The Web of Deceit

by Golfmann14

Rating: teen
Tags: Dark, Alternate Universe, Sad, Adventure
Length: 2719

A few weeks after the royal wedding, Ponyville is gearing up for another visit from the Princess. However, when everypony disappears, Twilight is thrust into a stark reality. The fate of millions will ride on one decision. One battle. One unicorn.

"Equestria as you know it, does not exist, Twilight Sparkle."

A few weeks after the royal wedding, Ponyville is gearing up for another visit from the Princess. However, when everypony disappears, Twilight is thrust into a stark reality: the real Equestria is on the brink of war.

The rules have changed. Spies walk among civilians and no one can be trusted. In the end, the fate of millions will ride on one decision. One battle. One unicorn.

Where lies the truth in a web of deceit?

(For those who have been following this fic, I have changed a few aspects of the story and am currently rewriting much of it. I apologize in a advance for the small amount of chapters.)

Published 1970-01-01 00:00:00 UTC
Last updated 2012-12-10 02:16:30 UTC

Chapter 1 - Morning

Chapter 1

Twilight awoke with a start. Raising her head off of the downy pillow,  she yawned and dragged her legs off the side of her bed. Touching the ice cold hardwood floor, Twilight winced and set herself down slowly. She yawned and walked through her room and down the creaky stairs. Feeling her way through the dim lighting, she bumped into the bathroom door and opened it with her magic. Twilight promptly shut it behind her and approached the oval mirror, gazing at her beautiful morning appearance. She spotted her comb sitting nearby and began teasing the sleep out of her mane.

As she combed over and over, Twilight's thoughts wandered. The last few days had been crazy with activity and her stress levels had risen along with it. The Princess was coming to Ponyville for another visit and Twilight did NOT want things to go as they had the last time. “Maybe everything will go according to plan with no parasprites or exploding birds.” Twilight thought. Chuckling to herself, she opened the door and crept quietly downstairs. Twilight had never been one for breakfast, but today was important. "I'll just take the bran muffin Pinkie gave me." she said, and levitated it from the kitchen. Now fully prepared, she trotted to the front door and stepped outside.

“Another beautiful day!”

The brisk morning air tickled Twilight’s skin with the glistening dew still fresh on the sharp blades of grass. The sun had just started to peak over the horizon, casting an orange glow over the countryside. Only a few ponies were out and about at this hour, preparing their decorations for today.  Twilight waved to a few of them as she trotted down the street, taking in everything as she went. Reaching City Hall, her eyes grew wide. They had worked on many of the decorations late into the night but in the morning's allure they looked even better! The circular porch surrounding the building was decorated with bright streamers and tapestries of every color that hung from the wooden beams overhead. Tied to the porch were bunches of balloons that swayed in the soft morning breeze. However, there were quite a few decorations still missing. Rarity had been working the entire day yesterday just to get them finished in time. Just then she spotted the mayor nearby, looking at her clipboard.

“Mayor Mare! Can I get your opinion on something?”

"Give me her chart."

Name: Twilight Sparkle

Patient No. 000001-A

Blood Pressure: 120/70

Blood Type: M

Race: Unicorn

Sex: Female

Notes: (See "Timestamps" on P.12)

Embryo is confirmed and stable in parent

Birth date: see P.4

1-A Sickness detected; Diagnosis: Common Cold - Ref. 234-8

Gained entrance to Magic School for Gifted Unicorns; Direct control assumed- authorization: X32-7459

Subject 1-A has adapted well to stimuli and passed all physical and magic strain tests.

Literacy/ Arithmetic mastery rate: Exponential- Commonness: Rare

Primary directive assigned to subject by leader.

Subject react code: 34B to Holos:1,3,4,5 Code35Y to Holos:2,6

Subject 1-A’s Directive: Success.

Subject has passed all tests.

Initiate Code: 93BP procedures until further instructed by both leaders.

"The need has arisen for Twilight’s abilities once again. It‘s as we have foreseen. We both agree. The time has come, Doctor."

"Are you sure she's ready?"

"Yes."

"Both of you are positive about this? We have already initiated her extraction as ordered, but the reemergence process could be dangerous. You remember our last subjects! 00083-B and 00084-M suffered cascading nervous system failures! Not to mention-"

"I am aware of 83 and 84, Doctor. Twilight is different. She'll survive. She must survive."

"At our current stage, the temporal processes are deteriorating. If she is to have any chance of survival, we have to do it now."

An eerie silence settled between the two as they gazed at the peaceful looking unicorn.

"Do it."

Chapter 2 - Gone

Chapter 2

“So I was thinking if we moved th-“

Twilight yelped in surprise. Mayor Mare had vanished. She whirled around trying to find where she had gone. “It’s physically impossible for an earth pony to teleport. Not to mention doing it without a flash. That’s a highly advanced study of magic that only the most skilled unicorns can do.” Twilight thought aloud. An eerie silence had settled around her and she snapped out of her trance, realizing just how quiet it had gotten. Twilight perked up her ears to listen. The pounding of the hammers, the morning chit chat of ponies getting ready for the day, everything had stopped.

