Author's Note

Hi everyone! this is a story I've been working on for about 4-5 years, and I finally decided to put it into writing! The story will be split up into separate parts, and I can't wait to share it all with you! All original characters have designs that are on my deviantart! https://www.deviantart.com/snonsy/gallery/94224603/zaf
Thank you for reading!

The beginning

Every year, the Zap Apple harvest brought with it a bounty of magical fruit, and from these apples came the beloved jars of Zap Apple Jam. Year after year, the Apple family followed their traditions to ensure the harvest went off without a hitch, and with each passing season, their products grew in popularity. Nopony could have ever imagined that something could go wrong—that the Zap Apples themselves would be at the root of such terror and tragedy. It seemed like any other harvest…

Big Mac and Applejack gathered the Zap Apples, while Granny Smith and Apple Bloom worked on turning them into jam. To the residents of Ponyville, everything appeared perfectly normal as they bought their jars.

"I reckon this might be our best year yet!" Applejack cheered, handing a satisfied customer their share. "I swear, Big Mac, those apples were bigger than ever this season!"

"Eeyup," her brother replied. He had noticed the unusual size as well. Although it struck them as odd, they didn’t think much of it—after all, they'd been giving the trees extra care. "I'll have to stop by Fluttershy's cottage later to see if she thinks this batch turned out better," Applejack mused. The gentle pegasus had been the first customer that morning, and AJ was eager to hear her thoughts on the latest harvest.

✦ . 　⁺ 　 . ✦ . 　⁺ 　 . ✦

Back in her cozy cottage, Fluttershy had just opened a jar of the delectable rainbow jam. "Oh my, this looks even more colorful than usual!" she hummed excitedly. "I bet it will be delicious!"

The pegasus set to work making herself a sandwich with the jam, her eyes sparkling with anticipation as she took a bite.

"Oh!" she gasped, her face lighting up. "It’s... absolutely wonderful! I’ll make Discord a snack too; I’m sure he’ll enjoy it."

Carefully wrapping the sandwich, Fluttershy tidied the counter and put everything away. Discord would be over for their usual tea later that afternoon, and she decided she would give him the sandwich then. Nothing felt amiss about what she had eaten, and the pegasus continued her day, eagerly anticipating the time she would spend with her beloved friend.

As the afternoon approached, Fluttershy began setting up for tea. She arranged a delightful spread of snack cakes for herself and Discord to enjoy. Her beloved pet bunny, Angel, kept trying to sneak bites when she wasn’t looking, leading to a playful chase as she attempted to reclaim the treats.

In the midst of this amusing ordeal, she hadn’t noticed that Discord had appeared right in the center of the room.

"Fluttershy, my dear," rang Discord’s voice, his tone laced with amusement. "What in Equestria are you doing?"

He couldn’t help but chuckle at the scene before him. As much as he adored his friend, he still relished the momentary chaos caused by her pet.

"Oh, Discord!" she squeaked, her cheeks flushing. "Angel was trying to take our food, and I, um... I guess I got a little sidetracked trying to get it back."

With a snap of his claws, Discord returned the food to its rightful place and guided Fluttershy and himself into their respective seats. "Well now, that should fix everything," he chuckled. "Now, my dear, do tell me what you have planned for us today?"

"Oh, right!" Fluttershy gasped. "Today marks the beginning of Zap Apple season! I bought a jar like I do every year, but this time it tastes absolutely out of this world." She stood from her seat and trotted into the kitchen to retrieve the sandwich she had prepared for her friend that morning. "It was so yummy that I wanted you to try it!"

The yellow pegasus beamed up at Discord as she handed him the snack. The Draconequus examined the sandwich closely, his curiosity piqued.

"Why, thank you, Fluttershy!" he exclaimed, taking a bite. As he savored the flavor, Discord sensed something unusual in the energy of the jam. However, he decided against mentioning it; he trusted that Fluttershy would never intentionally harm him. It tasted fine, after all—perhaps it was just in his head. On the other hoof, he couldn't help but notice that Fluttershy seemed a bit pale.

Fluttershy settled back into her seat, sipping her tea. She felt happy to share with Discord; after all, he was one of her dearest friends. The two exchanged stories from their week, laughing and enjoying each other’s company. All was well until Fluttershy suddenly erupted in a fit of coughing.

