asked.

"I'm sorry, I was hiding from a certain filly, whose determined to sell me more apples." The Doctor shuddered, leaves flew in all directions. He grinned and turned to the direction of the house.

"Why, where is Big Macintosh? Is he feeling under the weather?"

The other ponies nodded their heads in unison. Doctor Whooves rubbed his hoof under his chin, as if to contemplate the situation. He turned to Twilight Sparkle and whispered something inaudible into her ear. She nodded once, nudged her head towards the house, and walked towards the orchard. Spike quickly bounded off after her, desperately skipping every few seconds just to keep up.

"Miss Applejack, would I be intruding if I asked to see your brother?" Before he even got an answer, he turned to the bush and removed what looked like a medical bag. The others blinked a few times and tried to get a closer look at his bag. Doctor Whooves had to crane his neck up to get a good look at his intended target.

Applejack turned from one of the stands, her chin covered in small bits of fruit skins. She snatched a napkin from an adjacent stand and wiped her mouth clean.

"Sure. He's probably itchin' for some company right around now anyways, been cooped up in his room all day now.” She began to walk to the house, pushing her way through some of the customers on the way up the path. Doctor Whooves followed suit with his strange bag. Applejack stopped every few seconds to adjust or fix something in the market whether it be signs or baskets. Content with the settings, Applejack would progress to the house before repeating the cycle, much to Doctor Whooves dismay.

Eventually they did reach the house, only after Applejack had fixed a dozen signs and sold twice as many sweet granny apple baskets. The Doctor stood on the patio for a moment and saw Twilight off in the distance. From his point, her and Spike were just dots moving about a larger black chunk, which he could only assume was the meteorite.

“Ya’ll commin’ in, or are ya just gonna admire the view?” Applejack impatiently tapped her back foot on the wooden porch. Whooves shook his head and rushed inside.

Immediately, the two felt a surge of cold air hit the back of their manes. The Doctor dropped his bag from the unexpected shock. Applejack moved to one of the halls, out of sight behind one of the houses many walls.

“What the hay is- Mac! Didja change the thermostat to twenty degrees?” Her voice was sharp, as to easily demonstrate the power behind her words. Her only response was a low moan from one of the many adjoining rooms in the hall.

The Doctor picked up his bag and started towards the noise, alongside Applejack who was now truly surprised at the new development. They slowly approached the door, cautious as to not make any excess noise. When they reached the door, they exchanged a silent look then pushed the slightly ajar door even wider.

Macintosh was splayed on his bed, covers thrown in all directions, and heaving his pale chest with labored breath. Applejack tapped the back of her brothers hooves to get his attention. He swung his head around to face his visitors with visible effort and strain. The two just stared on in silent horror. Doctor Whooves even stepped back for a moment.

While it’s not unusual for a pony to become paler when they felt under the weather, Macintosh was far beyond just under the weather. His Red coat had faded to a light pink, with his even paler skin showing under the fur. Even odder was his face. His eyes had a faint yellow-golden glow to them, an unworldly look that frightened his onlookers. Even his teeth had begun to protrude from his mouth, taking on longer and slightly sharper traits.

His head twitched repeatedly and shivers rocked his body. The Doctor and Applejack just stood with their mouths slightly agape.

The doctor Placed his bag down, gently this time, then looked to Applejack.

“You say he was completely fine this morning?”

“Yeah, he was fine and dandy earlier,” Her quivering voice was totally out of character for her, “He even helped my pick up all the apples and put ‘em in a basket.”

The Doctor made some approving sounds. He opened his bag with a snap, reached inside, and pulled out a smaller bag. He walked over to the bedside, navigating through all the trash on the floor. The bag swung a bit in the air before he placed it on the bedside table, next to Macintosh’s thinning mane.

The Doctor was swift, and he quickly pulled out a series of medical based equipment. before Applejack could even ask, he had already placed down a needle, a stethoscope, some weird looking microscope, and a pack of collection vials. Big Macintosh watched his every move, following him with his glowing eyes at full attention.

“Mr. Macintosh, can you understand me?”

Big Mac blinked a few times. His head slowly moved up and down in response. The Doctor knitted his brow and picked up the needle, as well as a sample vial.

