The Mutant Wars

by DerpymuffinAuthor

Rating: mature
Tags: Dark, Alternate Universe, Sad, Tragedy, Human
Length: 3790

"For all the true Equestrians out there, run, head to Ponyville were you'll be safe." that was the last known words of Prince Lightning Sky to the Loyal Citizens of equestria

Ever since Prince Lightning Sky went missing, Equestria has changed. Mutants have been found out and hunted down , for fear they will be a threat. Ponies have fled to the small villages, most of Canterlot had been burned down during the Mutant War, along with half of Manehatten. Forests had become thick. Storm, Snowflake and Flame have fled from Cloudsdale, not wanting to be sent to war that had risen. Follow the mutants as they survive, bombings, gunfights, hunters, and the elements as they attempt to survive the Mutant War

Published 1970-01-01 00:00:00 UTC
Last updated 2015-02-21 01:59:32 UTC

The Burning of Canterlot

     Blossom walked through the busy streets of Canterlot. Her brain slightly throbbed, making her mentally groan. The sky was clear except for the clouds on the horizon. She stopped at a booth and looked over the produce. "I even got apples all the way from Sweet Apple Acres!" Blossom smiled and bought some apples, handing over some bits she headed home.

~Time Skip~

inside an apartment Blossom laid on her bed fast asleep, oblivious to the world outside. Outside the sun had set and clouds had covered most of the sky, sending darkness over the city as large groups of soldiers blocked the entrance to Canterlot. The  civilians unknowing of the soldiers walking through their city. The captain held a strange device in his hands. It began to beep loudly and he stopped. "Set fire to the city."

was all he said and the soldiers ran through the city, pulling out lighters and explosives and that's when the city went to burn.

BOOM!

Blossom yelped and fell from her bed, she stood up and looked around. She heard a faint crackle and felt a large migraine set in. "Ugh!" she groaned.

staggering from her room to the kitchen and opening the cabinet. She pulled out a bottle and opened it.

"Why?" she asked silently, chugging the bottle which was full of pills. The migraine instantly turned to a dull throb.

"Weird. Normally it goes away entirely." she stood up and headed to her window, only to be greeted with a horrible sight. Fire was bursting through windows, people were fleeing and screaming.

  She heard explosives go off and buildings were caving in on certain spots. Blossom gasped, turning to her kitchen, grabbing her satchel she filled her bag with plenty of food and several water bottles. She was confused as alarms went off through the city.

She grabbed all the bottles of pills and dumped them into her bag. She ran to her bedroom, grabbing her savings and several pieces of clothing. She ran to her door only to find it jammed shut. She groaned and placed her hands on the doors.

With a sudden burst of purple and green light the door was entwined in vines and ripped off the hinges. Blossom grabbed her hoodie and ran through the door frame, jumping over the shattered remains of the door and was only a couple feet away from her doorway when it exploded into flames. Blossom screamed and ran from the fire, throwing herself down the stairs.

She found debri and several other things scattered among the stairs, the stairway exploding into flames behind her.

She ran to the street. There were people running around screaming. She pulled her hood over he head and headed for the gates, only to find lines of debris blocking them. Blossom felt tears fill her eyes.

The city was becoming devoured in fire, burning people to death or suffocating them inside falling debris, slowly.....painfully. Blossom shook her head, pushing the painful thoughts from her mind, she jumped onto the piles of debris, being careful. There was cries and screams as people fled from their homes.

Then the ground shook with a giant explosion  and Blossom fell off the crumbled pillar she was trying to climb. She spun around to see a flaming building crumbling towards the ground at a frightening speed. She looked up to see planes flying over them, bombs diving down on the city. She turned to see a cloud of debris heading towards her.

She saw several bombs heading her direction as well. With no second thoughts Blossom dived into a small space provided between the debris, dust flew through the hole as the debris covered the hole, trapping Blossom inside as the world went quiet.

