The Aftermath
It all started with a simple cough. Rainbow Dash was charged with community service for her reckless acts against Ponyville and all its inhabitants. She had to clean up every single joke cookie that had been dropped during Pinkie's prank, which she found fair, because even she agreed that her behavior was reckless, and that she had gone too far. Her only tool to clean up the cookies was a simple aluminium stick with a metal spike on the end of it. She couldn't even use her hooves.
The first day was a cloudy day when she arrived just outside of the Sweet Apple Acres barnhouse. Along the way to the barnhouse, she had noticed the massive amounts of cookies she would have to clean up, and since she couldn't use her hooves, she couldn't just pick up the cookies along the way to Sweet Apple Acres. She knew it was part of her punishment, but seriously, did insult have to be added to her injury? She sighed, as she passed the gateway to Sweet Apple Acres.
Applejack was waiting for her just outside of the barn, where she would be watching Rainbow Dash, making sure that she did her job the RIGHT way. Applejack knew how Rainbow Dash was when it came to doing a job, and she wasn't going to get off easy.
"What? Did you seriously think that nopony wouldn't be watchin' ya' to make sure you did things right?" stated Applejack with a chuckle.
Rainbow Dash expressed an annoyed look, along with a small cough, as she walked into the barn, guided by Applejack, pointing her hoof into the barn. She had not realized just how many cookies had been consumed by Rarity, Applejack, and the CMC, until Celestia's sun shone upon the inside of the barn. Rainbow ink covered the barn floor in the areas where Rarity, Applejack, and the CMC had stood the night before, along with tons of cookie crumbs. Rainbow Dash sighed, as she stuck the metal spike into the very first cookie.
Applejack stood outside of the barn, leaning against the barn entrance with a single piece of hay in her mouth. Cookie after cookie was picked up, as Rainbow Dash caught a sniff of something among the barn. She figured it was just part of the natural smell of a barn, and quickly put it aside, continuing to peck at the cookie remains. The longer she continued her duties though, the more she could smell that same odor. The smell wasn't putrid, but almost a smell of a newly opened package. Something you normally wouldn't smell in a barn.
Barns would normally smell like three things. Barn animals, alfalfa, and barn wood. This smell was strange, and immediately made Rainbow question where the smell was coming from. Where could it be coming from? This barn was old, and the scent was of something new.
"Hey Applejack?" asked Rainbow Dash. "Do you smell that?"
Applejack lifted her hat from her eyes, and took a few good sniffs.
"The only thing I smell is somepony trying to get out of workin," replied Applejack in a stern voice.
"No, I'm serious," stated Rainbow Dash. "I swear I'm not making this up, AJ."
Applejack didn't respond, and just lowered her hat over her eyes once more. Rainbow Dash knew she wasn't going to get anywhere with Applejack, so she returned to her labor, attempting to ignore the smell. It was hard to ignore. The smell had become obvious, and even caused Rainbow Dash to cough massively. It was no small cough, but a scary one. She had coughed when she arrived as well, when she caught the same smell for the first time.
The longer she remained in the barn, the more the smell grew, making it hard for her to work. She wanted to say something, but that tactic had already failed flat on its face. She had only been in the barn for less than five minutes, and already she was getting a severe headache and even her stomach was starting to feel upset. Her vision had grown blurry from the strange smell as well, causing her eyes to water, and immediately she knew that it wasn't from the hay, because she never had allergies.
Her stomach grew more upset, and even had started to cough again, but this time, the severity of the cough had increased ten-fold. Something was definitely wrong with her, and even Applejack could see something was wrong.
"Rainbow, are you ok?" asked Applejack in a concerned tone.
Before Rainbow Dash even had a chance to respond, she dashed out of the barn. It was clear that she was in a hurry, but she didn't go far, only to the side of the barn. On the side of the barn, the pegasus vomited protrusively onto the dry ground. It wasn't just one full thrust of vomit, but five thrusts, as the pegasus started to cry from the burning in her throat. Applejack rounded the corner, noticing her friend in pain and agony. The sight frightened Applejack, as a cold sweat formed upon her forehead.
Rainbow coughed massively, as she planted her flank on the ground, and continued to cry. Applejack didn't know what to do, because she had never seen anypony this sick before. Apple Bloom had been sick with the flu before, but it was never this bad. What could have possibly caused it? It was clear that Rainbow Dash wasn't faking this. Without a doubt, this was real.