“This might sting, just think happy thoughts and relax, otherwise you’ll just feel it that much more. Now, here we go.” The Doctor lowered the tip. Taking his time, he slowly worked it into Big Macs soft, pale arm. Macintosh freaked for a brief moment as his dark red blood was pulled from his limb, but he did eventually settle back down into his splayed posture. The Doctor then filled a few of the vials and grabbed his bag again. His hoof fished around for a second, then emerged with a white stick.

He placed it in Macintosh’s mouth and started to tap his hoof. Thirty clops later, the Doctor removed the stick and thoroughly checked it out.

“Mr. Macintosh, your temperature... well, I don’t know how to really put this, but you’re much too hot to be...” the Doctor looked to the Microscope and audibly gulped. He placed the thermometer down and moved to the machine.

His hooves worked nimbly on the device, opening a side slot rapidly and inserting one of the many blood samples. He closed it and pressed a small switch to the right. A sound rang out, which was a complete mystery to Applejack and Macintosh as to what it really meant. Doctor Whooves, however, took it as some sort of signal and pressed his eyes up to the top, where two view ports were placed.

“Applejack,” The Doctors mane stood on end as his head rose back up, “May I have a minute of your time...outside?”

Applejack looked to her brother, who continued to twitch uncomfortably on his bed. She bit her lower lip and nodded. The Doctor put all his tools back into his bag and picked it up once again in his mouth. the two left the room, Applejack turning back one last time to look back.

Outside in the halls, Whooves closed the door and placed his bag down. His demeanor looked tense. His eyes were intense as well, as if he had seen something that had bothered him. Applejack was terrified of what he was going to say.

“I’m afraid to say it, but unfortunately, Big Macintosh’s condition is....unique. His current body temperature is almost twice what a normal Pony should be at, and it’s still rising.”

“What’s that supposed to mean?” Applejack felt her knees wobbling.

“It means that this is much worse than a fever, miss.” He began to pace a few steps.

“Well than, what the hay is is?”

“I have no clue. But it’s not good, whatever it is. Something in his blood is attacking his cells. It’s essentially cooking and eating him at the same time. I’ve never seen anything like it, ever.” The Doctor grabbed the bag and moved outside.

Twilight Sparkle had returned from her meteorite examination, as evidenced by Spike carrying a pile of notes almost as tall as he was. Wasting no time, he galloped to meet her, dropping the bag next to Spikes foot. They exchanged a series of inaudible words that caused Twilight's expression to change from a slight grin, to a worried grimace. Spike nodded once or twice and blew on the Bag, transporting it away.

The two ponies just stared at each other, their looks speaking louder than any words could.They turned suddenly to their left, where another Pony had collapsed and begun panting. More began to fall the same way, and panic arose in the group.

“What’s going on with everyone, Twilight?” Rainbow Dash hovered a few feet in the air, carrying a bag full of apples that she had already bought.

“I- I don’t know,” Twilight looked to the Doctor, “Whooves, what’s going on? Is this something having to do-”

“I’ll answer that as soon as we get the situation under control.” He interrupted.

Rainbow Dash shot him a look as she landed.

“What do you mean ‘we’? Is there someone you’re not telling us about?”

As if to answer the question, a large ring appeared a few feet behind Whooves, who didn’t even turn to witness the event. A few ponies turned away from their friends to see what had caused the gust that now blew across the market.

Emerging from the enigmatic blue ring, a dozen fully suited ponies marched onward. They wore clean white uniforms, complete with sealed masks and visors that gave them an almost robotic feel. They fanned out, silently taking positions behind fallen ponies and some went inside, most likely to gather Big Macintosh. They said nothing, just moved along with their private duties in a practiced fashion.

Twilight looked back to the orchard. three unicorns, dressed in almost the same manor, were moving the meteorite forward. Doctor Whooves approached one. It listened intently to the Doctor for a few moments before raising one of it’s hooves in the air. The others turned and watched. They then reached behind their backs, and all together pulled out small rods. they placed one on either side of their afflicted ponies and stood back.

Stretchers deployed from the rods, which allowed the mysterious ponies to pick up the sick ones with ease. They moved into rows and awaited even more instructions. The meteorite moved into the ring, along with the unicorns, and disappeared from sight. The ring began to change hues, shifting to an emerald coloring that emanated from inside the ring itself.

“Wha- what’s going on? Where are they taking everypony?” Fluttershy was hiding behind Pinkie Pie’s puffy mane. Rainbow Dash shot Doctor Whooves another look, along with Twilight. The Doctor said nothing, but he had a concerned frown on his face that reflected his deeper meaning.

