War for Equestria

by R-Dashiefan20

Rating: mature
Tags: Adventure, DJ P0N-3, Spitfire, Sunset Shimmer, Anthro, Main 6, My Little Pony: Friendship is Magic, Dark, Alternate Universe, Romance, Trixie
Length: 4826

Sombra rules Equestria with an iron fist... literally...

When Cadence and Shining have failed in their initial attempt to stop Sombra from returning and taking over Equestria, it's up to a small faction of resistance fighters to carry on what used to be...

Published 2016-01-31 22:40:01 UTC
Last updated 2016-12-13 01:04:30 UTC

Introduction

It has been five years since Sombra returned. It was a sudden change for the once peaceful land of Equestria. During the first few months of his new reign, he sought vengeance upon those who had tried to keep him at bay.

The first to fall was Princess Celestia. She had fought hard, but in the end Sombra got the better of her. Shortly after, Princess Luna fell to his dark magic.

With the princesses of sun and moon gone, the world of Equestria was bathed in a sort of limbo between day and night. The sun never fully rising and the moon never truly issuing night.

Several months went by as a moderate army of resistance fighters was formed, lead by Celestia's heir. He lead the resistance fighters to several victories, but unfortunately, fate had other plans for the son of Celestia.

During a frontal assault on Sombra's black castle, he made the mistake of getting cocky. He attempted to take on the king of darkness alone. With one near fatal blast of Sombra's dark energy, he was driven mad and his body broken. With the help of a newly developed stealth technology, the resistance fighters were able to rescue their injured leader and safely return him to their base.

Without proper technology to mend his broken mind, they had no choice but to place him in a form of hyper sleep after repairing his broken body. Time went on, both sides having victories.

The princess of love, Mi Amore Cadenza, was the next to fall to Sombra's blade. He made an example of her by displaying her severed head on a pike outside his black castle. This angered her newly wed husband and caused him to make the fatal mistake of charging right into a trap set by the dark king himself.

After a short battle, Prince Shining Armor was killed. His head joined his bride's outside Sombra's black castle. With Celestia's heir still out of commission, this left one pony to lead the resistance, Princess Twilight Sparkle. It wasn't long before she too fell to Sombra's dark ways. The loss their last princess was a huge hit on the moral of the resistance fighters. Many left and joined Sombra's mind controlled army willingly, seeing no other alternative.

This turn of events dwindled the resistance's already low numbers. The few scientists that had remained worked day and night to attempt to restore the mind of Celestia's lost heir and craft artificial limbs for those who were injured during battle. Even with their newest leader, Spitfire, the future and hope for Equestria looks grim...

Life in a stable

Rainbow Dash closed her field journal, having written down yet another page detailing her frustrations about her surroundings. She stuffed the small black and white journal back under the pillow of her cot and stood up.

She grimaced as she observed her surroundings for the millionth time. The room itself was painted a dull and faded gray. There were several more cots besides hers in the room, each was a bunk style bed. They were each dressed up in the same depressing stained white pillows and scratchy green wool blankets. Along the wall beside each bed was a locker to place personal belongings into.

She heaved a sigh as she grabbed her battered blue army fatigues from the locker, slipping them on and exited out into the dimly lit hallway. The long fluorescent lights buzzed and gave off a muted light as she made her way through the living quarters, passing each of the various rooms on either side of her.

Each room was exactly the same. Rows of cots, each with the same stained pillows and wool blankets. This makeshift base of theirs had, at one time, been built for the purpose of housing ponies during a nuclear disaster.

Stables, Rainbow Dash thought as she recalled the stories about them. She exited the living quarters and descended a flight of stairs, coming into a mess hall sort of area.

Along one wall was a small kitchen that only authorized cooks were allowed to enter. The other wall was lined with worn red benches. A few ponies sat at the benches eating various foods off of steel serving trays. Rainbow Dash approached the serving area of the kitchen and grabbed a tray.

