In This Cat and Mouse Game

by GoldSpringFox

Rating: teen
Tags: Discord, Violence, Dark, Alternate Universe, My Little Pony: Friendship is Magic, Rainbow Dash, Queen Chrysalis, Romance, Fluttershy, Adventure, Twilight Sparkle
Length: 2657

Fluttershy must go into hiding, assume a new identity, and to protect a source of dangerous information from the Changelings. Discord has agreed to round up the Elements to see which mare has said information.

After discovering a mysterious book in her cottage, Fluttershy finds herself on the run from Chrysalis' wrath. With her friends already spreading themselves across Equestria to keep Chrysalis guessing, Fluttershy must keep herself hidden, even if it means hiding in plain sight.

Will the plan succeed, or will Fluttershy be caught?

Either way, without help, it seems Equestria may be finished.

Set before Discord's reformation, major canon divergence.
Current Chapters are undergoing re-edits

Published 2018-02-24 06:50:12 UTC
Last updated 2019-11-07 23:03:26 UTC

There is A Book

The cries of terrified ponies rang throughout the city of Canterlot. A Pegasus the color of buttercream almost added her own scream to the throng as the nightmare causing this uproar crashed into the ground beside her.

“Fluttershy!” A blue blur rammed the Changeling’s head into the cobblestones with a sickening crunch.

“What are you doing?” The blue Pegasus began pushing her along, her yellow hooves clutching her saddlebags close to her chest. “You’ve gotta get outta here before it’s too late.”

“B-but I can’t-” Rainbow spotted a sewer entrance. Lifting the cover, she turned to her friend.

“There’s no time to be afraid, Flutters. There’s only one way this is going to work, and that’s splitting up and going as far from each other as possible.”

“M-maybe Twilight’s mistaken-” Rainbow grabbed her hoof, practically dragging her into the sewer system.

“Maybe she is, but it’s too late for an alternative. See ya on the flipside.”

And with that, the steel cover was set back in place, leaving a tearful mare to wonder how this could have happened.

Earlier that week……

Fluttershy was tending to her animals, as usual, when the sound of a scuffle caused her to look up to see a white rabbit and two ferrets exchanging blows.

“Angel, Basil, Lemon! Stop that!” As she moved to separate the fighting animals, one of the ferrets was thrown into the bookcase, dislodging several from their careful placements.

“ENOUGH!” The two still fighting stopped immediately, wincing at the tone and volume of the normally quiet mare’s voice.

“You should be ashamed. Corner, all of you.” Watching the guilty animals trudge to different corners, Fluttershy let out a sad sigh. For some reason, the animals were acting out, and it wasn’t an isolated incident. Rarity had told her Opal Essence would hardly come out from under the bed, scratching anypony who tried to retrieve her.

Applejack explained to her that Winona had suddenly turned into a nervous wreck, barking at shadows and howling in the middle of the night.

Owlowiscious refused to come near Ponyville at all.

Tank and Gummy were…. well, Tank and Gummy.

‘And none of them will tell me why.’ Fluttershy thought, frustrated. ‘Unless “a bad thing is coming” is it.’

When everything first started that was what all the animals told her, even the manticores. She’d told Twilight, who’d written Celestia, who’d replied back that nothing was wrong but to remain vigilant anyway.

Looking at the mess of books, she sighed. As she put them away her thoughts drifted. All this uncertainty and vagueness was causing her unnecessary stress.

‘Maybe an earthquake or some other natural disaster is on its way?’ She placed another book on the shelf.
‘But the animals aren’t running away like they should if that were the case. So why-’

“Huh?” There was one last book on the floor, but it wasn’t one she recognized. Not only that, but she was certain it hadn’t even come from her bookcase, as her books were all neatly in place. There was no space for this book to have fallen, and she never left books lying on the ground.

Picking it up, she read the title embossed on the cover.

“History Expanded: Secrets Explained and Revealed.”

Curious, she opened it up to the first page.

Until recently, history has been focused on the reigns and fallings of monarchs, wizards and species. Much of the information we read about these, sadly, are viewed and taught as old pony tales and are not taken seriously.
I am writing this book with the permission of the Princesses, under the condition it goes to them so that they may read of my findings as well.

Chapter One: Changelings

Changelings are a race that little is known about. What we know for certain, is they feed off of a pony’s love, making the pony weak. They also have a hive mentality, with one Queen acting as ruler and mother to the drones.
Though these are the facts we are familiar with, I have found evidence of -

“Fluttershy!” The Pegasus yelped, the book fumbling in her grasp. Rainbow stood in the doorway to her cottage, a look of concern on her face.

“You okay? You didn’t answer when I knocked on the door. Her rose-colored eyes fell on the book. “If you wanted to read that, you’d better save it for the train ride.”

That caught Fluttershy’s attention.