After several minute Blossom pushed at the concrete chunks above her, letting in the light as she was freed from her hiding. The sky was covered in clouds, some of them being smoke from the still going fires.

Blossom turned to the city she knew as home her whole life.

Tears filled her eyes as she watched buildings collapse. She turned and climbed over the debris and landed on the other side. Then the city exploded behind her. She stared for several minutes before the clouds began to pour onto the city.

Blossom turned around and fled, tears falling from her face the entirety of the way as she headed to the only place she knew safe. Appleoosa.

The Prince

     "Storm! Storm!" a orange haired boy cried out, slamming his fists into a door. After several minutes of him mercilessly pounding the door, a boy with coal black hair opened it. "Flame? Flame what are you doing?" Flame pointed out the window. Confused, Storm walked over to the window and looked out.

  Storm and Flame were friends that lived in a house with several other ponies, one being Snowflake, a beautiful, blue-eyed mutant.

Yes mutant, Storm, Flame, and Snowflake were three of the few mutants of Equestria. They had found out Snowflake's secret not too long ago.

  "N-No." Storm stammered, staring at a group of soldiers as they began knocking on the door to their house.

"I'll get Snowflake!" Flame told him and ran to the girls room. Storm ran into his room and grabbed a bunch of clothing and his special belongings, shoving them inside his bag and running downstairs to find Flame and Snowflake, theirs bags full of their belongings and extra clothing.

We grabbed our jackets, except Snowflake who shoved it into her backpack and pulled out a sachel full of water and food, including some medication.

"Excuse me. We need to examine this house." the three spun around to see one of their friends at the door, speaking with a captain

"Okay?" Storm turned to his friends

"Hurry! We need to go now!" the three ran up the stairs and stopped a large window.

"Wings?" Snowflake asked and the boys nodded, firey wings came from Flame's back while two ice like ones came from Snowflake's. Storm's wings were thick and furry like a dog.

"The sensor's signal is going mad!" and the three heard soldiers walking up the stairs.

"I FOUND THEM!" a soldier came running towards them. In a quick reflex he was thrown into a wall by Flame's pheonix-like wings. The three hurled through the window, shattering it to pieces. They heard gunfire but they flew past unharmed. Then Storm noticed that Flame was covering them in a fire shield.

"Quick! Head to Canterlot! We need to find Prince Lightning Sky!" and the trio flew to Canterlot.

    When the three reached Canterlot they were shocked, the sky was storming on it and smoke was rising from it. People littered the city, burnt and crying or dead.

"T-The castle!" Snowflake called out, flying towards the castle, only to see smoke coming from some windows.

The trio flew into the room Lightning lived in.

"Lightning Sky!? she called out and a boy ran over, he wore a golden circlet with blue gems, his hair was a bright blue and his eyes were green. He wore a night designed cape and blue clothing.

"What are you doing here?" Flame pointed at the chaos going on in Canterlot

"Do you see this?!" he nodded, picking up a backpack

"I was on my way out. There are bunch of soldiers searching the castle. But you belong in Cloudsdale." She shook her head

"They're storming Cloudsdale." and then there was a loud banging on the door.

"LET US IN LIGHTNING!" Lightning turned to the three and handed them some guns and ammo.

"You might need these. I want you to head to Appleoosa, there's a friend of mine there, his name is Braeburn Apple, he has a bunch of rebels with him, they know about the soldiers that are attacking Equestrian Mutants or suspects. Give him this" and Lightning handed Storm a folded piece of paper

"B-But y-your stuck in here unless you fly!" right then the door crashed into the floor.

"I'll hold them off. Gather the remaining loyal Equestrians together! Rescue Equestria!" Lightning Screamed, pulling out guns and shooting the soldiers

"HURRY!" and the three fled from the castle, Snowflake crying as she clutched the paper to her chest.