"Rainbow? Are you okay?" asked Applejack, keeping her distance.
Rainbow didn't answer, as she slowly turned her head toward Applejack. Rainbow Dash's face was as pale as a ghost, her tears were not tears, but blood drops, and the content that Rainbow had vomited was nothing but a pure massive puddle of what looked like blood. Applejack jumped back from the sight she was seeing, as Rainbow Dash muttered something.
"H-H-Help me," muttered Rainbow Dash, as she collapsed to the ground.
"RAINBOW DASH!" yelled Applejack, rushing to Rainbow Dash's aid.
She watched, as Rainbow's mouth started to leak a massive amount of blood, and the pegasus grew weaker with each passing second. Applejack was more scared than ever before, as she felt tears escape her eyes.
"SOMEPONY HELP!" she yelled, attempting to keep Rainbow Dash conscious. "Stay with me, Rainbow! Stay with me!"
At Ponyville Hospital, Applejack sat in the hall just outside of Rainbow Dash's room, awaiting the results of the tests that were ran on the pegasus. Applejack had not decided to tell the others yet, until Rainbow Dash's condition was determined to be severe or mild. It had to be severe though. Rainbow was crying blood drops, and was throwing up blood. Not your common flu or cold. Applejack was still traumatized at the sight of Rainbow Dash's condition.
From out of Rainbow Dash's room, Nurse Redheart stepped out of the room, closing the door behind her. Once the door was shut, she approached Applejack with a clipboard in her grip.
"Well?!" asked Applejack.
"After running multiple tests on her, the results all come back negative," assured Nurse Redheart. "Nothing was found in her blood tests and her oxygen and blood pressure is normal. Sorry to say, but we can't find anything wrong with her, so the best thing we can do, is give her some medication for her nausea."
"Ya'll can't be serious?!" exclaimed Applejack. "She was crying blood! She was vomiting blood! Something is wrong with her, and as doctors ya'll should be able to fix her!"
"I'm sorry, but there's nothing we can do," concluded Nurse Redheart. "My suggestion is for your friend to get lots of rest, and if her condition worsens, take her to Canterlot. I'm sure that she can get some professional help there. For now, have your friend take these."
Nurse Redheart held out her hoof, holding a small bottle of nausea medication. Applejack took the small bottle and placed it under her hat.
"I wish there was more we could do, but best of luck to you and your friend," said Nurse Redheart, as she turned away, and walked off.
Applejack stood from the bench, and clenched her hoof.
"I'm not going to let Rainbow suffer," she stated. "I'm sure Twi' can figure somethin' out in her collection of books. Just gotta stay positive, and not jump to conclusions."
She took a seat again, waiting for a doctor to come and discharge Rainbow. In her heart, she struggled to figure out what could be wrong with Rainbow, but nothing came in the silent hall.
Once Rainbow Dash had been discharged from the hospital, Applejack wasted no time in taking the suffering pegasus to Twilight's castle, where she hoped Twilight could find out what the cause was. To prevent any other pony from getting sick, Twilight cast a spell on Rainbow, so that she was enclosed in a bubble of magic. Much like what Cadance had done when they had to take care of a not-so-sick Discord.
Twilight scrambled through the countless books she had on severe illnesses, focusing on looking for keywords. The alicorn was surprised when Applejack had mentioned Rainbow crying blood. That's usually something that you'd only hear or see in a horror story, but for it to really be happening, frightened Twilight.
She continued to flip through every book, page after page, only to find nothing on an illness like Rainbow's. There were similar illnesses that involved severe nausea where the victim of the illness vomited blood, but nothing came up on the victim crying blood. The more time that passed, the worse Rainbow's condition became. She was coughing horribly, and all that came out of the cough was blood. Rainbow looked weak, and her blue coat and rainbow mane had fallen to pale colors. Everypony was starting to assume the worst, but what could possibly have caused this?
Out of her frustration, Twilight tossed aside her last book on severe illnesses.
"I can't find anything!" said Twilight, harshly. "I've looked through every single book I have, and nothing comes up on somepony crying blood!"