“Train ride?”

“Yeah. Celestia’s summoned us and I got a really bad feeling.”

Fluttershy nodded as she reached for her saddlebags, pausing a moment to stare at the book before placing it in.

“Be good while I’m gone.” She called out to the animals in timeout. Unlocking the animal door so that they could come and go, she went on her way.

She didn’t see the look of fear and concern that crossed their little faces.

On the train, her friends were talking and laughing, trying to ignore the bad feeling they all seemed to share. Fluttershy had the book open on her lap, but couldn't bring herself to actually read it as something unpleasant settled in her gut. Her thoughts went to her animals and what they'd been trying to tell everyone.

'What if the "bad thing" is what we're all heading towards right now?'

"Hey, Fluttershy, is that a new book?" Fluttershy looked up, startled by the sudden question. Twilight was looking at her, a small smile on her lips.

"Um, yeah. I just found it in my cottage this morning." Twilight looked confused.

"You mean you didn't know that it was there?"

"No. You see some of my animals had a quarrel, and ended up knocking into my bookcase. After I put them in time out, I was cleaning up the mess, and this book was there. But the thing is, it wasn't there this morning so I have no idea where it came from."

Twilight put a hoof to her chin in thought.

"Maybe somepony sent it to you by mistake. Like they were trying to practice their magic and accidentally teleported it off their intended target?"

"Oh, my!" Fluttershy looked at the book in her hooves, a sense of guilt and shame settling over her.

'If that's so, then I shouldn't be reading this. It's somepony else's property.'

Closing the book with a sigh, she placed it back in her saddlebags, vowing to return it to whomever it belonged to.

But as the train draws closer to its destination, it would've been wiser to have stayed in Ponyville.

There is Another Chapter

Author's Note

So just a heads up.... Major-- and I mean MAJOR-- canon divergence. Like, throughout this entire thing.

I hope you enjoy. :D

There is Another Chapter

The sun was just peeking over the mountains in the east when a cold sense of dread washed over the ruler of Equestria. Startled, Celestia let the spell on the sun slip, causing it to momentarily dip back down on the horizon.
After regaining control and finishing her duty, the white alicorn remained where she was standing, trembling and breathless.

"It cannot be." She muttered under her breath.

Quickly, she turned and darted into her chambers. Celestia began searching her wardrobe just as a dark alicorn entered the room, a concerned look on her face.

"Sister, I fear something is amiss. I felt this strange, magical surge coming from the direction of Ponyville-"

"I know," Celestia spoke firmly, cutting her sister off.

"I had always feared this happening, but with recent events, I had grown complacent." There was a noise of victory as the eldest brought from the hidden depths of her wardrobe, a small dusty book.

Luna blinked in surprise. "What is that?"

Celestia said nothing as she opened the book and began flipping through it.

"There are many things you have missed, Dear Sister. And, regretfully, this was something I should not have attempted on my own. However, there was only one pony that could have pulled it off flawlessly, and he died before he finished hiding them all." She stopped somewhere towards the end of the book, going silent as she read the familiar hoof writing.

"I am aware of the time we spent apart, Sister," Luna spoke lowly, "but I am more concerned over the sudden release of magic that I cannot tell whether it is Unicorn, Chaos, or our own somewhere in the same vicinity as your beloved student and here you are reading your old diary like a filly. Is your old coltfriend's name still there?"

Sighing, the white monarch shook her head.

“Luna,” she started before stopping herself, pushing past her sister to the hall to see if anypony was there. She saw no pony, but still, cast a privacy spell on the room to be safe. Turning to Luna, she continued, “I understand your frustrations. Believe me, I do. I will tell you everything I know pertaining to this matter, but first, we must gather the Elements. Twilight and her friends must know what they are up against.”

The younger princess frowned, worried.

............................................................................................................................................................

The Canterlot Mines

Far below the streets of Canterlot, in the darkest depths of the mines, something gave a shiver as the scent of great magic suddenly filled the air. Something it had thought lost had returned, the first piece of a puzzle finally reappearing after fifty, long years.

There is a buzzing of wings as the thing laughs, the time was nearing.

Soon, Equestria would be hers.

...............................................................................................................................................................

The Friendship Express

Fluttershy was walking through the train cars, searching for something. As she searched, an Earth Pony stallion walked beside her, keeping pace.

"Don't lose hope," he was saying. "They'll find you when the time comes. Take your time."

"But it's important that I gather all of them?" she asked, though she didn't know what "they" referred to.

"Not yet, and not so fast. Many seek their hidden power, though within plain sight it be."

Normally, Fluttershy would ask what that meant, but what came from her mouth was, "But I must protect the spell in its entirety, for it is Harmony that is in jeopardy."

She looked down at herself. There were stripes over her yellow fur. The stallion chuckled.