Discord was by her side in an instant. "Oh dear," he said, his brows furrowed with concern. "Fluttershy, are you all right?"

Fluttershy’s coughing continued for a moment before it settled into a soft wheeze. She breathed heavily until she could speak again. "Yes, I think I'm okay," she whimpered. "I’m so sorry, Discord. I have no idea what just came over me."

The Draconequus frowned, gently picking her up in his arms. "Nonsense! You don’t need to apologize for coughing, but you are going to bed."

Discord carried Fluttershy up to her room, gently tucking her into bed. "What you need right now is rest, my dear," he said. "If you need anything, just call my name."

In a flash, he was gone, leaving Fluttershy alone in her room. She hadn’t even noticed how unwell she was feeling. "I hope I didn't get anypony else sick by being out today," she sighed, turning onto her side and nestling under her blanket. Her head was pounding, and her thoughts felt a bit clouded.

✦ . 　⁺ 　 . ✦ . 　⁺ 　 . ✦

About a week had passed since the Zap Apple harvest. The Apple family had made considerably more this year than in previous seasons, and Applejack was thrilled to tackle the long list of chores around the farm. Old wood had been replaced, peeling and faded paint refreshed, and critter pens repaired. She and Big Mac had worked hard to get as much done as possible.

Wiping the sweat from her brow, the orange earth pony smiled up at the freshly painted barn. "Now that’s what I call a good day’s work," she said with satisfaction.

Applejack put her tools away and took a much-needed stretch. She was happy to have finished the work; it had been a busy week, and she hadn’t had much time to see her friends. Eager to catch up, she headed into town after a refreshing shower.

It didn’t take long to find most of the group. Rainbow Dash, Pinkie Pie, Rarity, and Twilight all greeted her warmly, but the absence of a certain soft-spoken pegasus was noticeable to Applejack.

"Say," Applejack spoke up, "where's Fluttershy? I'm mighty surprised she's not here with y'all."

The mares exchanged worried glances before Rarity stepped forward. "Oh dear, she’s been quite sick the past few days," the unicorn said with concern. "She’s practically bedridden. Discord’s been taking care of her."

Applejack’s brow furrowed. Fluttershy rarely got sick. Tipping her hat to her friends, she said, "I think I’d better go check on her." She turned toward the direction of Fluttershy’s cottage. "I’ll catch y’all later, okay?"

With a quick kick of dust, Applejack took off running, while her friends waved and called their goodbyes. They were all worried—Fluttershy had been acting a bit erratic lately.

It didn’t take long for Applejack to reach the small cottage. She knocked softly on the door. "Shy? You doin' alright?" she called. "I came to check on you."

Silence followed for a moment before the door creaked open. Applejack furrowed her brow—nopony had opened the door. Then, she felt a soft tapping on her hoof. Looking down, she saw Angel. The little bunny motioned for her to follow, guiding her upstairs to Fluttershy’s room, though he seemed hesitant to let her in.

From behind the door, quiet banging could be heard.

"Fluttershy?" Applejack asked quietly. "What’s going on in there?"

A grotesque groan echoed from the other side of the door before Fluttershy’s strained voice rasped, "Apple...Jack?"

The earth pony entered slowly, careful not to disturb her friend. The room was dark—so dark she could barely see. As her eyes adjusted, she noticed the shadows of overturned furniture, and she moved cautiously to avoid tripping.

"Fluttershy, where are you?" she asked, squinting in the dimness, trying to make out her friend's form. "I can't see a thing in here."

Slowly, a shadowy figure crept from the corner of the room, stumbling over the cluttered floor. Soft wheezing, followed by fits of coughing, filled the air as Fluttershy approached. "I'm sorry, Applejack. It's just so bright outside, it hurts my eyes," she rasped, coughing into her wing. "I apologize for the mess. It's... a little hard to see where I'm going."

Applejack instinctively covered her snout with her hat as Fluttershy continued to cough. "Don’t worry about it, Shy," she said, her voice muffled behind the brim. "The girls said you’ve been sick. Are you feelin’ any better?"

Fluttershy shook her head weakly. "Um... not really. I... I think I'm getting worse. I can’t keep anything down anymore."

"You really should go to the doctor, Fluttershy," Applejack said firmly. "It ain't good for you to be cooped up like this when you're so sick. I can take you if you need help."

