The Rising of the Silence

by KodyMcQ

Rating: teen
Tags: Original Character, My Little Pony: Friendship is Magic, Other, Adventure, Octavia, Tragedy, DJ P0N-3, Dark, Alternate Universe, Doctor Whooves, Sad
Length: 3213

When Equestria is threatened by a mysterious cult of faceless ponies, who is there to help?

Equestria has always been a big, fun, happy family. But what if there has always been a species controlling the actions of Ponies? The Silence, a species which has hardwired the universe to forget about them should you look away, has been attacking Equestria. And after Vinyl and The Doctor's honeymoon, they return to Ponyville, to reunite with Vinyl's family. But what can save Equestria, when there is no Doctor to help?

The third story in the Re-Written Equestria Saga. Go read the other two if you want the first couple of chapters to make sense!
#1 Octaves of Time
#2 Cadence for a Shy Alicorn

Cover Art again by Me!

Published 2012-06-18 16:24:02 UTC
Last updated 2012-06-18 16:24:02 UTC

Prologue: Scootaloo Takes a Fun Ride

"Seeya later, Scootaloo!" Apple Bloom called out from behind the speeding Pegasus. They had just spent their day crusading for their Cutie Marks, with things such as Apple Painting, Apple Eating and Apple Sculptures. All of course, to no avail. Sweetie Belle had missed out on the party, having to be a model for Rarity on the extremely sunny day.

"Bye Apple Bloom!" Scootaloo yelled out, barely able to hear herself over the high pitched whine of her wings roaring to life. She shut her saddlebag with her wing, and messily shoved her purple helmet over her hair. Her scooter began to move, her senses telling her to put her hooves on the handles. She did as her gut told her, and began to speed over the hills by Sweet Apple Acres.

She passed dozens of trees, plants, and fauna, occasionally passing another pony, wishing her luck with her Cutie Mark, or just saying hi. That was the type of town she lived in. Calm, gentle, caring, loving. Ponyville. On the outside, she enjoyed the serenity of the place, but on the inside, she wished there would be something at least a little different. But no, her wishes never came true. Every day, it was always the same ponies, passing by and saying hello.

Scootaloo sighed and continued down the path, bounding over small rocks and roots. Looking up, she noticed the sun was going down relatively quickly, and was just on the horizon now. She passed by a few houses, and ducked into the bright pastel coloured alley behind them. More rocks vibrated her and her scooter, as she continued bounding down to her cottage home at incredible speeds.

She finally raced down a steep hill, and then back up halfway. She jumped off her scooter with almost no sound, and then dragged it down to where the deepest part of the small valley was. The sight at the bottom was something of a cartoon to her, twinkling water under the sunset, only disrupted by the waterfall racing off of a steep cliff. To the left, was a slow river, and a small path carved out beside it. To the right was more hill, and a small cottage. Scootaloo took the path to the left on her scooter, this time a little slowly, to avoid falling in.

The river slowly began to race faster as she got further, and small granite rocks poked their heads above the waters. Scootaloo didn't care for the sights though, as she was lost in thought, looking down at her feet on the scooter.

'I'm nopony important.' She thought, still meandering down the path. 'Maybe I haven't gotten my cutie mark yet because I have no special talents. I mean, what kind of Pegasus can't fly? Even Fluttershy can do it, why can't I?'

Scootaloo continued down the path, as she has hundreds of times. She could do it in her sleep, she's passed by this area so much. But something was new this time. And she didn't realize the new, unknown Pony standing in front of her until she bumped into it.

"Oh! Sorry! I wasn't watching where I was going!" She worried, jumping off her scooter and looking up at the tall pony. And as soon as she had seen the face, or lack of face, she suddenly wished she hadn't looked up.

The gray, faceless pony simply stood there, it's dark maroon mane flowing lightly in the wind. It towered over the small orange Filly in front of it, ignoring it's presence. Slowly, it's head looked down at the shivering Filly, seeming to bring up a dark cloud behind it's head.

Scootaloo continued to shiver in front of the strange Pony before her, never seeing something like it. It didn't even have a cutie mark. It was just a blank, colorless pony, with a deep dark maroon mane.

"You have made a deep mistake." She heard, but not knowing from where. Slowly she realized that the voice seemed to emanate inside her head, meaning to her the pony had some form of mind speaking power.