"You are quite right. The bugs will be coming soon, and you've barely started. You must teach yourself my teachings to survive the trials ahead. Don't worry though. There's a reason why-- Fluttershy"

"Fluttershy-"

"Fluttershy!"

Fluttershy yelped as she jerked awake. Rainbow had her hoof on the other mare's shoulder, having been shaking her.

"C'mon sleepyhead! The princesses are waiting!"

With that, the cyan pegasus bolted out the train to meet their friends on the platform. Fluttershy hoisted her saddlebag onto her back and followed, trying to make sense of the dream that was already fading away.

There is a Problem?

Celestia sat in the throne room, one golden-shoed hoof tapping the stone step in front of her. Luna sat by her, glancing over on occasion. Her sister's worry was contagious it seemed, as many of the palace staff had similarly been on edge throughout the day. Luna took note of the more rigid stances the guards had, due to their mere proximity to Celestia.
She nudged her sister, causing Celestia to turn her attention to the Night Princess.
"You'll poke a hole in the tiles, Sister." She said lightly, a teasing smirk on her lips. Softer, so that the guards wouldn't hear, "They just got off the train. They'll arrive soon."
Celestia composed herself. "Thank you, Sister. But I cannot help my worrying. I swore to him..." the last part petered off, Celestia lost to her thoughts. When she spoke again, Luna had to strain her ears as she whispered, "Faust, help the one who found it."

As the Mane Six made their way through the streets of Canterlot, they chattered amongst themselves, expressing a light concern. What was the reason Celestia wanted to see them? Hopefully, it was nothing too serious.
As the group walked, Fluttershy felt a growing unease settle like a rock in her stomach. Like someone was watching her closely, their eyes burning a hole in the back of her head. She wanted to turn, at least to confirm whether or not someone was staring at her, but the words from her dream came back to her, ringing around her head like alarm bells.
The bugs will be coming soon.
"Fluttershy?"
The yellow pegasus gave a start as she looked up to see Applejack, her pace slowed to match her friend's. Fluttershy hadn't realized that she'd begun to walk slower. Her head felt fuzzy.
"Are you alright, sugarcube?" AJ asked, her voice low. Mild worry was etched into her face.
"Oh, I'm fine," Fluttershy mumbled. There was a buzzing now, and the world seemed slower than her line of sight. They were almost to the gates of Canterlot Castle, when AJ said,
It's time again.
"Time again for what?" Fluttershy asked.
"What do you mean?"
Fluttershy frowned. Wasn't it AJ who made the comment tho-
Don't keep me waiting, Miss Fluttershy.
The buzzing suddenly intensified, the sound digging into her brain as the world around her was lost in a blur of piercing light and colors.
She gave a small gasp and fainted.
As the world around her faded, she heard AJ call out her name. She could hear the girls panic as they realize what's happened. And that strange voice, saying:
Time is almost up.

When Fluttershy woke, she was lying in her usual room in Canterlot. Looking around, she found herself alone, confused, and a little scared. Clutching her comforter in her hooves, she tried to remember how she got here, but all she remembers is fainting.
The girls must have brought me up, she concluded, embarrassed. Just what was happening? Could she be coming down with something?
Fluttershy rested her hoof on her forehead a moment, checking for fever, before thinking that that probably wouldn't help if she did have one. A fever can only be confirmed by another individual or a thermometer, neither of which were in sight.
She sighs, settling back onto her pillow. If she was coming down with something, then she should stay put. No use risking other ponies' health.
Turning onto her side, she spots her saddlebag on the nightstand. She reaches out to grab it when she stops. Remembering the conversation on the train. This was somepony else's book, their property.
Although, if it was just a textbook, a tool for learning, then it wouldn't matter, right?
Right, and....
What was she getting all worked up about? It's only a textbook. And besides, all books are made to be read. Why write a book if no pony was going to read it?
Shrugging off the weird mood she'd been entertaining, Fluttershy grabs her bag, takes out the book, and begins from where she left off.

Meanwhile, in the throne room...

Luna watched her sister from over the lip of her teacup. She'd ordered some refreshments, in the hopes it would quell some of Celestia's worry. The normally poised ruler barely nibbled on the small snacks, and her cup was only brought to her lips, no tea actually being sipped.
Luna was beginning to catch her sister's anxiety, it seemed, as she began fidgeting in her seat and glancing every so often at the door.
She was just about to open her mouth to ask Celestia something, possibly along the lines of, "What do you suppose is stalling them?" when the door flew open, and the Mane six dashed into the throne room in a clamor. The sudden entrance made everypony in the room startle, and only slightly relax when they realize who it was.
"Celestia, you have-"
"-in tarnation-"
"-just disappeared!"
"-PURPLE PONY EATERS!"
The two rulers sat there, dumbstruck. What had happened on the group's way here?