She extended a hoof to her friend, but Fluttershy backed away.

"Oh no, Applejack," she protested. "I couldn't possibly go out and risk getting other ponies sick!"

"Sugarcube, it’s not your fault if you need help," Applejack insisted gently. "You're sick, and you need to see a doctor."

Fluttershy let out a wheezing sigh, lowering her head. She didn’t want to leave the comfort of her home, but deep down, she knew she needed medical attention.

"Okay, Applejack..." she relented. "Just let me find a mask to wear..."

Once ready, the pair set off toward town, with Applejack staying close to Fluttershy's side. She steadied the pegasus when she stumbled and gently warded off other ponies to give her some space.

"I promise you'll be fine, Fluttershy," Applejack reassured her, offering a kind smile.

Fluttershy, concealed behind a mask, sunglasses, and a large coat, walked quietly, not wanting anypony to notice her until they reached the hospital.

Upon arriving, Applejack held the door open as Fluttershy walked in. The receptionist greeted them warmly and quickly checked in the ailing pegasus. Soon, they were escorted to a room, with Applejack sticking close by Fluttershy's side.

"Don’t you worry, sugarcube," Applejack reassured her, resting a comforting hoof on her shoulder. "Doctor Stitch will have you feelin’ better in no time!"

It wasn’t long before the Doctor entered the room and began his routine checkup on the ailing pegasus. Fluttershy was unusually nervous and irritable, a stark contrast to her usual timid demeanor. She hesitated to remove her coat, but eventually complied, bolstered by Applejack’s reassuring presence.

As the coat fell away, both Doctor Stitch and Applejack stood in shock, their mouths agape. Fluttershy had lost a considerable amount of weight in just a week, and the sight was not only concerning but dangerous.

"Oh Celestia..." the orange mare whispered, her voice filled with worry. "Shy... what happened to you?"

Fluttershy furrowed her brow at her friend’s remark and quickly moved to cover her body with her wings. "I told you I... I can’t keep a-anything down..." she huffed, averting her gaze to the wall.

Taking this moment, the doctor checked her eyes, frowning at the sight before him. Fluttershy's eyes had a barely visible glaze, colorful and swirling, unlike anything he had ever seen. It only heightened his concerns.

"Miss Shy," he cleared his throat, "I’d like you to stay overnight for closer observation. We’ll administer an IV to push fluids and keep a close... eye... on your condition."

The pegasus flinched. She didn’t want to stay; she didn’t even want to be there. Her heart raced as she felt cornered.

"I-I... I don’t want t-to be here!" she cried out, her voice filled with panic. "You can’t make me stay! I just want to go home!"

Applejack tried to calm her friend, but her attempts only deepened Fluttershy’s distress. The pegasus was not acting like herself, and it was beginning to frighten Applejack. Amidst the growing commotion, the doctor paged a nurse to bring a sedative, which he quickly administered. Fluttershy’s resistance faded, and she soon collapsed onto the patient bed.

"Apologies for this," he said, noting the worried expression on Applejack's face. "It was the best course of action, given her rising temper. We’ll be moving her to an inpatient room for closer monitoring. You’re free to return home now."

Feeling uneasy, Applejack left the hospital and hurried to meet up with her friends. She quickly informed them of Fluttershy’s ordeal and suggested they reach out to Discord as well. They all agreed, but when he finally appeared in response to their call, it became evident that he was also unwell.

This marked the beginning of the end.

✦•······················•✦•······················•✦

Discord was clearly ill; his body had thinned out more than usual, and his eyes were glazed over with the same swirling colors as Fluttershy. In addition to these symptoms, he was also coughing up a foamy, rainbow-hued saliva. Twilight wasted no time in manifesting protective masks for herself and her friends, eager to prevent them from catching this unknown ailment.

"Discord, what happened?" she inquired, concern etched on her face. "Both you and Fluttershy have the same symptoms—minus the, erm... foam."

The draconequus coughed violently, hacking up more of the substance. "That jam did this," he spat, glaring at Applejack. "Fluttershy, being the wonderful friend she is, made me a sandwich with it. Ever since eating it, I've only gotten more sick!"

His mood shifted rapidly, anger bubbling to the surface almost out of nowhere. Twilight and the others kept their distance as his frustration grew.