The gray pony began to move it's left hoof towards Scootaloo, changing the colors of the clouds to a deep, dark blood red. She gave up - Scootaloo ran. She ran as fast as she could around the bend in the path, fluttering her wings for less weight, and added lift for speed. She was so shocked by what she had seen, she couldn't even scream. Or see the other faceless pony she had bumped into around the bend.

The next gray pony was exactly the same, dark gray, maroon mane, and faceless. The only difference was this pony stood taller, Scootaloo's head barely reaching it's belly. It too, began reaching a hoof towards Scootaloo, this time it's hoof surrounded by some form of deep, blood red lightning. Scootaloo lost it.

She jumped into the river.

Her body was immediately swooped away by a change in the rapid current, dragging her along at a speed that could rival Pinkie breaking the 4th wall. Her body tumbled helplessly, bounding off of rocks and being whipped around by waves. She tried to reach out her wings, to see if she could lift herself up. What really happened was her landing on her side, and breaking her wing. Her right wing now flopped at an awkward angle, with her tumbling body yelping in pain.

"HEEEEEEEELP!"

Scootaloo grabbed on to the next rock she could find, bracing herself against the rapid water. It pulled her along, and she took a small glance at what she was about to head into. She saw nothing, but water dropping off of a steep cliff, and her cottage home resting beside her. She knew this cliff, she was always told as a child to not go near it.

"Now Scootaloo, don't get too close to the water! You might get swept away!" Her mother called out, as a young baby Scootaloo played on the shore. She had built a small, but very decent Sand Castle, just out of reach from the waves. She ignored her mother's calling, and continued to frolic by the shoreline, enjoying her childhood. She dipped her hooves in the water, then immediately bounded out, and started crying.

"Oh Scootaloo! Was the water cold?" Her mother sulked at her, as Scootaloo muttered a sobbing "mhmm". Scootaloo's mother picked her up and threw her on her back, holding Scootaloo between her wings and spinning in circles. This immediately got Scootaloo out of the bad mood, and she began to laugh and giggle.

Scootaloo's brother heard the giggles, and being only slightly older than her, loathed for the attention. His life was spent to staying in the attic of their riverside cottage, too young to go to school, but too old to frolic by the shoreline. He watched solemnly as his mother spent all of her attention on his baby sister, wishing that he could get some. Then he remembered her mother's words, "Don't get too close to the water. It could sweep you up and over the cliff." She had told him, when he was Scootaloo's age.

He rushed down the stairs, and burst through the doors. Going around the happy and cheerful sight, he ducked into the trees, and felt his hooves sink into mucky leaves and water. He sighed, before taking a leap into the river. It wasn't very strong, but it was strong enough to carry him.

Scootaloo and her mother continued to play by the shoreline, building another sand castle. This bugged her brother, and he reached out to the shore with a his magic, pulling out a seashell from the sand and tapping his baby sister on the head with it. Scootaloo whipped around, obviously interested in this strange feeling of confusion.

Scootaloo began to walk towards the water, whilst her mother continued on the castle. Her mother didn't take long to look up though, and she saw both her children in the river, being swept away (albeit slowly) by the current.

"Scootaloo! Cuso!" She cried out, before flying above the water, and plucking Scootaloo out of the water by her mouth. Scootaloo was deposited on the shore, giggling at the feeling of water drying on her coat. Scootaloo observed the scene of her mother pulling her brother out of the water, turning her head to the side in a very adorable manner.

"Cuso! What are you doing in the water?" The mother asked, tugging on her son's hooves to pull him to shore.

"You spent way too much time with the baby, mom. Why can't I get love like that? WHY DON'T I GET LOVE LIKE THAT?" He shouted, before his magic began to kick in and make the river go faster. The tide rose, slowly getting the attention of his baby sister, and drawing her closer. Their mother began to tug harder, as they neared the edge of the cliff. The mother saw Scootaloo get swept up by the river, and let go of Cuso. At speeds faster than ever recorded, she plucked Scootaloo up and tossed her on the back porch of the cottage, then quickly flew back to her son.

"Cuso, I love you. Scootaloo loves you. Just, calm the river!" She cried, submerging herself in the water and using all of her force to try and push the son out. He simply closed his eyes.