Through the long open window of the service area, she could see a small stove with a couple of pots cooking food to be eaten later. Also in the kitchen was a moderately sized fridge with a small pantry just beside it. Just above the stove sat a crudely made wooden spice rack that was depressingly barren. She was shaken from her thoughts as she realized the cook was talking to her.

"... to eat, miss Dash?" He asked. She shook her head to clear it.

"I-I'm sorry... what was it?" She answered.

He chuckled lightly.

"What would you like to eat, miss Dash?" He asked again.

She managed a weak smile.

"Just an apple and some cider will do, Joe." She replied as the cook brought out a magically grown apple and some cider made from the same apples.

He set the items on her tray and waved to her as she made her way to one of the benches and took a seat beside a pink earth pony with dull flat hair. She sat down and sighed again as she listened to the hum of the generators that kept the place lit. When she sat down, the pink earth pony stood and saluted her.

"Good morning captain Dash!" The earth pony yelled as Dash took a bite of her apple and lazily saluted back.

"At ease, Corporal Pie." Rainbow Dash replied.

The earth pony dropped her hand and sat back down.

"The soldiers are awaiting you in the training room for daily drills ma'am." Corporal Pie said.

"Thanks..." Rainbow Dash replied with a roll of her eyes.

The same routine everyday had taken its toll on her mental state, making the slightest thing such as waking up, a chore. Rainbow Dash finished her apple and polished off her cider and stood.

"Corporal Pie, inform the soldiers I will be with them momentarily. I have business to take care of first." Rainbow Dash said.

"Right away, Captain Dash!" Corporal Pie saluted and ran off in the direction of the training facility.

Memories

Rainbow Dash slid her hand down the surface of the tank, the metal scraping softly against the glass. She turned from the tank, heaving a long sigh as shed headed for the exit. As she was leaving, she noticed a folder with 'PROJECT FREEDOM' stamped across it in large red letters. Against her better judgement, she picked it up and opened it. The crisp white pages blew a gentle breeze across her face as she leafed through it. As she read the contents, her face started to flush and her blood pressure rose.

She slammed the file shut and stormed out of the room, stomping through the various halls. The annoying buzz from the halogen lights only fueled her anger as she walked with clenched fists and gritted teeth. She reached her destination, a large door with 'CAPTAIN' printed across it.

She wasted no time and kicked it open, startling the occupant. The flame-haired mare inside dropped the clipboard she was holding and slipped a T-shirt on over her previously bare chest. "Doesn't anyone knock?!" She yelled.

Rainbow simply threw the file folder at her, a few of the pages flying out and onto the floor.

"Explain this! Now!" Dash demanded.

"Well... Uh..." Spitfire stuttered, picking up the loose papers and stuffing them back into the folder.

Dash slammed the door shut and cracked her knuckles.

"Start talking." Dash said through gritted teeth.

Spitfire set the folder on her desk and tapped her fingers against it.

"This is just a contingency plan for if things go too far south during the war. Spitfire replied with a cool expression.

"So, you had him turned into a fucking war machine?!" Dash screamed in response.

Spitfire took a deep breath and looked at Dash.

"You know how I feel about him!" Dash continued to yell.

"Rainbow Dash... I just made him indestructible... and maybe added a few modifications..." Spitfire replied cooly.

"What else are you hiding from me?" Dash asked, her anger still blatantly present.

"There is one other project the scientists have been working on, but Jet swore me into secrecy." Spitfire said, avoiding eye contact.

"Does that project involve someone else I care about being turned into fucking a war machine!?" Dash asked, rather loudly.

Spitfire only shook her head in response. Dash sighed and sat next to Spitfire on the bed.

"Are there any risks to this?" She asked.

"Not that we are aware of." Spitfire replied.

Dash grabbed the file and leafed through it again.

"If it comes down to it, I want to be the one to give the activation order." Dash said, after getting through the entire file. Spitfire nodded to this.

"Of course, the authorization code is on this paper." Spitfire said as she produced a slip of paper from her bed side table. Dash quickly took it and stuffed it into her right breast pocket. She stood to leave, stopping just at the doorway.