Silence.

Twilight methodically scanned the direction she had come but her eyes were met only by the bright decorations blowing around. The chilly morning breeze had turned into an ice cold wind. Dark clouds had also begun to roll in, blocking the sun's comforting rays.

"That's odd. Where did everypony go? They were right there just a minute ago." she said, puzzled.

Just then, a raindrop plopped on Twilight's nose.

"I'd better hurry and find where they went before this storm hits." she said, and took off down the street.

"Now where do I start? Sugarcube Corner is probably the closest." Running through the market, Twilight dodged vendor stands and houses until she finally slid to a halt in front of the bright pink door. Twilight raised her hoof and rapped on the wood. The sudden noise echoed ominously through the streets. She waited a moment and knocked again. "Hello?" she said, pushing on the door handle. It was unlocked.

The door swung open with a hollow creak and Twilight peeked inside. All of the lights were on and so was the display case. Stepping out of the doorway, she glanced around.

"Nothing seems to be out of place." she murmured.

Continuing her search, Twilight peered into the kitchen. "Nothing there either."

"Maybe the Cakes are out making a delivery. Pinkie should be right upstairs looking after the kids. "

Twilight nodded to herself thoughtfully and walked upstairs, confident Pinkie would be right there, playing with the kids. Rounding the corner, she froze. Not only was there no Pinkie, but there were no kids either!

"The Cakes couldn't have just moved away and left their entire store unlocked!"

Twilight scratched her head in frustration. Nothing made sense!

"Okay, so maybe Cakes are gone. There has to be somepony here somwhere." She said. Stepping back out into the cold street, Twilight raced towards Carousel Boutique.

The cold torrent of rain lashed at Twilight, mixing with her hot tears.  The distant thunder rumbled ominously, and flashes of lightening ripped through the pitch black sky. Darkness had fallen long ago, but Twilight didn’t care anymore.

After looking in Sugarcube Corner, Twilight had gone to Fluttershy's hut, Rarity's boutique, Sweet Apple Acres, all of them! She even went to houses of ponies she'd barely knew! All of them with houses unlocked, cooking projects abandoned, fireplaces burning.

Every last pony in Ponyville was gone.

Twilight walked through the melancholy streets, her sobs muffled against the storm’s roar. She had nowhere to go. She couldn’t take the heartache of returning to an empty house. She just couldn't.

There were too many memories.

A sudden crack of lightening echoed across the landscape and Twilight jumped in terror. However, as she was shaking in fear, she saw something.

Twilight turned and squinted to see through the pouring rain. Then she spotted it: a lamp was flickering inside the window of Lyra and Bon Bon’s house. Her spirits rising,  she picked her hooves out of the mud and trotted quickly towards the dark shape of the house.

"Ugh, why won't this whelp shut up?"

The Changeling Queen had been sitting her throne for the last twenty minutes listening to this defector's poor excuses.Thank goodness she hadn’t converted him into a changeling when she’d had the chance. Chrysalis had tuned him out a long ago, and continued to probe her way through the collective absent mindedly. She could sense the growing boredom in her guards. "At least I'm not the only one." She thought to herself, and sent them each a small amount of love for putting up with this idiot's shenanigans. They straightened up immediately, fully focused on their duty. Chrysalis groaned to herself.

"I've been queen for thousands of years but the stupidity of  ponies seems to be timeless."

Just then, a drone brushed against her mind and she connected with him.

“I hope this is important.”

“My Queen, there is news from our spies. Princess Celestia and Princess Luna are attempting to awaken Twilight Sparkle.”

Chrysalis bolted upright in her chair, startling the oblivious pony in front of her. The guards sensed her distress and snarled threateningly.

“What did you say?'”

“It’s true, my Queen. The information we have received was from a reliable source. Twilight Sparkle is returning.”

Chysalis sat back for a moment. But then she laughed loudly and smiled, exposing her sharp fangs.

“Guards, get this pathetic excuse for a pony out of my sight.” She said, “As for you drone, gather our allies. The time for my vengeance has come."

Chapter 3 - Memory

Chapter 3

Twilight's hooves squished in the mud as she stopped in front of the door. She couldn't believe her luck! "If somepony is left, then maybe they know what's going on." she said to herself. "Or someone just left a light on and I really am the last one left." Twilight said, bowing her head. She had to find out. Summoning her courage, she straightened up, reached out a hoof, and opened the door.

Stepping into the living room,  it was nearly pitch black. A few streaks of light trickled down the nearby staircase and casted ominous shadows onto the floor. She took a gulped and began to tiptoe through the room, but immediately whacked her knee into a coffee table. "Horse apples!" Twilight cringed. "Who in Equestria puts a coffee table right in front of the door?!" She whispered. Rubbing her leg, she dodged the remaining furniture until she was directly below the staircase.