The Letter

   The sky was dark as rain poured over Equestria, as if it were mourning for the losses of massive cities and citizens that no one could save

Among the dark drizzle in the desert was three people, walking towards a settlement. When they reached the entrance one read it "Welcome to Appleoosa.."

the girl with purple hair stated and the other person beside them just stared

"You sure its safe here?" the person turned

"Of course Sweetie Belle. I wouldn't lie to you." Sweetie Belle stared at the person

"But what if the soldiers are there! Scootaloo W-What if-" she was stopped by her friend's hand.

"Hide!" and the two slid behind a boulder.

"This is it!" the three stared at the teenagers in front of them, the three quickly noticed the food and water they had, the three younger girls having nothing but clothes and half empty water bottles.

"Let's go look for Braeburn then." the one with coal black hair said and the trio walked into the town.

The girl with the pink bow looked at her friends before getting up. "C'mon. They're looking for Braeburn too!" but Sweetie Belle grabbed her friend's hand.

"But they might have something bad in store for him!" Scootaloo stood up

"We should follow them. After all we've gone through. We can't let them hurt Braeburn." and the few walked into the town, Scootaloo pulled up her orange hood to hide her face. Sweetie Belle wrapped herself tighter in her white hoodie. They followed the trio to the saloon were they walked in. The Crusaders watched from outside as the trio walked up to the bar, receiving odd glances from the Appleoosans at the tables.

"Excuse me. Do you know were I can find someone?" the bartender looked up

"Look pal. I don't provide information. I provide drinks. Now if you want I can get you one for a couple bits." Storm narrowed his eyes. Flame crossed his arms.

"Excuse me but we just want to-"

"Look. I don't provide information. I providedrinks. If you don't want a drink than you can just leave."

Flame narrowed his eyes and let out a exasperated growl, his eyes flickering with faint fire. Then Snowflake slammed her hand on the table, grabbing the attention of the bartender. "Look. I don't think you've noticed. But this is a war. And we just survived a storming in our city, Now." she said and crossed her arms.

"We're looking for a guy. We were told he lives here in Appaloosa." the bartender looked at her "Of course lass. Who may that be?" Snowflake set the envelope on the bar.

"This is  a letter from someone in Canterlot. We were sent to speak with someone named Braeburn Apple."

the bar went silent.

A guy with a dark purple hoode looked up, the only visible feature was a set of glasses.

"What do you want with him?" Flame turned "business...war business." the boy next to the hooded man stood up

"What kind of war business?" Snowflake stood in front of Flame.

"There has been a couple bombings. We would go to Prince Lightning Sky. But we already did." the guy stood up and walked up to Storm.

"What do you mean?" Storm grabbed the letter and held it in front of the guy

"He sent us with this." the crusaders slid into the bar, avoiding the gazes of the Appleoosans. "We're looking for Braeburn Apple too." Scootaloo spoke up, grabbing the group's attention.

"Mah sis says that he needs this." and the girl with the bow and held up a tattered piece of paper. The boy looked at them before turning to the hooded man. "Want me to go get him?" the hooded man shook his head.

"No. We'll take them to him. They'll be lucky he doesn't send them to the jail if they're spies."

"We aren't spies! We're just kids! You don't know what we've been through! I swear we just went through hell ta reach ya!" the girl with the bow snapped. The man nodded, turning to the group.

"Follow me." and he led the visitors towards a building.

Inside the building he led them to a staircase that led to what looked like a basement. But when the reached it they found it to be a very tech filled base, people at computers and glass doors that showed offices.

"He's in here." the man said and opened the door. Inside sat a man with brown hair, a cow boy hat, a vest and his waist was decorated with loaded guns.

"Ace? Who are they?" the man asked, staring at the people who had just entered

"Visitors Sir. They said they were sent with letters. One from Prince Lightning Sky." at the mention of Lightning Sky the man jumped up.

"Apple Bloom!" and Apple Bloom was wrapped up in an embrace faster than you could say "apple"

"What brings you three here?" He ask in a confused voice

"Apple Jack. She sent this to you," Apple Bloom handed him the paper. Braeburn looked at the others.