"Calm down," the princess said soothingly. "What do you mean the jam did this? It's just food!"

He let out an annoyed growl. "That jam isn’t right. Its magic is all messed up—bad, even. It may taste fine, but I know the difference."

Discord's furious gaze remained locked on Applejack. She had sold that jar to Fluttershy; she had gotten Fluttershy sick, and now she was the reason he was suffering too. Whatever that jam did to their immune systems, his magic was mixing with it, making this illness incurable. He already sensed that time was running out as the illness progressed. Despite his lack of full control, he was painfully aware of what was happening and how he was treating his friends.

Discord didn’t want this. Ever since he learned the true meaning of friendship, his only desire had been to protect his dear friends. But the longer they stayed near him, the more they risked sharing the same doomed fate. He knew Fluttershy’s illness couldn’t be cured, and deep down, he recognized that it was his fault for being near her after contracting it himself—that he was the reason she would perish.

"Heed my warning, Twilight," he rasped. "Tell everypony to get rid of the jam—ALL of it. Quarantine the healthy ponies and lock the rest away."

With a snap of his claws, he vanished in a flash. Discord's words lingered in the air, haunting and striking deep fear into the mares.

"D-do you girls think that was a joke?" Pinkie asked, giggling nervously. "H-he didn’t sound like he was joking... Please tell me he was joking?"

Rarity and Rainbow Dash exchanged worried glances. He wasn’t joking; Discord had been all too serious, and they all knew it.

"Come on, girls!" Twilight urged, motioning for the other mares to follow her with her wing. "We have to warn everypony. Whatever this is, it’s bad, and we need to make sure nopony else catches it!"

The group raced toward Twilight's castle. She wanted Spike to send a letter to Princess Celestia right away. In her haste, Twilight practically snatched the little dragon up by his tail with her magic, bringing a quill and paper along as they hurried to Town Hall.

"Spike, take a letter," she huffed, settling him on her back with the supplies. "Princess Celestia, I am writing to you with utmost urgency: Ponyville is experiencing a potential viral outbreak. We need quarantine equipment and the best doctors available. I’m unsure how dire this illness is, but Discord has contracted it and warned us to take action immediately. We are doing everything we can to prepare. I am eagerly awaiting your response. Your faithful student, Twilight."

With a small burst of green fire, Spike sent the letter off to Princess Celestia. The group arrived at Town Hall, nearly barreling into Mayor Mare. Startled by their sudden intrusion, the mayor’s eyes widened as all five mares began talking at once, each trying to explain the situation.

"Easy, girls!" Mayor Mare stammered, raising a hoof to calm them. She glanced between each of them, her confusion growing. "One at a time, please!"

Twilight took a deep breath and quickly relayed what they had learned to the mayor, her tone urgent and laced with worry.

"We need to make an official announcement, warning everypony!" she gasped, still out of breath from the run. "Everypony has to stay indoors until further notice. Food will be distributed by ponies in protective gear."

Mayor Mare blinked, clearly overwhelmed by the sudden flood of information. But after a brief pause, she nodded firmly. "An announcement will be made at once," she affirmed.

✦•······················•✦•······················•✦

It had been a month since the outbreak first began, and many ponies had fallen ill after coming into contact with the infected. Princess Celestia had dispatched royal guards and medical staff to Ponyville, and a magical forcefield now encased the town, preventing anypony infected from leaving. A large hospital outpost had been constructed at the edge of town, dedicated to caring for the sick. The outpost became the central hub for managing the crisis, housing countless patients as the mysterious illness spread.

As the first doctor to examine this phenomenon, Quick Stitch had been transferred to the outpost, along with his primary patient—Fluttershy. Despite the best efforts of the medical staff, Fluttershy’s condition had continued to deteriorate. Quick Stitch spent countless hours monitoring her, trying to find any clue as to the cause or cure of the illness.

"Fluttershy, it's Doctor Stitch," came the doctor's voice through the intercom beside the window to the pegasus' containment room. "How are you feeling today? Do you feel well enough to eat?"

Quick Stitch peered into the dim, shadowy space, watching the faint outline of Fluttershy in the center of the room. The infected couldn’t stand the light—it was too agonizing for them, causing screams and wails until they were left in the darkness. Fluttershy's chest heaved as she lay slumped, her mane and tail tangled and unkempt. She had wasted away to a skeletal form, her body unable to hold down any food. Everything she consumed came back up in sickly rainbow bile.

