All alone again

by The_Archivist

Rating: mature
Tags: Twilight Sparkle, Profanity, Gore, Violence, Dark, Death, Alternate Universe, My Little Pony: Friendship is Magic, Rarity, Horror, Queen Chrysalis
Length: 1981

Summary: Twilight Sparkle awakens within her Library only to discover that Ponyville is void of any and all its former inhabitants, she must find somepony soon otherwise she might have to return to Canterlot in hopes of discovering what was wrong.

Summary: Princess Twilight Sparkle awakens in her Library within Ponyville only to learn that everypony has vanished from the town, she wants to find everypony however they all seem to have just vanished from sight.

Can Twilight find everypony? Or will she need to find Princess Celestia and Princess Luna before things get so much worse.

Published 2023-09-16 17:30:00 UTC
Last updated 2023-09-16 17:30:00 UTC

Chapter One: Discovery

Twilight was resting peacefully in her bed as the midnight blue star coated blanket drooped over the sides of the bed frame then Twilight was startled away by something crashing near her desk, that made her violet eyes shoot around the room hoping to find some sort of intruder until she noticed the ink pot shattered on the wooden planks near her desk. Twilight sighed softly and raised her hooves and hung them down the edge of the bed feeling her hooves gently tap against the wooden floor beneath her.

"Oh come on. That doesn't even make sense. I didn't leave any of those ink pots out...At least I don't remember leaving one there? Maybe Spike forgot to return one of them to my cabinet?" Twilight began to think to herself with step she took over to the desk.

Twilight blinks as she looks at her desk only to realize now that she was closer to the to the desk that nothing else had been disturbed which was impossible, Twilight stared at the desk in confusion then she glanced at the ground below to see the shattered remains of the ink pot.

"That heck? That can't be possible...The rest of my equipment can't have just been...Completely ignored if all of the other stuff was completely untouched...Something isn't right here" Twilight heard her thoughts echoing through her mind as she tried understanding what could possibly be happening right now.

Twilight felt her horn flare up with light raspberry coloured magic swirled around her horn then the shards of the ink pot were surrounded with the magical aura, Twilight used a thought to push each shard together then she raised all the shards up and levitates them over to the nearby trash can.

"Hm. Where's Spike? Wait...What the hell? How'd I not notice that...Where did Spike go?!" Twilight felt her heartbeat rising from the fear that was now surging through her body until she heard the sound of pans hitting each other from down in the kitchen, this sound made Twilight sigh in relief as she approached the doorway to her bedroom which was completely open revealing the staircase down into the library below.

Twilight stared into the darkness as her mind began swirling with horrific monsters that were waiting for her in the dark but she shook the thoughts away and briskly walks down the stairs, Twilight continued her travels until she stopped on at the doorway leading to the Library when she felt something in her mind telling her to wait and listen to any further sounds. Twilight was confused at the feeling in her mind so she just shrugged to herself and pressed the side of her head against the wooden surface of the door only to hear absolutely nothing on the other side, Twilight's eyes narrowed in confusion then her eyes widened in concern when she was unable to hear the sounds of the stove or oven generating some sort of humming sound.

"That...That isn't possible, Spike isn't down there..." Twilight's voice came out like a whimper as she whispered each and every word yet she couldn't understand how it could be so silent now, Twilight closed her eyes as a million possibilities were racing through her mind then she landed on a single option she could follow.

Twilight raised her right hoof and pressed it against the door handle slowly pushing it down then Twilight delicately pushed the door open which slowly revealed the silent and empty library below, Twilight's eyes widened in terror but she kept her composure and remained silent as she gently stepped out into the upper floor of the library hoping to catch a glimpse at something in the library below yet she saw nothing.

"Nothing...How can that be possible? Alright...Whoever is down there must still be in the kitchen..." Twilight's voice stuck down to the volume of a whisper as she walks over to the staircase leading down to the library below, Twilight was immediately frozen in place as she heard the sound of a voice swearing in annoyance as the creature was trying to find something from the drawers and cabinets of Twilight's kitchen.

"Damnit. Where is it?! That damn mare must have left it somewhere around here! If it isn't in the library itself then she must've hidden the damned thing around here" The pony shaped creature was using some form of brilliant green magic to open and slam drawers closed in some attempt to find what Twilight assumed were the Elements Of Harmony, Twilight carefully stepped down the remaining stairs but she missed the bottom step and slipped off the staircase once she became unbalanced only to painfully hit the ground.

Twilight groaned softly and rubbed her head with her front hooves as the sound of magic ceased then the taller pony shaped mare stepped out into view, Twilight shook her head and glanced at the pony shaped mare causing her eyes to widen so much she thought they'd fall out of their sockets as she looked upon the tired and dishevelled form of Queen Chrysalis. Queen Chrysalis stared at Twilight Sparkle allowing Twilight to notice how short and dirty Chrysalis's hair had become along with her hooves and parts of her body were stained with dried blood causing Twilight to pull backwards for more space away from Chrysalis.