The room fell to silence for a moment, until it was interrupted by the sound of Rainbow coughing again, and the sound of blood splatter against the dome of magic following it. The pegasus was on her final lifeline, and Rainbow knew it. Applejack felt guilt come over her, looking at her suffering friend. She suddenly remembered something that could possibly have something to do with Rainbow's sickness. With no further options, she had nothing to lose, except her friend, so she spoke out.
"I-I actually have an idea of what could've caused this," said Applejack in a low tone.
"What is it?" asked Twilight.
"Well, Rainbow was doin' her community service, and somethin' kept botherin' her in the barn," replied Applejack, feeling tears form in her eyes. "Some sort of smell."
Twilight looked at Applejack with a confused look.
"A smell?" said Twilight.
Applejack nodded her head as a response.
"What kind of smell?" asked Twilight.
"I don't know," replied Applejack, her voice full of sadness. "I thought she was tryin' to get out of workin', so I didn't ask her about the smell."
Twilight could see that Applejack was troubled, and she didn't want to question Rainbow Dash, due to her current condition.
"Well, there's only one way to find out, I suppose," stated Twilight.
Applejack knew what Twilight meant, but deep down, she was afraid to go back. The sight of Rainbow crying blood would forever haunt her memories for as long as she lived, but she knew that Twilight was right. It might be too late for Rainbow, but it wasn't too late to prevent another death, so she nodded her head.
"Spike can watch Rainbow while we're gone," assured Twilight. "As long as the spell holds out, he should be fine. Let's just hope that Rainbow's condition improves by the time we get back. Otherwise, I'm afraid we might have to accept the truth."
Applejack agreed, as her along with Twilight trotted out of the room, not hearing Rainbow's warning.
"D-Don't go. It's n-not s-safe."
Back at the barn, Twilight and Applejack arrived, approaching the area with caution. It didn't take less than a second of stepping into the barn for the smell to hit both of them. It had grown stronger since Rainbow Dash's sudden sickness, and to suppress the smell, both of them covered their nostrils.
"What is that smell!?" exclaimed Twilight. "It smells like somepony's mane being burned!"
The smell was terrible, causing an immediate headache to build up in both of their heads. It was unbearable, causing both of the mares to immediately back out of the barn, attempting to breathe in as much fresh air as possible. One question still remained though; where was the smell coming from? Seeing that she had already failed her friend once, Applejack took the task of finding the source.
"I'll go," stated Applejack. "It's the least I can do for Rainbow Dash."
"Just be careful," concluded Twilight.
"I will, sugarcube," replied Applejack, stepping back into the barn.
She kept her nose covered, approaching the area where Rainbow Dash was when the events of that day went downhill. Applejack's head pounded as she came to a stop, noticing that the smell had become stronger. The source was near, so she quickly looked around, trying to find the source of the smell. Her eyes had started to water, making it hard to focus, but for her friend, she was going to find the source. All that was in the area was hay, so the source had be coming from somewhere she wouldn't expect.
Out of the corner of her eye, she spotted some of the joke cookie rainbow filling smothered on the ground, next to the large number of boxes of the other joke cookies.
"Could that be..."
She stuck her nostrils down toward the rainbow filling, and took one sniff. Immediately, the smell had caused her nose to burn, and her stomach to turn. The source was the joke cookie filling, but why would such a harmless thing cause somepony to get deathly ill, and what was causing the foul odor? She didn't waste no time in trotting out of the barn, and took in heavy breaths of fresh air.
"Did you find the source?" asked Twilight.
Applejack raised her head.
"It's the rainbow fillin' from the joke cookies," she confirmed.
"What?" questioned Twilight.
"I don't know what it is, but there's something in the rainbow fillin' that makes ponies sicker than a desert on a harvest moon," replied Applejack.
Twilight's face fell to a look of horror, knowing that Applejack was being serious.
"That's good. Now we know the cause, so all we need to do is dispose of the joke cookies," stated Twilight.
"I'm afraid it's not that easy, Twi," spoke Applejack in an unsettling tone. "Ponyville is littered with those cookies, and unless somepony has a cookie magnet, we're in trouble."
Twilight's eyes widened, as she looked at Applejack, noticing blood starting to leak from her eye sockets. Her entire body shivered, as she backed away.
"Twi? Are you okay?" asked Applejack, following an unexpected cough.