"Do you really think we need a WMD?" She asked.

"I pray that we don't Rainbow Dash, I pray that we don't." Spitfire replied as Dash opened the door and stepped into the hallway again.

The bright white of the halls and ceiling stinging her eyes a bit. She rubbed the tears from her eyes as she went. As she walked, the soft thud of her boots on the tile was almost hypnotic and causing her mind to wander. Her mind drifted back to the that day of first grade when she met Jet.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

It was a fairly cold fall day, a thin sheet of multi-colored leaves covering the ground. A cool breeze sweeping through the parking lot of the school, blowing the leaves into small twisters. She walked with her dad towards the entrance, her Wonderbolts backpack tapping gently against the back of her light blue jacket. She and her dad walked inside, passing a couple classrooms along the way. Inside each room was the same scene, other kids putting their things into their respective cubby holes. As they approached her classroom, Rainbow Dash could see Cheerilee waiting outside the door to greet the parents like usual. Cheerilee smiled warmly when she saw the two rainbow haired pegasi. She wore her usual sunflower adorned dress with a pink shawl over her shoulders to keep the cold breeze at bay.

"Good morning mister Blitz." Cheerilee said chipperly.

Rainbow Blitz smiled at her.

"Good morning Miss Cheerilee, how are you today?" He asked as Rainbow Dash let go of his hand and rifled through her backpack.

"I'm quite fine mister Blitz. I managed to get my promotion to teach the sixth grade students, starting next year." Cheerilee replied happily.

"Oh, that's wonderful news. Have you by chance thought about my offer to join us for Hearth's Warming?" He asked hopefully.

"I'm not sure yet, it might be conflict of interest. On the other hand, it would be nice to spend the holidays with a handsome stallion." She replied with a wink.

Blitz's face reddened a bit as Dash pulled out a piece of paper with a crayon drawing on it and handed it to Cheerilee.

"This is for you Miss Cheeriwee." Dash said as Cheerilee took it and looked it over.

It pictured a rainbow maned stallion holding hands with a two-tone pink maned. It was Cheerilee's turn to blush.

"Oh, well this is nice Rainbow Dash. Thank you." She said.

"Daddy reawwy wikes you." Dash said with a giggle and darted off into the classroom.

Blitz chuckled awkwardly.

"Kids say the darnedest things, right?" He said quickly.

Cheerilee giggled and twirled a piece of hair around her finger.

"Well, the sentiment is rather sweet regardless. She replied as the bell rang. "I'll see you later handsome." She said, giving him a quick peck on the cheek before heading into the classroom.

Blitz smiled widely as he walked back outside. Cheerilee shut the door behind her.

"Ok class, please be seated." Cheerilee said nicely.

The students quietly took their seats as Cheerilee stepped in front of the blackboard.

"Thank you. Now, first we have a new student joining us today. Please come in and introduce yourself." She said.

The door opened and a black and red haired pegasus colt stepped inside. He had on an old looking black hoodie and stained jeans. He slowly made his way to where Cheerilee was standing, his head down.

"No need to be shy dear, just start with your name." Cheerilee said, smiling at the nervous little colt.

He simply shook his head in response.

"That's okay dear, maybe later. Just take a seat anywhere." She said.

He walked quickly towards and empty seat in the back next to Rainbow Dash. He sat down just as Cheerilee started on her daily math lesson. Dash looked over at the new colt, noticing a set of silver dog tags on a chain around his neck. She just barely make out the engraving on them.

'Jet Stream; Ponyville Orphanage; (757)051-1950.'

She gasped quietly as Cheerilee passed out some worksheets. Dash groaned, she hated math.

"E-Excuse me... Do you h-have a spare p-pencil?" A soft voice said from beside her.

She turned to see the new colt looking at her timidly. She smiled warmly and nodded, pulling a pencil box from her backpack and handed him a pre-sharpened pencil.

"Th-Thanks..." He said as he took it and started on the worksheet.