“We’re taking them to the hospital. Until a time comes that I can conclude that this outbreak is completely safe, I hereby initiate a quarantine on the infected with the lawful power vested in me by Princess Luna herself. For now, just go home. Only those who are positive for trait symptoms will be affected.” Doctor Whooves rushed forward and whispered something to another suited pony.

“Attention, all Bio-con Ponies,” His voice was obviously projected through some form of a megaphone build into his mask, “All afflicted subjects are to be placed in the care of the Ponyville Medical Center and issued an immediate Ice dipping. Stop for nothing, and for nopony!”

The Ponies galloped through the portal, leaving only Doctor Whooves, the commanding pony, and the crowd of very confused onlookers. The commander pressed a button on his leg and turned. A unicorn wearing a similar uniform emerged. A flick of it’s head and the portal behind it closed.

Doctor Whooves turned to crowd.

“Anypony notice anything that all the ponies from earlier were all doing? Did they all touch something, maybe walked in a certain area?”

“I think I saw a bunch of them eating those apples over there!” Pinkie Pie shouted. It was hard to tell if she was taking this seriously from the excitement in her voice.

Applejack looked to see a barrel half full of apples. A small gasp escaped from her mouth, which caught the attention of all three science ponies. She rushed over and double checked the sign on the the front of the barrel, and unfortunately, she was right about her suspicion.

“They’re the apples me and Big Mac picked up after the rock hit. He even ate one to prove they were still good.” She turned to face her friends, tears forming in her eyes.

“Whooves!” Twilight snapped her head towards the Doctor, “What the buck is going on? What does the meteorite have to do with this. It shows to traces of magic!”

“Twilight, this is not a magical ailment. From what I’ve seen, in basic field observations at least, this is completely science oriented. That means in falls into my domain.”

“Hold on. Are you trying to tell me that there’s something affecting the ponies, that doesn’t have any magical roots?”

“Precisely. I believe this outbreak is Viral in origin,” His hoof scratched the underside of his chin, “And it must be hyper-sensitive, considering it doesn’t seem to be airborne.”

Rainbow Dash looked to Fluttershy, how had started to shake violently in fear. She flew behind her and tried to pat her gently. Then she looked back to the Doctor.

“So what are we supposed to do? Just sit here and watch?”

“You’re to go home. And someone will have to provide housing for the Apple farm’s residence. This area now falls under the full authority of the E.S.R.D.”

The girls didn’t argue. They looked back and forth, sighed, and then started to walk off. Other ponies started to disband as well, wandering off to their homes in town. Doctor Whooves continued to talk with his fellow science ponies as though the entire routine was normal.

“I hope they all turn out okay.” Fluttershy had curled herself up, in spite of the efforts her friends went through to calm her down.

“I’m sure they’re fine, dear.” Rarity lifted up a kettle and poured another round of calming tea for the group. Twilight kept pacing back and forth in front of the window, impatient as ever. the other ponies kept trying to calm Fluttershy down, and Pinkie even baked her a single slice of cake, just to help her out.

“This doesn’t make sense. Whooves always tells me about his findings, why would he keep me out now?” Twilight sat back and stared out into the night.

“Now just hear me out,” Rainbow replied, “Maybe he can’t?”

“What do you mean ‘can’t?”

“You saw his army of robo-pony drones. This looks serious!”

Applejack stood up and circled herself. She had been worried sick all night because of Big Macintosh, and even Rairty’s tea wouldn’t help. Neither could Pinkie Pie’s sweets. She was alone and homeless now, and there was nothing she could do about it. Rainbow Dash kept raising her voice while Twilight argued that she should’ve been told everything. All the wile Applejack just sat solemnly in the corner, contemplating Macintosh’s condition.

“Just because he usually tells you doesn’t mean he has to!” Shouted Rainbow Dash.

“Ladies, lets be civilized for a moment.” Rarity wiggled between the conflicting ponies, “I’m certain that this Doctor gentlecolt has a perfectly good reason for not telling you. Maybe it’s not that he doesn’t want to, but rather he can’t, like Dash said.”

Twilight scowled, but her face softened after a moment.

“Yeah, maybe you’re right, Rarity. I just wish I knew what was going on. For Applejack’s sake.” She looked to her friend in the corner. It just wasn’t fair being left in the dark like this, without any clue as to what was happening.