Tears started to fill Twilight's eyes, knowing her friend had come down with the same sickness as Rainbow Dash. She didn't want to see Applejack suffer a slow and painful death, so she decided to put her friend out of her misery.
"I'm sorry," said Twilight in a low voice. "Please forgive me for this."
Twilight shot a powerful beam of magic from her horn, hitting Applejack and throwing her against a nearby apple tree. The impact had managed to break Applejack's spine, along with countless other bones. Twilight felt horrible, as she approached her friend. Applejack was bleeding horribly against the tree, as she saw Twilight approach closer.
"Twilight!" she pleaded, coughing out massive amounts of blood. "Wait! Please!"
Twilight didn't hold back this time, and charged a stronger mass of magic, firing it directly at her friend. Applejack didn't speak or breathe, as she died seconds after impact with Twilight's blast. The farm pony was gone, and free from dying a horrible death. Twilight fell to her knees, and cried massively. She felt horrible. She had just killed her friend. One of the first friends she had made when she came to Ponyville.
Despite her killing a friend, she couldn't let Applejack die in vain. Ponyville was in deep peril, and even though she felt it was already too late, she pressed onward into Ponyville.
"Please, let there still be time," she pleaded, as she trotted toward Ponyville.
Along the way to Ponyville, the worst had become obvious. She spotted countless ponies on the sides of the street, each deathly ill and in a pile of their own blood. How could something like this happen to Ponyville? A place of happiness and friendship. The one place you would never expect something like this to happen. It dawned upon Twilight. It was already too late. The smell had plagued Ponyville, and everypony had become infected.
It became obvious, as Twilight came to Ponyville Center, where she saw countless ponies struggling to stand. All of them were as pale as a ghost, and were coughing massively. From among these ponies, she saw Fluttershy and Rarity, each with tear streams of blood down their faces. Fluttershy. A pegasus of pure kindness, infected with a ruthless disease. Rarity. A unicorn of fashion and generosity, doomed to a slow and horrid death.
Twilight didn't know if she could handle killing another friend, but at the same time, she didn't want to see her friends suffer. She was unsure of what to do, until she heard Fluttershy speak out as loud as her weak voice could manage.
"Twilight, please, make the pain go away!" pleaded Fluttershy, her voice full of sadness and pain.
That was a plea for death that she couldn't turn down. Fluttershy was her friend, and as a true friend, she was not going to let the kind-hearted pegasus suffer. Twilight approached Fluttershy, and placed her hoof against the neck of the tender pegasus. She couldn't watch, so Twilight closed her eyes, and pressurized her hoof downward, until she heard the neck of the pegasus snap. That was one sound that Twilight would never forget.
Tears escaped Twilight's eyes, waiting for Rarity to ask the same request, but until Twilight opened her eyes, she didn't realize that Rarity was already dead. The unicorn's neck had been snapped by somepony, and it didn't even take a second for Twilight to figure out that Fluttershy had put Rarity out of her misery. That was three of her friends, dead.
She had no idea what to do now. Go back to the castle? Look for Pinkie? Try to find a cure? If she went back to the castle, she would only be confronted with a dead Rainbow Dash and a progressing Spike. There was no need to go looking for a lost cause. If everypony was affected, not even Pinkie Pie, an earth pony able to break the laws of physics could escape an epidemic. Even if she was gone from Ponyville, it would eventually spread. Lastly, she was already infected, so a cure wouldn't matter.
Her only hope was that this entire thing was just a terrible dream, and that she'd wake up any second. She blinked multiple times, and after about the third try, it became obvious that this was no dream. This was real. Hope was gone.
28 days later
Population of Ponyville: 1
The once populated Ponyville is now a land of rotting corpses, with only the smell of the joke cookie filling being present in the air. All business is dead. All ponies are dead. All except one. Princess Twilight Sparkle. 28 days have passed since she was infected, and slowly the effects have taken hold, but she still lives among the many ponies she once knew as her friends. Her strength weakens, her body deteriorates, her grip on reality slips. A noise in the distance erupts among the quiet town, the sound of numerous bones shattering, and blood leaking from open wounds.
A distant heartbeat fades to nothing, as the town falls to pure dead silence. Her torture ends, as a new sound fills the air. Pecks from the vultures that have circled the town for weeks. It's done.
Population of Ponyville: 0