After several grueling minutes, Dash finished just as Cheerilee was coming by to collect the sheets. Cheerilee took them to her desk to be graded later.

"Okay class, as usual we're going to be having our weekly spelling test." She said as the class let out a collective groan.

This made Cheerilee roll her eyes in amusement. "Don't sound so disappointed. Please, take out a piece of paper." She said.

The room being filled with the sound of rattling paper as the students got paper from various notebooks and binders. Dash tore an extra sheet out and offered it to the new colt. He took it with a smile. Cheerilee began listing off the various words, the students writing them down and spelling as best as they could. After the test, Cheerilee took up everyone's papers and set them on her desk next to the math worksheets.

"Okay class, please get out your History of Equestriabooks and turn to page 104." Cheerilee said, the class doing so.

Some of them taking out notebooks to take notes in. Dash, however stared blankly out the window. She watched as a large white duck flew by, late for its' migration. She imagined herself out there flying, Wind Rider and the Wonderbolts with her. Her imagination took hold, drowning out Cheerilee's lesson. She saw herself helping perform the Wonderbolts signature stunts. As her mind began to drift further, she was suddenly snapped back to reality by the high-pitched ring of the school bell, signaling lunch. Cheerilee jumped a bit at the sudden noise.

"Oh, well I suppose it's lunch time." She said, walking over and opening the door.

The class stood and stretched their muscles. After a few satisfied groans, the students headed towards the door. They grabbed their coats and hats along the way, for recess afterwards. Dash was second to last out the door, the new colt behind her. They all filed down the hall towards the cafeteria with the other two classes in the school. The students formed a line around the lunchroom, the clean white tables arranged in neat rows. Dash sighed as the line slowly progressed, the new colt still silent behind her. By the time she got through the line and got her tray, the others were already seated. She looked around the cafeteria at the various tables, most already full. She noticed the new colt heading for an empty table. Without even realizing it, she found herself sitting across from him at the empty table. He looked up from his tray nervously then looked around, as if expecting something.

"W-What do you want?" He asked timidly.

She shrugged.

"You never towd anyone your name." She stated matter of factly.

He gulped down a bite of apple.

"I-It's Jet S-Stream." He replied.

She stuck her hand out towards him, causing him to flinch. He had his face covered with his wing.

"Are you okay?" Dash asked, keeping her hand where it was.

He peeked at her from above his wing, his blue eyes darting between her hand and her face. She felt something click inside her as she looked into his eyes. She didn't know what the new feeling was, but it made her pulse quicken and her palms sweaty. Slowly, he lowered his wing and extended his own shaky hand. As their hands met, Rainbow's smile widened a bit, she liked this new feeling.

"I, um, I'm Rainbow D-Dash." She said, surprised by her own sudden lack of speech.

Jet managed a weak smile, the bell for recess ringing as the cafeteria quickly emptied out. During all the commotion, Dash and Jet got separated. She started looking around for him when a commotion by the swingset caught her attention. There was a small group of kids gathered in a circle around something. She walked over.

"What's going on guys?" She asked.

She noticed something shiny in one of the colt's hands. It was a set of dog tags on a chain. The side she could see had a sun engraved on it.

"G-Give it b-back..." She heard a familiar voice say.

She looked past the group to see Jet huddled at the center, face red with tears.

"What're ya gonna do, tell your mommy?" One of the bullies said, the whole group bursting into laughter.

Rainbow Dash snatched the dog tags out of the bully's hand and glared at him.

"Weave him awone!" She yelled, Jet looking up from under his wing.

"Or what, Rainbow Crash?" The bully asked, getting in Dash's face.

She gritted her teeth clenched her fist, drawing it back. Just as she was about to swing, a golden aura surrounded the both of them.

"What's going on here?" A sweet voice said from behind them.

A mare in an ankle-length white dress with long flowing multi-colored hair stepped into view. Everyone gasped as Celestia herself walked over, examining the situation.