"I'll see you in hell, mom." He said. He gave the river a push, increasing the speed of it. His mother rose from the river, crying out to her daughter.

"Scootaloo! I'm so sorry!"
Her last words were drowned out, as both her and Cuso were swept off the cliff, falling a good 30-50 feet.

Scootaloo's eyes began to water, as she recalled the memory as vivid as if it were happening before her. The river began to race faster and faster, thrusting against her with each wave. Her hoof slipped, and she lost all focus on the rock as her body was quickly swept up and thrown off of the cliff.

When Scootaloo opened her eyes, she was sitting on the shore of a small pool. It looked almost identical to the sight she'd seen in the valley, but the cliff was much larger. Her wing was bent awkwardly on her side, still broken. She took a deep heavy breath, and stopped when she felt the sharp jabbing pain in her chest.

'Broken ribs. Great.'

Slowly she gained enough strength to stand up, wobbling and taking a few experimental steps. For the first time, she observed her new environment. Large, leafy green jungle trees surrounded her and the shore, occasionally broken by the dense undergrowth. She took another small sigh, and began to fumble her way around in the jungle, before smacking her face into something soft. Something gray and soft.

Looking up, she gulped as she stared into the faceless Pony she'd encountered earlier. She was quickly forced to the ground by a strong hoof, and it placed itself on her chest. She simply gave in, too tired to try and escape.

"You will pay for your mistake." The deep voice once again echoed through her head, sending a shiver down her spine. The hoof began to glow with the blood red lightning, scaring Scootaloo greatly.

"Who... Who are you?" She managed to choke out.

Scootaloo got no answer, as the lightning rose in volts and fried her mind. Scootaloo's heart slowly came to a stop, before being shocked back to working again. Slowly, the blood red lightning began to cover her lifeless body, draining the color from her coat. Her mane began to change color, catching fire, then extinguishing, revealing dark maroon hair. Her facial figures began to corrode and change to ashes, melting down her gray face.

"Doctor"

"Hmm"

"Doctor..."

"Hmm. Interesting."

"Oh Doctor!"

"Hmm."

"DOCTOR."

"Oh what?" He answered, looking up from his invigorating book on cats.

"I've been calling you for half an hour, sweetie. We're back in Ponyville." Vinyl responded, rising from her seat across the Doctor.

"Oh."

The Doctor followed her out the door, regretfully putting down his book. He tightened his bowtie, and followed suite of where his Wife was taking him.

The Time Couple came to Ponyville for their honeymoon, after getting married on some planet by a Frozen Star. The Doctor still wasn't sure how a star could be frozen, but it has happened twice to him so far, so he just began to accept it. The universe is weird, especially to a Time Colt who's wife is forcing him to wear a bowtie everywhere he goes. When she'd first made him wear it, he was resilient, but it grew on him quickly, and now he won't go anywhere without it.

"Doctor."

"I hear you, Vinyl. What's wrong?" He answered immediately, popping up right behind his wife. Vinyl simply nudged her head upwards, towards the blood red clouds, circling and twirling in every direction.

"Funny." He answered. He'd never seen something quite like it, in all of his years of living.

"They're twirling, and rising in colors and amounts." Vinyl noted.

"Pony made. But not necessarily Unicorn." He responded. He began trotting into Ponyville, which seemed desolate and empty. Usually it was bounding with life.

"Vinyl, do you remember where your mother lives?" He asked her, receiving a nod of agreement. "Good, we're coming for a quick family visit."

Octavia and Starburst watched their new excited young Foal bound around the house with excitement, enjoying the strange blood red tint coming from the sky. These clouds were popping up all over Equestria lately, with no explanation as to why. And there were even some rumors that Ponies were going missing during the appearance of these clouds. Fluttershy sat in the other room, having opted to stay back from the Time Couple's private wedding. Her home had been destroyed by a hurricane in her months of travelling with The Doctor, and as friends of the Time Colt, the family had gladly let the fourth member live with them for a few days.

"Diaton, calm down please honey. The Doctor's coming for another visit." Octavia said in a monotone voice, tired with attempting to calm down the child. Starburst had already finished his attempts, and was now happily taking a nap on Octavia's shoulder. Diaton still continued bounding around the home, ignorant of his mother's wishes.

Fluttershy's head poked from the side of the doorframe, inquiring if she was needed. Her question was met with a desperate mother's nod, and Fluttershy emerged from the Guest's Room.