"What do you have from Lightning Sky?" Braeburn asked and Snowflake handed him the letter. "This."

"Yeah. He also gave us these guns for self defense." Flame said and Braeburn picked up the letter, opening it.

"Ace." Braeburn asked, turning to the cloaked male. "Gather the recruits. I have some news for them." Ace nodded and left.

"Are you friends of Lightning Sky?" the trio nodded "he's friends with all the mutant-Erm...." Flame stuttered as he said it. Storm shot him a glare

FLAME!!! Storm thought as Braeburn stared at him "Your mutants?" Snowflake stared at her feet. "Yes." Braeburn shrugged

"Any friend of the Prince is a friend of mine!" and they left the office, heading to a big area with a platform. Bunch of rag tag people filled the spacious, high ceiling, room.

"My fellow rebels. I have just found my little cu Apple Bloom. She has traveled all the way from Sweet Apple Acres with her friends Scootaloo and Sweetie Belle with a note from Apple Jack." the meeting area was filled with cheering as the crusaders made their way onto the platform, the other trio stayed hidden behind the wall with Ace and the boy. "I also have received word from an old friend. Prince Lightning Sky. It was personally delivered by these three." and the trio walked out "But this letter. Holds information not all of us may like." and Braeburn pulled out the letter, taking a deep breath he read into the microphone.

Dear Braeburn and whoever else is reading this. If you are reading this it most likely.....Most likely means I am dead.....There has just recently been a searching throughout various cities in Equestria. And Canterlot has been bombed, I was lucky enough to be in my castle.

I knew they would attack us. They are known as 'The Force' I have no clue who leads them, but I know what they want. They are trying to rule Equestria for its valuable resources, and sadly enough, Mutants. I hope you understand that this letter holds information that not even Celestia herself knew of.

I, Prince Lightning Sky, am a mutant. I have three friends who should be here soon. The soldiers are sieging Canterlot Castle. The Force has created a complicated device, the only one of its existence, The Hunter.

It makes loud noises when Mutants are nearby. I have a good stock of guns. The Force is trying to capture mutants. But most are killed for being 'useless.'

I am sorry that you may never see me again. I am a sign of hope for Equestria Mutants, and they want to destroy it. I want you all to run. Stock up on resources, my army has been sent to Las Pegasus to check up on siege, the remaining half is some were else, scattered by the bombings. As for what mutant I am- I cannot write much more, I can see the silhouettes of Flame, Storm, and Snowflake. When you receive this message, I am most likely dead.

Your dearest Prince, Lightning Sky of Equestria.

The area was silent and some quiet sobs were heard. "Now..." Braeburn said after finding his voice.  "Everyone may head back to their offices. I want a patrol on the borders of Appaloosa to watch for soldiers. Good Day." and Braeburn left the platform, walking down the hall, only to be followed by the visitors. "Now." he said turning to them. "Ace. Tour them around and introduce them. Oh and by the way. Ask if they wish to join 'The Protectors'" and with that he left.

Tour

     Storm walked after Ace. Why does he wear that hood. Wait. What is that design?

Ace's cloak had a big red design on the back. It looked like wind coming from an oustretched hand, surrounded in a circle

    "This is were all the technological and hacking stuff happens!" Ace said with a surprisingly young voice.

"h-Hacking?" Snowflake asked, It didn't sound very...good guy.

"yeah. Were do you think we get our information and machinery? Its not like Celestia wasn't alive when this base was built. She didn't 'certify' this place. But Lightning did ,under the desk that is."

"Are you trying to hack the Force's Device?" Flame asked and Ace nodded

"Yup. Problem is we don't have good enough hackers."

"If only we knew how to hack..." Sweetie Belle muttered, making her friend perk up.

"You need a Hacker?" Scootaloo asked and Ace stared at her "Y-yes?"

   "Then show me what you got!" and Scootaloo ran to the closest computer that no one was using.