“We should just relax. I’m absolutely positive that this won’t a problem for too long.” Rarity started up the stairs. The others all breathed out sighs and began to curl up. Fluttershy and Pinkie shared a cushion, while Rainbow laid down on top of one of the many shelves. Twilight felt Spike put his head on her back, trying to use her as a makeshift pillow. Her eyes slowly drifted to Applejack, who had covered herself in a blanket.

The halls of the hospital were silent, despite being full of all the new patients. Bio-suit pony patrols littered the halls in a silent and monotonous manner. Many of the nurses had been busy all day, since all the new sick ponies needed immediate attention. Most of the new charges were issued ice dips to counteract the rising temperature, but it did little to help. Sometimes, the ice melted upon dipping the subject, as if they were a furnace wrapped in fur.

The Bio-suits did very little to help with the load, and seemed more concerned in keeping them in the hospital than actually healing them of their ailment. They didn’t even notice that half the patients, including Big Macintosh, were no longer in their rooms.

“Bio-Con Pony Alpha-25 reporting in on third wing. No visible issues in affected ponies. Awaiting update from project head, over.”

Alpha-25 trotted through the hallways with a determined demeanor. His sealed suit flashed with dials and reminders of the current quarantine status. The constant beep was the only sound in the halls, since all the patients were apparently looked in their rooms. He checked a few rooms, peering through the plastic sealing that had been installed on the interior of the door. There was some fog, but otherwise it was pretty clear.

Inside, a Pony was laying in a cooling unit, a desperate attempt to lower it’s body temperature. It was sad to see such a nice creature hooked up to a series of monitors and tubes. Alpha just looked on with mild interest. As a Bio-Con unit, his entire job was to further the study of science in Equestria, which had, until Doctor Whooves had appeared, been a relatively under-developed field. As such, it was insisted that this outbreak be handled by the E.S.R.D, or Equestrian Research and Science Division, rather than a magical cure.

Not like magic could help. For some reason, it had no affect. Especially on Patient Zero, or “Big Macintosh”, who actually exhibited accelerated symptoms upon exposure to healing magic. He was then confined to the lower, secure levels after he attacked a nurse and two of the Bio-Con units, Gamma and Theta.

Alpha turned his head up. While lost in his thoughts, he had reached the edge of the hall, and now stood at the elevator entrance. He shrugged and tapped the button with his hoof. The light showed an up arrow. He started to whistle a little tune, just trying to kill the time. The doors let out a soft ‘ping’ and promptly opened. Alpha moved inside with haste.

The elevator shuddered for a moment before closing the doors and starting down. The ride was smooth enough, but Alpha couldn’t help but feel like something was off. He looked to the guide, which was currently heading to the basement level. he decided he might as well check it out. The red number above the dashboard lowered in digits every second, until it finally pinged again, now displaying a a letter. ‘B’

As the doors slide apart, Alpha found himself shoved into a network of pipes, and cables. Steam shot out in places where the pipes didn’t full meet. Alpha also noticed that in some places, the pipes were missing entirely, ripped from the walls, and the same case went for metal wall sidings. It was as if the building had been scavenged from the inside. Alpha started moving along the walls, noting that even more and more metal, sometimes even cables, were missing. In some areas, the excess material had been completely removed, leaving only the framework of the halls.

“Hisssssssssss”

Alpha turned his head. Had he been a regular nurse, he would have assumed it was just another pipe letting off steam, but he was a conditioned Biological Containment pony. He instinctively knew that in a quarantined outbreak, it was his duty to inspect the cause of mysterious events. A smile spread on his face, and he thought about how cool that just sounded.

He weaved through the pipes, following the series of hisses and various groans to what he perceived to be the source. Soon, he began to hear the clanging of metal on metal. Something snagged his front hoof, drawing his attention downwards.

A bundle of cables had been routed into the wall, glowing a faint and pulsating yellowish orange, and then tangled onto his leg when he wasn’t looking. The cables lead out under a loading dock garage door.

Must be the heavy equipment storage, Alpha thought to himself, maybe a few guys are just moving around some new tech.

Alpha snuck around to a door on the other end of the wall. Instead of having to use the loading controls, somepony had been smart enough to install a regular, knob operated door. Alpha quietly turned the handle and let the door swing ajar.

His first reaction was to call for help, but his voice got lost in his throat as soon as the thought occurred to him.

