Scootaloo hurriedly but silently made her way through the trees and towards a house. She was carrying a small saddlebag that contained food. Or, what could be called food these days: some cans of beans, corn and peas, a stale piece of bread, some moldy apples and three bottles of water. She approached the desolate house and slowly made her way inside. The filly trotted into the room, which was dark but illuminated by the moonlight that peaked through a broken window. She briefly looked at the moon and cursed the princesses for letting this happen.
Scootaloo sat down near a drawer and lighted the tiny lamp that sat next to it. The small pony basked in the light while she caught her breath. She took off her saddlebag and put her items on the drawer. Her eyes scanned the picture that was on top of the drawer: her and Rainbow Dash gleefully hoof bumping. In an instant, Scootaloo's mood soured even more. She loved that picture, and she loved Rainbow Dash even more, but that picture kept reminding her that it was the only thing that still connected her to Rainbow Dash. The filly tried her best to suppress the memories, but she just couldn't stop thinking about Rainbow Dash, especially since this Celestia damned virus started. She didn't want to believe that her dear sister was infected, and Scootaloo was sure she wasn't, even if sometimes she thought she saw her as one of those abominations.
"No, she isn't infected. Rainbow is too awesome and strong to let that happen to her. I bet she just flew somewhere safe to gather the Wonderbolts or the Princesses in order to save me!", Scootaloo thought while shaking her head determinately.
The orange pegasus decided that it's best to keep herself distracted, so she opened a can of beans and slowly started eating while thinking about her two friends, the rest of the Cutie Mark Crusaders. The last time she heard from them was when this whole thing started, when AppleBloom came to her and told her that something is wrong with some of the ponies in town. Scootaloo didn't know what to make of this, but AB told her to talk with Rainbow Dash if she could, and then to go stay in her home like Twilight instructed. When Scootaloo asked about Sweetie Belle's whereabouts, Apple Bloom told her that she is already at Rarity, staying with her. Then, the earth pony filly told her something that worried the pegasus.
"I...I also heard that Rarity wants to take Sweetie Belle to her parents, just to be extra safe. That's all I know, I don't know when she will leave or when she will come back." Scootaloo looked sad at this statement, but nodded her head at her friend. After all, it was more important for Sweetie to be safe, at this moment. Speaking of which...
"What exactly is happening, AB?"
Apple Bloom averted her gaze when her friend asker her that, but she decided to answer her nonetheless.
"I don't know all the details, but I was with AJ when Twilight came to her and told her that the ponies that were sick a few days ago, started becoming extremely aggressive for no reason whatsoever. And she also added that they started to look...weird. Like, more sickly and almost...almost dead." The filly shuddered while she mentioned this, then continued.
"Twilight then told AppleJack that they should split up and make the other ponies in town aware of what's happening and to advise them to stay inside. My sister told me to go to the farm, but I wanted to inform you. Now, with Sweetie also safe, I'm gonna go inside my home too. Stay safe Scoots." With that, the two ponies embraced eachother and departed.
After some time, Scootaloo came to understand how grave the situation was:zombie like ponies, rotting and with contorted bodies started roaming around Ponyville. The worst thing was that the little filly recognized some of these ponies, including her once teacher, Cherilee. She couldn't be sure since she was focused on her own survival, but she really hoped that her friends were safe. The pegasus even tried to check just to be sure, but she couldn't gain access to both Sweet Apple Acres or The Carousel Boutique, so she just thought that if she couldn't enter, then the infected couldn't either. She prayed to Celestia and hoped that she was right.
As she was deep in thoughts regarding her friends, Scootaloo didn't hear the slow hoofsteps approaching her home. All she knew was that suddenly somepony...or SOMETHING, was nearing her window. Just to be safe, the filly blew out the light from her lamp and listened intently while trembling slightly.
"...hello?", said the voice as the pony slowly approached the window.
"It's...Rainbow...Dash", the voice croaked.
Scootaloo started crying, but not from joy. That was not how Rainbow Dash sounded, and Scootaloo's worst fears came to fruition when the creature that called itself Rainbow Dash put its hooves on the windowpane. The small orange pegasus started trembling harder from fear. The creature that stared intently at her resembled Rainbow Dash, but more in a mocking, grotesque parody of the former blue pegasus: her body was lithe and longer, resembling that of an alicorn. Her body was rotting, with fur almost missing completely and her skin a nauseating shade of greenish gray. She had a deep gash on one of her hindlegs, so deep that her bone was visible through it. Her neck was crooked and her face was looking like something from the filly's deepest and darkest nightmares:Rainbow's mouth was split at each end, giving her a macabre grin, while the inside of her mouth was adorned with small, sharp teeth. Her nose and eyes were black and oozing a thick, black substance, making her appear like she was crying. Her beautiful rainbow mane was almost gray, rotten and thin and her wings, her once pride and joy, were missing from her body. Scootaloo didn't know if they simply rotted away or if they were forcefully plucked from her body.
The infected Rainbow Dash tilted her head slowly at the small pegasus, as if she somehow recognized her, then she slowly began crawling her way into the destroyed home through the broken window. Scootaloo wanted to move, she really wanted, but she was paralized with fear. And not only fear, but also disgust, contempt and desperation. The only thing she could do was cry and watch in disbelief the slowly approaching dead pony. Was this truly the state of her idol?Was this disgusting creature really Rainbow Dash in the first place...?
Her train of thought was suddenly interrupted when her rotting idol lunged at her without any hint of hesitation. Screams of agony overpowered the sound of Rainbow Dash eating her adopted sister alive. Scootaloo could feel the mangled mare's sharp teeth biting and pulling out her flesh. Rainbow was so ravenous that Scootaloo could already see her ribs and leg bones protruding from her chest and hooves. As the darkness and the cold embrace of death started taking her, the last thing the filly saw was her ex sister standing above her, looking almost proud and smiling.
"We'll...be...together...soon", croaked Rainbow again.
Author's Note
My first "MLP infection AU" fic. Hope you enjoyed it 