"Hmm, bullying huh? What's your name young man?" She asked, looking towards the bully still in Dash's face.

"Um... I-It's Ch-Chuck ma'am..." He said, shaking a bit.

The aura focused on just him.

"Well Charles, do you know the punishment for bullying in my day?" She asked.

He shook his head in reply.

"The punishment was to have your tongue removed so you could never say hurtful words again and have your hands cut off to stop you from committing violence." She said with a stern face, looking over the group.

They ran away in fear, Chuck trembling in Celestia's magical grasp. He had tears streaming down his face.

"I'm going to let you go now, but no more bullying, or else. Got it?" She asked, bringing him to eye level with her.

He nodded quickly, wetting himself. She dropped him. He hit the ground with a heavy thud, quickly getting up and running off. Celestia turned to Rainbow Dash and Jet. She walked closer and knelt beside them.

"What's your name young lady?" She asked.

"Rainbow Dash, ma'am." Dash replied confidently.

Celestia smiled warmly and gently brushed Dash's hair back.

"That was very noble of you Miss Dash." Celestia said.

"I just fewt I shouwd hewp." Dash replied.

"Oh, and why is that?" Celestia asked with a raised eyebrow.

Dash shrugged.

"He... He makes me feew weird, but good weird..." She explained as best as she could.

"Hmm, I see." Celestia replied, turning towards Jet and slowly extending a hand. Jet sniffled and lowered his wing, looking between her and Dash. He slowly took her hand, Celestia gently helping him to his feet. He let go of her hand and stood there, arms crossed. Both ladies let out a small gasp as they looked him over. One of his eyes was blackened, both elbows skinned, shirt ripped, hair frazzled, and one wing was bent at a painful looking angle.

"My goodness, you are a mess dear." Celestia said.

She took the dog tags from Dash and moving back to Jet. She gently put the necklace back on him and kissed his forehead. A golden aura surrounding him. When the aura faded, he was healed. His eye good as new, his elbows healed over, his hair brushed out, his shirt mended, and his wing bent back correctly.

"There, good as new." Celestia said with a smile.

Jet smiled back.

"Th-Thank you princess..." He said.

She stood back up.

"Just remember, in the end, love conquers all." She said as she turned to leave.

"Love?" Dash and Jet said together, exchanging a look.

Celestia only giggled as she headed inside.

Visiting an old friend

Rainbow Dash slowly stood, stretching her aching muscles. She grabbed her tray and set it on the conveyor by the service station to be taken back to the kitchen to be washed. She heaved another sigh and looked down the hallway to the science wing, her current destination.

She walked slowly toward the entrance of it and swiped her key card, the door opening with a hiss of compressed air. She entered the hallway and made her way through. Along the hall was a series of doors, each giving way to rooms where the few scientists they had were working on equations and various mechanical replacement appendages.

She lifted her left arm into her line of sight. What was once a part of her own light blue flesh, was now replaced by a beaten silver length of steel. She flexed the fingers on it as a mechanical whirring sound came from the silver limb. While she stared at the artificial part, her wings inadvertently twitched, causing her to look back at them. The dim light of the hallway gleamed off her right wing, also a cybernetic falsie. She remembered the day she got the 'enhancements'. She remembered all too well, sometimes the memories coming back as a nightmare.

It was during a battle to retake Canterlot castle, one that was unfortunately lost to them. She had misjudged one of Sombra's warrior's speed and it had caused her wing to be severed as he struck with a painfully sharp spear. After that had happened, she tried to retreat with the rest of the army. She was almost out of the castle walls when a chunk of rubble fell and hit her, it had pinned her arm and crushed it beneath the weight.

With no options and Sombra closing in on her, she had used her dagger to sever the arm a few inches below her shoulder. With a loud cry of pain, she sliced though the skin and bone in one swift move. She tore the sleeve from her other arm and quickly tied it tightly around her now armless nub. With the help of their first general, Celestia's son, she had managed to get back to the base and he had ordered that they give her the artificial limbs they were working on creating.