Standing a mere dozen feet away were half of the detained ponies. Except they didn’t look like true ponies anymore. they’re eyes were all glowing that bright yellow they had seen before, but now, that light was constricted by a black growth on the outside of the eyes, which gave them a tunnel-vision look about them. Their fur had fallen off, leaving their pale hides exposed in the faint working lights they had set up.

One turned to another one, speaking some language that didn’t sound like anything Alpha had ever heard. On each of their backs was a metallic saddle, adorned with what appeared to be a screw sticking out of the back, glowing the same faint yellow as the cable leading into the room. Two additional screws were riveted into the hips of the device, connected to the main screw through hoses.

All around them was the fruits of their labors. They had built some strange devices and glass pods, which were stuffed full of weird cocoons. Above that, weird lights glowed from the metal sheets that had been cut into triangular shapes. More monsters were lining the room, all tending to pods, or strange, dark metal saddles with four large stacks that emanated heat. In a cell a few yards away, three nurses desperately knocked against the glass prison, screaming silent pleas.

One of the laborers stumbles over and pressed a button on one of the consoles. the nurses turned their heads to another side of the prison, to a vent in the wall. The vent began to shake, then violently burst apart and spewed out a swarm of beetles. They attacked the nurses, attempting to crawl into their noses and mouths as if they were like a walking nest just waiting to be colonized. The nurses eventually fainted, and the insects wasted no time in entering their new hosts.

Another strain of the creatures emerged from one of the pods in the corner. It, like the ones around it, was completely hairless and pale. However, it was a bit more unique, and much more monstrous. Six glowing eyes penetrated the dim lighting around it, 3 eyes lining either side of it’s head. In place of its mane were a series of spikes, all placed in a straight line down the center of its skull and stopping around the middle.

A laborer rocked back onto it’s hind legs, revealing cloven hooves that seemed to bend like some sort of manipulator. It walked, hunched over like some sort of dinosaur, to one of the saddle racks. It hefted off one of the four pronged ones and turned back to the new creature. The new one had collapsed to the floor, growling with a mouth containing saber-like fangs. It helplessly clawed at the ground with the same cloven hooves as the workers, desperate to escape from some form of pain unseen by Alpha.

The laborer bent over and placed the saddle gently on its back, then slammed it down with both feet. Blood trickled from the edges of the saddle as the creature writhed in even further agony. Cables shot out from the base of each rectangular tower and drilled into the elbows of it’s legs and the sides of the torso. Steam shot out from all the tips at once, and the creature went silent. It pushed itself up and tested the stability of the new attachment.

“What in the name of Celestia-” Alpha placed his hoof over his mouth to stop himself, but it was too late. They heard it.

All the creatures swung their heads around, their glowing eyes reflecting cruelty in just a simple glance. The laborers hissed violently at the intruder, and the new one roared.

Instinctively, Alpha turned and started for the exit behind him, backtracking to the elevator.he got to the two sliding metal doors of the elevator and smashed the button repeatedly. The light flickered, but no sound indicated how close the elevator really was.

The creatures behind him quickly pursued as he abandoned his wait at the elevator, and made a break for the nearest stairwell. They were deceptively fast after what he had witnessed in their sluggish movement. Their cloven hooves tore any stray wires out of the way, and he could only imagine what they’d do to him.

Alpha made his way threw the maze-like basement in search of the exit door. He turned the corridor to see a long hallway to a large door marked with a sign ‘stairs’. Frantically, his legs began to move on their own. He broke into a full gallop for the stairs, but before he could get half way there, his hoof caught on a wire, causing him to stumble for a few steps.

The pony recovered his balance, but not before one of the monsters was able to tackle him. He tried to squirm and get free, but the weight of the monster held him down. Alpha stopped his fight as a large shadow loomed over him. He felt something turning him over, and upon being forced belly-up, he was met eye to glowing-eye with one of the larger ones. On it’s wrist dangled a few scraps of paper, labeled with a messy but still legible name: Big Macintosh. Alpha felt a hoof slam into his face and then everything went black.

While drifting in and out of unconsciousness, they threw him into the same room the nurses had been, only after they had removed his sealed helmet of course. He pushed himself up with some extra effort and looked outside from the cell, obtaining a small glimpse of a large framework that held multiple pods seemingly filled with the beetles that he observed earlier. Near one of the ends, some of the labor drones were attaching some form of an advanced engine. Immediately, it dawned on him what they were going to do with such a thing.