"You hack?" Cloud asked out of no were. Scootaloo shrugged

"Yeah. I used to hack all the time. Since I had no sister to spend time with." Scootaloo said coolly and began to press the keys and mouse.

"You trust her?" Ace asked and Cloud just playfully shoved him. "Your so distrusting. You know that?" Ace shrugged and watched as the girl hacked. "Who taught you this?" Apple bloom asked "Rainbow dash. Obviously." Storm tilted his head Isn't that the girl that made gold in the last three Equestria games? Scootaloo turned "Yup! She only knows basic hacking though."

Storm flinched at her and she smiled. "BTW I have this." she pulled a device from her face which everyone realized had been disguised to match Scootaloo's face. "By the way Ace. I hacked through the first fire wall already." Scootaloo said dismissivly, putting the device back on. "That's so cool!" Sweetie Belle chirped. "I wish I could be useful."

Snowflake smiled and looked at Ace "Should we continue the tour?" and Ace nodded and led them down a hall. "These are the offices and down there is the bunkers." Apple Bloom looked at Ace. "Why are there bunkers?" Ace looked at her

   "Do you think people don't attempt to bomb us?" Apple Bloom looked at Ace. "Never thought about it.." Ace nodded and led everyone to another corridor that had sliding doors with numbers on them (Imagine the Fallout corridor)  "This is were people sometimes stay when stuff goes down. You guys can stay here." and Ace pressed his hand to a pad and the door to room 909 opened. The group walked in and observed the room. It was like an apartment really, there was a couple bedrooms and two bathrooms.

"So yeah. I am in the room with the purple door." and he walked away.  Apple Bloom walked to a bedroom which had three small beds and a wardrobe.

"Guess me and mah friends sleep here." she said and set her bag on a bed and Sweetie belle put hers on the bed in the middle. Snowflake got her own room, leaving Flame and Storm to the last bedroom.

Everyone then met after unpacking in the main room which had a table in the corner with a couch like chair and it had some chairs and a computer. Apple Bloom had been kind enough to unpack Scootaloo's stuff. As they all sat down Scootaloo walked in, her eyes were filled with exhaustion. "Scootaloo? How did the hacking go?" Apple bloom asked and Scootaloo just flopped onto a chair.

"That...was the hardest hacking session...ever.." she muttered and slumped back.

"Really?" Scootaloo nodded "The Force went overboard to protect that device. Want to know how many fire walls there are?"

"Sure." Sweetie Belle answered and Scootaloo took a deep breathe.

" 30." she answered in a dull tone "How many did you break?"

"...... The rebels were only able to breach 19. I breached 23." everyone just stared "Can't we just....burn it?" Flame asked and Storm nearly face palmed

"No....I would suggest trying to hack and make it explode but they still have the design plans. We would have to go to their base which is who know's hell were! and then we would have to break in and hack all their computer data and burn all the documents. Then we would have to kill whoever created the device or brain wash them. Then escape with the data and most likely just break it. So not a lot of burning."

"Awww...." Flame made frowning face and Scootaloo cocked an eyebrow.

"Erm.." Storm stood up 'I'm gonna go....do stuff." and he left, walking down the hall, passing rebels and such. Then he found a purple door with a red design similar to the one on Ace's cape

"I wonder what Ace is doing..." he realized the door was slightly open and he looked inside, not wanting to interrupt Ace if he was doing something. The room was decorated with book shelves. In one corner was a desk covered with books. In the center of the room was a purple circle carpet but what intrigued him most was this.

There was guy in the center of the book, cross legged. It was Ace. Then the books that were open around him began to levitate. Storm stared in shock as Ace and the books levitated. Then he was surrounded in purple and his cloak flew off.  Ace had bright purple aura surrounding him and in a quick flash Ace was in a standing position. Then the room went dark and Ace fell onto the ground.

Ace struggled into a sitting position and wiped something off his face. Blood Storm backed up and walked away.