Like Discord and the others, Fluttershy constantly spit up a glowing, iridescent foam—an eerie, unnatural hue that hinted at the magic that had tainted them.

"Fluttershy?" Quick Stitch called again, his voice a touch more urgent this time. "Miss Shy, are you able to answer at all?"

For a moment, there was no response—only the sound of her labored breathing.

Doctor Stitch's brow furrowed as the silence stretched on. Fluttershy’s mental state had been steadily declining—two weeks ago, she would have at least muttered a response. Now, the silence spoke volumes. He sighed, turning away from the window to jot down notes, his quill scratching across the paper in an otherwise still room.

But then a sudden thud broke the quiet.

His head snapped up, eyes darting back to the glass window. Fluttershy had thrown herself against it, her frail body trembling as she pressed her face and hooves against the pane. Glowing foam dribbled from her mouth, smeared across the glass as she weakly smacked it with a trembling hoof. Her eyes, glazed and swirling with unnatural colors, locked onto him in desperation.

The doctor’s heart pounded as he froze in place, dread settling in his chest. Fluttershy, who had once been so kind and gentle, was now barely recognizable—a shell of her former self.

"Fluttershy!" he called out instinctively, rushing back to the window. "Fluttershy, please—stay calm. We’re doing everything we can."

But the pegasus didn’t respond with words. She only banged the glass again, more foam spilling from her mouth, her eyes wild and frantic.

The sight made his stomach churn. Whatever had overtaken her was far more sinister than he had anticipated.

The doctor pressed a button on the control panel next to the window, causing metal shutters to descend over the glass and door. This precaution was intended to prevent the mare from escaping should she somehow find the strength to break the glass. With a sigh, the stallion made his way upstairs to convene a meeting.

As everypony arrived and took their seats, a discussion commenced regarding the disease. It remained unnamed, as they had yet to agree on what to call it.

"Thank you all for coming," the stallion began, clearing his throat. "A rather... unexpected symptom has emerged in Miss Fluttershy."

The ponies at the table exchanged worried glances. Clover Cure, another doctor from Ponyville, spoke up. "What is this symptom? Why has it appeared now?"

Quick Stitch nodded in acknowledgment of her question. "The aggression we've been documenting has escalated into violence. Miss Fluttershy threw herself against the window of her room, attempting to break through. She was unresponsive to verbal prompts, and I fear this disease has taken away her last ability to communicate."

Iron Hoof, a sergeant from the royal guard, slammed a hoof on the table in frustration. "This situation is spiraling out of control! You all have tried countless remedies, yet not one has shown any promise in alleviating the infections or stabilizing these ponies!"

Swiftstrike and Shieldbreaker, two guards accompanying him, nodded in agreement. The smaller of the two, Swiftstrike, spoke up. "The sergeant is right. It's time we take decisive action."

Soothewing, a doctor from Canterlot, shook their head in disapproval. "We can't take action against something for which we haven't found a cure. These ponies are suffering, and it is our duty as their physicians to help them! I will not allow you to bring harm to my patients just because you believe they are a lost cause."

Sergeant Hoof shot them a fierce glare, puffing up his wings in anger. "The longer we wait, the more ponies we put at risk, Doctor." The emphasis on the last word was laced with disdain.

He and the other guards appeared ready to take drastic measures against the infected, as it seemed to be the only course of action left. Clover Cure spoke up again, raising her own concerns. "We must continue searching for a way to stabilize them, at the very least. It is cruel to consider giving up so soon."

Doctor Stitch nodded in agreement with his colleagues. "We will not give in yet. For now, we need to continue documenting symptoms and changes in behavior, while exploring any possible avenues for progress."

The guards scoffed but relented; the decision to take physical action was not theirs to make. All final decisions had been left to the head doctors on the team.

Soothewing adjusted their glasses, positioning them more securely on their snout. "As for a name... has anypony found something suitable yet? We need a term for our official statements."

The ponies exchanged thoughtful glances before Shieldbreaker spoke up. "Erm, some of us guards have been calling it Zap Apple Fever..."

Doctor Stitch repeated the words to himself. This was perfect. The disease afflicting so many ponies would henceforth be known as Zap Apple Fever.