"Princess Twilight Sparkle? You're still here...You weren't taken...You are the only other living pony or creature that I've seen in hours. I hate myself for saying this but. I am overjoyed to see you right now." Chrysalis was panting softly as her short bug-like wings began fluttering in some form of joy as she looked upon the frightened form of Twilight, Chrysalis rolled her eyes and made her own abnormally curved horn flare up with brilliant green magic once again which spread to Twilight and surrounded her body helping Twilight to her feet while Chrysalis began circling Twilight causing her magical aura to dissipate.

"Chrysalis...What the heck are you doing here?! Why are you in my kitchen and why are you searching for the Elements of Harmony! And...Why are you covered in blood? I...Did...Did you hurt somepony?" Twilight felt her wings fluttering in concern as Twilight prepared to escape if the possibility made itself known but this was stopped once Chrysalis stopped her movements, Twilight felt her wings slowly curling up against the sides of her back as Chrysalis looks at the ground and just started to cry softly which made Twilight's eyes fill with worry at Chrysalis's reaction.

"No. I never harmed anypony here. I haven't killed anypony here or anywhere else in Equestria. This blood isn't from your little subjects. This blood is from my own children. Some creature came into the Changeling Forest and entered my hive while I slept. And slaughtered my children in their beds while they slept! I thought it was you Ponies but then I found Sweet Apple Acres looking void and completely empty of life, even the apple trees weren't touched by any member of the Apple Family." The former Changeling Queen scoffed when Twilight gasped at the mention of the Apple Family disappearing which Twilight realized was fairly insensitive considering the Changelings were all dead, Twilight lowered her head as an apology which Chrysalis chose to accept and just turned to look at each of the bookshelves around them hoping something around them would have some sort of answer to what was happening.

"I am very sorry, that was very insensitive to you. I am sorry about what happened to your children, but that doesn't really explain where all that blood came from. Did you take their bodies somewhere or something?" Twilight heard the suspicion in her voice and before she could try to explain herself the air was filled with aggressive hissing and snarling, Twilight shut her eyes and stepped backwards while Chrysalis was expressing her anger at Twilight then Chrysalis sighed and flared her horn up again this time she cast a memory spell out so Twilight could see her own memories of what truly happened in the Changeling Hive.

Chrysalis awoke on her stony bed and felt the presence of abnormal silence within her hive so she rushed off her bed and galloped out of her room until she emerged out into the sleeping chamber of her subjects, Chrysalis was horrified to see all the blood on the stone below that was forming giant puddles of red liquid on the slightly dipped down areas so Chrysalis began pushing each corpse aside trying to desperately find at least one of her children to still be alive. Chrysalis spent over two hours searching through the mangled and brutalised remains of her children hoping that she'd missed something until she looked upon to remains of her own spawn, Chrysalis saw each claw mark in every available patch of flesh along with the broken bones visible beneath the pale black skin of her children yet Chrysalis could only stare for a moment before she just let out a pained and enraged scream into the sky from the sheer loss of every one of her children.

Chrysalis dispelled her magic causing Twilight's glowing white eyes to instantly revert to normal causing Twilight to desperately look around almost like she was searching for something that didn't exist, Chrysalis was looking at the side while Twilight was trying to properly understand what was happening in Equestria at this point after getting such a clear look into Chrysalis's memories.

"They...Oh my Celestia...That was horrible...I...I've seen predators hunting and killing prey but that's just natural...Animals do that to feed instead of just butchering an entire species...I don't know what caused that to happen but I will help you get justice. If you swear to me that you won't continue to put Equestria in more danger. We don't need to be enemies Chrysalis. We can be allies, you need love to survive and remain magically enhanced. This is something we can help with. But only if you understand that we aren't enemies. Friendship is powerful and it might seem scary at first. But everything seems scary at first" Twilight felt her eyes glistening with magic as her horns sent out a few short lived magical sparks as Chrysalis was just thinking to herself clearly not sure how to respond, Twilight noticed how Chrysalis was struggling to think of an answer so she just raised her left hoof in response just to make sure that Chrysalis knew that she didn't need to answer yet.

Twilight glanced at the doorway which she galloped over to and used her magic to pull the door open revealing the outside after wanting to be sure that Ponyville truly was empty which was proven to be correct as she was unable to see anypony around, Twilight took a step outside hoping that she missed something yet she was still unable to see anything nearby so she just sighed softly and turned to return to the library until she heard the familiar sound of hooves crushing dirt so Twilight spun around and opened her wings wide causing her horn to glare up with magical energy. Twilight glared at the other Pony causing her horn to lose its magical glow almost instantly as she stared at the frightened and confused form of Rarity who was staring at Twilight in fear.

"T...Twilight...I...I need your help, everypony has disappeared and I can't find Sweetie Belle! I need your help please!" Rarity felt the tears in her eyes slowly sliding down her cheeks as she took a step forward but Twilight reacted much faster than Rarity could, Twilight rushed forward and wrapped her forehooves around Rarity's neck to hold her as closely as possible even when Chrysalis stepped out of the library which caused Rarity to scream out in terror which echoed down the streets.