Big Mac approached the console with the button and looked at him with his glowing yellow eyes. there was a complete absence of emotion in the mares gaze, confirming that whatever this thing was, Big Macintosh was long gone from its conscious mind. The creature hissed, pressed the button, then turned away to perform other tasks in the workshop. Alpha’s eyes wandered up to the dreaded vent, where the sound of wings and tumbling bodies began to ring out. His throat tightened.

And then the vent burst.

“C’mon guys, just a little farther!” Pinkie hopped around the group, as enthusiastic as ever. Applejack kept her head down the entire time they walked, still feeling upset over the development of yesterday.

The mane six were headed to the Apples Orchard that had recently been quarantined. Over the long night, a large, white plastic fence had been erected around the entirety of the farm, which was consistently guarded by a Bio-Con pony every few yards. They were all in the same white sealed uniform as the ones from last night. In fact, they might as well have been the exact same ponies as last night.

When the group got close to the wall, two of the White ponies jumped out, waving some sort of baton.

“Return to your home, citizens. this area is under the jurisdiction of the E.S.R.D. That means it’s off limits to the populous for the time being.” The Bio-Con pony spoke with a calm and detached tonality, speaking from a script rather than to fellow ponies.

“This is my home,” Applejack began to move closer to the guards, “You no-good, uniformed wearin’ pans-”

Twilight shoved a hoof in front of her friends mouth, cutting her off. Rainbow Dash wasted no time in grabbing the back legs of Applejack. She pulled back at an angle, stopping the forward march, and keeping the angry farmer at bay. Twilight looked to the guard and shot im a look.

“Tell Doctor Whooves that his friend, Twilight Sparkle is here. He’ll give us clearance.”

The guards turned to each-other. The made some form of silent exchange under their masks before the smaller one closet to the group nodded and galloped off. Guard number two slowly pan his head across the group, his eyes examining the all behind his dark visor.

He inclined his head to the left and began randomly to randomly nod. The baton shrank down, and he placed the smaller rod on his belt, where it clipped on with a confirming ‘click’.

“You’ve received clearance, civilians. Please follow me to Doctor Whoove’s work station. We also apologize for any misunderstanding that has occurred.”

“Thank you. lead the way.” Twilight nudged her head at the group, issuing a silent ‘follow me’. The others all nodded and followed, but only after Rainbow Dash let go of Applejack’s back feet. Dash landed and tried to apologize, but Applejack had already started off after the group, so instead, she lowered and shook her head.

The camp inside was unlike anything the group had seen before. Tents were scattered all around the center, and the trees had been encased in wrappings. Dozens of horses littered to paths, some heading into the orchard beyond the sight of the group, while others still headed through the house itself. They all seemed to meet, however, in the main tent, the largest one that lay in the center of the mighty operation.

Ponies in strange suits trotted back and forth, carrying out various tasks in silence as efficiently as possible. Fluttershy began to shake. Rarity began to whisper some comforting words to her, trying to keep her going long enough to reach the central tent. The guard looked over his shoulder at the group again, then pulled the plastic sheet away from the entrance.

Inside the tent, dozens of Ponies were working on machines of various sizes, some twice as big as the ponies themselves. There were plastic boxes set on tables, where ponies worked through thick gloves sealed to the box, interacting with glowing chemicals and pouring solutions. Occasionally, a second pony would walk by and pick up a box of sealed samples, moving them to another table where a third pony would take them away once again.

“Now what’n the hay could they be up to in here?” Applejack’s eyes remained in a scowl, which frightened some of the other busy ponies.

“Ladies, I’m glad you came!” The Doctor lifted up a pair of goggles from his eyes, “I was getting ready to send for you. We’ve made some amazing breakthroughs in just the night alone!”

The mane six stopped and glared at the Doctor. He blinked a few times before picking up on the vibes they were sending him. He cleared his throat and turned back to the table. There was a moment of silence between the groups, which was broken when the Doctor waved them over to his workstation. They grudgingly complied and approached his table.

There were notes splayed over the table, with scribblings covering every inch of the paper’s space. Numbers and calculations dotted notebooks that surrounded the Doctor himself. He leaned back, using both his front hooves to move the paper around. He worked quickly, retrieving one of his many folders. Manila in color, it was emblazoned with a bright red stamp reading ‘CLASSIFIED’ across the front.