Shortly after, she awoke to the sight of the general standing over her smiling. She slowly got up from the gurney she was on and looked at herself in a mirror on the opposite wall of the infirmary room she was in. She had come to the realization that she was standing in front of him wearing only her sports bra and underwear, quickly moving to cover herself as she blushed deeply. He chuckled behind her.

"Relax. Not like I haven't seen you nude before." He had said jokingly.

She relaxed a bit and glared at him. She looked into the mirror, a look of shock crossing her face as she saw that her arm and wing both were now robotic in nature. She could still feel a phantom pain from her severed limbs and shuddered. She had no idea she would end up like this.

She snapped back to reality as she bumped into a scientist unicorn carrying a clipboard and pencil, causing her to drop a folder of papers.

"S-Sorry..." Rainbow Dash apologized.

The unicorn knelt to pick up her fallen papers and waved a hand at Rainbow Dash.

"Quite alright Captain Dash. It was completely my fault, I was lost in my reseach." The unicorn said politely.

Rainbow Dash managed a weak smile and knelt to help her pick up the various papers. Rainbow Dash stopped with her hand on a particuliar page that caught her eye. It showed a recent brain scan.

"Is that... from him?" Rainbow Dash asked hopefully.

The unicorn nodded and picked up the paper, showing it to her.

"The scan revealed that his psyche is fighting the effects of Sombra's dark magic." She said.

"Does... does that mean there's hope to get him back?" Rainbow asked.

The unicorn thought for a moment.

"Well... I suppose if his psyche were to continue to fight off the madness, then in theory he could come out of it unscathed. Although, with the state his body is in, we cannot be sure the shear shock of it won't drive his senses back into a state of madness." The unicorn said bluntly.

"Oh... I-I see..." Rainbow looked at the floor, covered in a thin sheen of dust.

"I am sorry, Captain Dash. We are doing all we can to help bring him back to us. But, if I may... why do you always come in to see him? We would willingly send news if there was ever a change in his state." The unicorn said as she stuffed the papers back into the folder, a bit messily.

"Uh... personal reasons..." Rainbow replied, a light blush visible on her face.

The unicorn placed a hand gently on Rainbow's shoulder.

"I understand." She said before standing up again and heading into one of the rooms along the hallway.

Rainbow slowly stood and brushed a bit of dirt from the knee of her pants and headed into a brighter lit room at the end of the hallway.

The room was about the size of a high school football field, but rounded off on all sides. To her left sat a table with wheels that had random medical equipment sitting on it. Off to the right was a doorway that led to the scientist's personal areas, such as bedding areas and perhaps even a rec room. Along the opposite wall was a large computer console that had various screens showing multiple diagnostic things about the main part of the room.

In the center of the room was a large tube like construct that had a single control panel extending from it's base. The tube itself was filled with a liquid substance that was one part water and two parts artificially created nutrients. What was inside the tube was what concerned Rainbow though. Inside the hypersleep container, as the 'eggheads' called it, was the son of Celestia himself.

He floated in the ooze inside the tube. There were various hoses connected to his body from the outside of the tube. One was leading from his mouth and nose to a device that kept him breathing, another led from his chest to a makeshift defibrillator that kept his heart pumping, and a third hose led from the middle of his back to an electrical type device that kept his newly fashioned cybernetics in working order on the off chance he'd come around again.

When she had seen him brought in, his body destroyed and his mind shattered, Rainbow Dash had broken down in tears. They had to replace almost his entire body with cybernetic upgrades so he would live.

She didn't like to admit it, but she liked him. They had been close friends since first grade. He had grown up his entire life as an orphan, his mother leaving him there as a result of a stupid law that restricted royalty from having children if they were unwed. It wasn't until Sombra started his rule that Celestia had claimed him as her child.

Rainbow Dash placed her hand on the glass of the container, a soft tinking could be heard as her metal fingers touched the surface.

"One day... one day we'll have you back... I'll have you back..." Rainbow said quietly as she looked into the closed eyes of her closest friend.