"Diaton dear?" Fluttershy asked in her hushed voice.

Diaton immediately stopped and turned to Fluttershy, giving her his full attention.

"Mommy and Daddy need you to go to bed now. Could you do that for them?" She asked him, giving him a hopeful look.

Diaton shook his head.

"Would you do that for Aunty Fluttershy?" She asked again, using the pet-name their family had adopted for her.

Diaton quickly nodded his head and rushed off to his room, shut the door, and wasn't heard from.

Fluttershy smiled, satisfied with her ways. She nodded to the drowsy Octavia, who was now falling asleep on Starburst's head. She trotted back to her room, and used her wing to quietly shut the door.

BANG.

Fluttershy winced, thinking she had made the sound closing her door, but in reality, Vinyl and The Doctor had burst through the family's home.

"Wee'rre back!"

The house erupted into cheers, as every tired essence in them was drained out. Even Diaton, who had apparently 'Gone to bed', was now bounding around his older sister. Octavia gave Vinyl a bearhug, then gave The Doctor a bearhug as well.

"How's it been you two?" She asked, stepping back and allowing her extended family to sit.

"Great. What's up with the fancy weather? Aliens? Daleks? K9? Please tell me it's K9. I miss him." The Doctor asked, bounding over to a chair, and leaping into it.

"No, nothing of the sort."

The Doctor paused to think. 'Strange red clouds, swirling and tumbling in the sky...'

"Have Ponies been disappearing in these storms?"

Octavia gave a small nod.

"Well then. It's obviously..." He paused. "I have no idea. But it's nothing natural, and nothing Unicorns could make. Not living unicorns anyways. Mayb-"

He was cut off by a blood curdling scream, coming from somewhere between SugarCube Corner and the home. The Doctor, Vinyl, and Octavia quickly rushed through the door, leaving Starburst with Diaton. The took a left, and saw the source of the scream.

A blue unicorn, with a lighter blue highlight in her hair was running away from a much taller Pony. The taller pony was dark gray, with deep maroon hair. The Doctor took a few steps, and a closer look at the Pony's face. But he saw that there was none.

"What in god's name is THAT." He asked, turning to the shocked ponies behind him. They'd obviously seen the faceless Pony as well, and simply shrugged at The Doctor.

"Well. That's new. Something I've never come across. Let's go say hi!" He said, bounding up and down with excitement.

"Doctor..." Vinyl asked.

"Maybe we can be friends with it!"

"Doctor..."

"It could come with us, Vinyl!"

"Doctor, we don-"

"Here you go Vinyl. It could be our adopted child!"

"DOCTOR WOULD YOU LISTEN!" Vinyl shouted, attracting the attention of the Time Colt. She again nudged her head, pointing behind him. The Doctor gulped, and faced the tower behind him.

He took a look up, and was staring into the faceless visage of the gray pony.

It's gray coat was a contrast to it's deep maroon mane, and was easily recognizable to The Doctor as long as he was looking at it.

"Hello, Silence." He said. Vinyl shuddered and glued her eyes to the tall gray pony.

"Silence?" Octavia asked.

"Some of the oldest aliens in the universe. They can, quite literally, erase themselves from your memory. Specifically, as soon as you look away." The Doctor said, still looking towards the Silence towering over him. The Silence slowly raised a hoof towards the Doctor, gaining an inquiring look.

"Never seen one do this before." He added.

The hoof began to glow with blood red lightning, and struck the Doctor on the back, eliciting a scream of pain. The Doctor then focused, and began to glow with small gold specks of dust. Soon, they began to erupt from his hooves.

"What's happening?" Octavia asked, freaking out at the strange sight.

"He's regenerating mom, he'll be-" Octavia was interrupted by another scream from the Doctor.

Looking over, she saw the Silence once again strike the Doctor with it's hoof, ending the regeneration process. Vinyl almost collapsed at the sight.

"Vinyl, what's wrong. Why'd he stop regenerating." Octavia asked, worrying more and more through her calm british accent.

The Silence looked directly at the mother and daughter.

"Time Ponies have two hearts... That's why we can't die... When you try to kill one, it'll regenerate. But if you kill it while it's regenerating... It's dead."

"What does that mean, Vinyl. Tell me!"

"The Doctor is dead."