Inside were a series of notes, all marked with the letters E.S.R.D in the corner. He picked up a few and placed them down, then made a motion with his hoof to another pony. It brought over a thick case, covered by a clouded plastic wrap and gently placed it on the table.

“I ask that you not share what you see. In fact, I’m only showing this to you as an apology for not telling all of you earlier.” And with that, he ripped off the sheet.

Inside the case was a beetle the size of a grasshopper. It hopped around and clawed at the casing, causing some of the girls to jump back. Dash squinted and tried to get a closer look. She noticed the large incisors and sharp wings that fluttered about in the insects impatience

“What does this have anything to do with people becoming sick?” She asked while turning her head to view the insect from multiple angles.

“Everything, actually. What you see here is a mutation that occurs in the insect populace that find themselves exposed to the viral strain.” The Doctor placed a note next to the case, which Twilight quickly picked up and skimmed through.

“‘Exposed subjects exhibit rapid mutation into new species’? What do you mean by that?” The group leaned over Twilight’s shoulder, trying to get a peak at the notes.

“It means what it says, Twilight. Any organism exposed to the viral contaminant undergoes a mutation that affects the genetic code. This little bug could have been something such as a lady-bug before exposure. You can see the results of a simple insects exposure, now imagine what this could do to the populous should it break out.”

Applejack turned her head side to side, as if looking for something.

“What about that barrel of apples, you know, the one all them ponies ate out of and started dropping like flies?”

“Those apples were destroyed after we retrieved a sample of the purest strain from that strange dust coat. In fact,” The Doctor lifted another file up and plopped it onto the desk, “Those insects in the casing were extracted from the barrel, but at the time they were just crickets.”

“This thing was once a cricket?” Rainbow asked, a touch of disbelief in her voice.

“Now do you understand why we had to quarantine the area?”

“Um, I’m sorry to interrupt, but what about all the other ponies who were getting sick?” The group turned to look at Fluttershy, whose voice was barely audible in the busy environment. All eyes moved back to the Doctor, expecting an answer.

“We ran some tests on the blood from Subject Zero, er, I mean Big Macintosh. I’m afraid the results were similar. The viral agents were converting his cells and reprogramming them the same way that these insects were.”

Applejack took a step back. that couldn’t be possible, it wasn’t possible. Nothing could turn somepony into something else. Pinkie Pie had even stopped hopping at this point, stunned at the shocking news. The air suddenly grew chilly between Doctor Whooves and the mane six. Nopony said a word, they just tried to take everything in.

Finally, Rainbow Dash broke the silence

“If they’re changing, what are they changing into?”

“I have named the strain after the ancient mythical monsters of Equestrian lore, the fearsome Chimera, which was supposedly a conglomerate of many different creatures. However, someone in our upper departments has dubbed it the Chimare virus, since it seems designed to be most effective against the equestrian population.”

“Chimare? Is it reversible?” Twilight placed the notes back on his desk.

“We’re not sure, but I can promise you that we’re working on this as intently as possible. As long as we can contain the outbreak to the hospital, then we should be able to continue our research and hopefully find a cure. Luckily, the virus needs a colder vector than our current environment.” Doctor Whooves pointed to the orchard, “For example, this air is perfectly safe to breathe and interact freely in. The viral presence also disappeared on the apples after a few hours from the heat.”

“Then whats the condition of the other ponies, the ones at the hospital?” Asked Twilight.

The Doctor furrowed his brow and turned to one of the suited ponies next to him.

“When was the last report?”

Without warning, a blaring siren erupted from a pillar outside, giving a very distinct air-raid horn tonality. Every Bio-Con pony dropped their tasks and galloped outside. Even Doctor Whooves appeared to be frightened. He looked back to the group, frowned and motioned to follow him outside. They wasted no time and trotted right after him.

The ponies all stared into the sky, staring in wonderment. A large black streak was tearing through clouds Their first assumption was that is was the works of some of the pegasi, but when they looked closer, they noticed a large conical missile. It appeared to be the origin of the contrails that crawled across the sky, quickly making its way to the center of Ponyville.

“What in Celestia’s name is that?” Applejack shouted, fighting to be heard over the siren.

Doctor Whooves stepped forward, focused completely on the new problem.

“It’s nothing good, nothing good at all.”

And with that, the missile began it’s descent, right into the heart of Ponyville.

To be continued...