Twilight climbed the stairs swiftly and stood in front of the white nondescript door. Pressing her ear against the cold wood, she could hear the sound of beeping and the dull scrape of metal on wood. "What could that noise be?" she thought. She reached out a hoof, and twisted the knob slowly. Suddenly, the door was wrenched out of her grasp. She screamed. The wold began to spin out of control around her.

"Hello. Twilight Sparkle."

Thunk.

"Ugh. What happened?"

Twilight blinked open her eyes and recoiled. Standing right above her head was the dark figure. She screamed and flailed her hooves frantically, trying to get away.  "Do not be afraid Twilight." the figure said, stepping into the light.

"Princess Luna!" Twilight said, relieved.

"Do not try to move too quickly. You took a nasty spill down those stairs. Here, let me help." she said, reaching out a hoof. Twilight took it, lifting herself back onto her feet.

"Thanks, you have no idea how comforting it is to finally find somepony!" Twilight said.

"Actually that is the reason why I am here, Twilight. Under normal circumstances, I would be back at Canterlot. But this is not Equestria." Luna said as Twilight's smile vanished.

"What do you mean? I've been all over town today. We're in Lyra and Bon Bon's house right now!"

"Follow me upstairs."

Twilight followed along behind; her mind absent. She slowly digested what the Princess had said. "I can only imagine what you must think. But I assure you, I speak the truth." she said, stepping through the door. When Twilight reached the top of the stairs, her eyes went wide. Inside the dimly lit room were several large metal boxes, which were hooked to small screens that scrolled images across them. To the left was a portable chalkboard where complicated algorithms were scrawled. To the right were thick black cables that ran from a central control panel and attached to a large blue telephone booth. Everything buzzed and chirped with excitement.

"But how?" Twilight said, "That technology has to be hundreds of years ahead of its time! What are they doing here?"

"Listen to me carefully Twilight Sparkle. This technology comes from the present. Right now in the real Equestria, you are sitting in a cryostasis chamber deep below Canterlot. You have been that way for exactly one thousand years. The place you are in now is actually a dream. This is all simulated to seamlessly interact with the conscious mind in creating a new reality."

Twilight stared back at her, backtracking the events. "Wait, when did I get put in there? I don't remember anything like that happening." she said.

"After you defeated Nightmare Moon, my sister explained the situation, and you agreed to be willingly placed inside. However, for your own protection we used a memory spell. If you are so willing, I can unlock the memory. It may answer some of your lingering questions."

Twilight thought for a moment and nodded.

"Spike, take a note please. I, Princess Celestia, hereby decree that the unicorn Twilight Sparkle shall take on a new mission for Equestria. She must continue to study the magic of friendship. She must report to me her findings from her new home in Ponyville."

"Oh, thank you Princess Celestia! I'll study harder than ever before!"

"Before we get too far into the festivities, may I have a word in private with you?"

"Absolutely. I'll see you guys at the party!" Twilight said, pushing her way out of the group hug.

Princess Celestia led Twilight back to the library and closed the door behind them.

"Twilight, what I am about to tell you is for your ears only. Under any circumstances, do not relay this to anypony else. Understand?"

Twilight nodded slowly.

"Good." she said, pulling a dusty book from the shelf. "Do you recall this book?" Twilight brushed the thick layer of dust from the cover. "No. It doesn't say anything on the front." said Twilight, bewildered. Princess Celestia nodded, "That's because this book is strictly forbidden in a wing of the castle that is heavily guarded. It contains Equestria's most well kept secrets from hundreds of thousands of years even before me." she paused, "However, it also contains prophesies." Twilight looked at her teacher. "So what does this have to do with me?"

Princess Celestia levitated the book upwards and opened to a page.

Etched in charcoal was a drawing of a unicorn. Squinting, Twilight examined it closer. "Wait a second. That's my cutie mark!" she said, taken aback. "But how? If this book is hundreds of thousands of years old, how am I in it?"

"The world works in strange ways, my student. I've translated it over and over but the result is the same. Exactly one thousand years from now, there will be a terrible war between us and the Changeling Army." Princess Celestia closed the book and poofed another one into existence. "This one is from my private collection. It explains everything we currently know about the changelings. However, if you agree to my proposal, there will be no need to read about them."

"What do you mean?"

"Back in Canterlot, my top scientists and I have been working on a new technology that will, for lack of a better term, preserve you for one thousand years. From there we can place you in an alternate reality where this conversation never happened and simulate possible scenarios to allow you to gain experience on defeating them and hopefully prevent a war in the first place." she said, pausing for a moment. "I realize that you may be apprehensive as to believing in myths and legends. However, we believe there is sufficient evidence to warrant concern."

"I believe you, Princess. I'll do whatever you ask of me." Twilight looked up sadly. "But what about my friends?"

"I'll explain the circumstances of the situation to them. Also, with our technology it will be like they never left."

Twilight looked longingly out the door, listening to the faint noises of the party. A tear rolled slowly down her cheek.

"Can I at least say goodbye?"

"Take all the time you need."