The Mane Six

by Cartoonlover13

Rating: mature
Tags: Alternate Universe, Anthro, Main 6, Drama, Gore, My Little Pony: Friendship is Magic, Other, Romance, Adventure, Sex, Sunset Shimmer, Discord, Princess Celestia, Dark
Length: 4333

Six Supervillians come together as team to go to the wreaked city of Canterlot to defeat the Spirit Of Chaos, Discord.

[In an alternate universe where Luna never became Nightmare Moon and Rainbow Dash never exceeded the speed to do a rainboom]

Equestria has seen better days...to the Celestia and Luna's surprise their old foe, Discord has returned. Desperate and rubbing out of time, the two rulers resort to the the last thing possible: recruit Twilight Sparkle, Rainbow Dash, Pinkamena Diane Pie, Applejack, Rarity, and Fluttershy, the six most dangerous ponies Equestrian has seen.

The team is led by Sunset Shimmer. Will these six mates succeed or fail their mission?

All ponies are in anthro form.

Cover art is from Ashley Nichol on Devianart.

DC Comics mostly Suicide Squad inspired this story.

Note: Twilight passed her magic test and hatched Spike and lose control of her magic without the rainboom and became Celestia's student.

Edited by: Phillyphil, ARTL, and Jaws4

This story is now on Deviantart but you have to an account to look at it, because of mature content.

This Picture inspired this story.

Note: Story is currently going through some revisions

Published 2016-03-27 19:20:01 UTC
Last updated 2016-05-18 12:03:21 UTC

Chapter 1 (updated) (re-edited)

"C'mon, get up!" shouted a female voice. All of the Wonderbolts slowly got up from the voice “Coming to” would work better here, “woke up from the voice” messes with the sentence structure. “Got up” would also work

The Wonderbolts, consisting of thirteen ponies including Spitfire, Fleetfoot, and Soarin, were all shocked to feel absolutely nothing. They weren't in the bar they were getting hammered drunk at, instead, they were at a worn down barn. The coldness from the outside made its way through the holes in the ceiling and walls. Their bodies were placed in a sitting position on the barn floor with their backs to the wall, the smell of hay and manure attacking their nostrils.

"Like it? We got some unicorn to do a spell that paralyzes ponies," another female voice said.

The Wonderbolts looked up and saw twelve pegasuses dressed in darker colored versions of uniforms like their own, the cutie mark on the suit was a winged skull.

Spitfire's eyes widened as she recognized six of the seven ponies, the seventh one had her goggles on and the uniform also covering her face. "Sour Sweet! Sunny Flare! Sugarcoat! Lemon Zest! Indigo Zap! Lightning Dust! WHO THE HELL ARE YOU!?"

"QUIET!" shouted Sour Sweet, startling the Wonderbolts.

Soarin opened his mouth to scream, causing Sugarcoat to glare at him. "Don't even try, idiot. Nopony would hear you if you did."

The unidentified pegasus took out a pistol and so did all the other ponies.

"Are you scared!" shouted Indigo Zap to Fleetfoot’s face, fleetfoot responded by spitting in Indigo's face. "You should be"

BANG!

The Wonderbolts hearts stopped for a few seconds from shock as Fleetfoot's insides were splattered all over the barn floor and on their faces. All of the Wonderbolts screamed as their friend fell over onto the ground dead. Figured this sounded more dramatic :D

"Consider that your future, assholes," Lightning Dust said, grinning at High Winds who were passed out cold on the floor.

Wave Chill didn’t he faint? had shock plastered on his face seeing his teammate die. "WHY ARE YOU DOING THIS!"

Lemon Zest rolled her eyes. "Please, don't fucking act like you don't know!"

Sunny Flare scoffed "You all said the same bullshit excuse, that we were all reckless and have no fucking teamwork. Yeah we do have teamwork! We're working as a team to bring you down!"

"THIS IS BECAUSE WE DECLINED YOU?!" Soarin shouted in anger.

The unidentified pegasus walked up to the Wonderbolts and had a short laugh. "After you declined them, their lives fell apart. Now they're gonna end you!" The mare then took off the goggles.

All of the surviving Wonderbolts looked at the mare, recognizing her voice. That rasp, those magenta eyes, and the fact Rainbow Dash was the only Wonderbolt not here suddenly made sense.

"R-Rainbow?!" Spitfire's brain was a mess and thoughts were scrambling all over.

"It's about time you figured it out." Sugarcoat rolled her eyes.

"Why...why Rainbow Dash? WHY!?" screamed Fire Streak.

"Because Fire," said Rainbow, walking to him and aiming the gun to his head. "Haven't you all realized you're all incompetent assholes?"

"RAINBOW NO!, STOP NOW!" Misty Fly was screaming at her limbs to move.

"You are not Rainbow Dash! The real one would never stoop so low!" spit out Rapid Fire.

"I am Rainbow Dash, and I am sick and tired of all of you!" Rainbow then lowered the gun away from Fire Streak's head, causing him to exhale in relief.

All of the twelve Wonderbolts stared into Rainbow's eyes. She was a terrible liar and she was telling the truth.

"No, I-I don't believe it," mumbled Surprise the formerly happy and careless pony of the group.

"Oh my Celestia!, are you deaf? That's sooooooo sad," said Sunny Flare in a condescending reply.

"No, what did you do? WHAT DID YOU DO TO HER?!" screamed Soarin, trying to get up. He then grunted in pain as Sugarcoat stomped her foot on his head.

"Wow, that spell that unicorn did really did work on him," whispered Indigo to Lightning Dust.

"C'mon, Nightmarebolts, let's go," said Rainbow Dash. The Nightmarebolts complied.

"HEY WHERE DO YOU THINK YOU'RE GOING!" screamed Soarin.

The Nightmarebolts ignored the screams and wails of the Wonderbolts. As Lightning Dust exited the barn she had a face mixed with glee and bloodlust, "Ten seconds, everypony!"

The Wonderbolts, well the ones conscious had vomit in the back if their throats, almost having a panic attack.

"Ten....SECONDS!?" shouted High Winds in panic.

Spitfire's eyes shifted all around the barn in fear "Wha–?"

https://m.youtube.com/watch?v=ngXjJoNCzu4

Rainbow Dash awoke from the dream, no, not a dream but a memory that had started it all. The pegasus wasn't in a barn; She was in her bed in her prison cell in Crystal-MAX in the extremely cold Crystal Mountains. It had been two years since all that happened, why was she still getting that dream about her killing those assholes?

Rainbow Dash sighed and lied back down with her head resting on her pillow and tried to get back to sleep. Ugh, of all times to get fucking haunted by that dream, why now? I swear if I get that fucking dream again I will kill somepony. The mare closed her eyes and took a deep breath.

"We need a new plan!" exclaimed Princess Celestia in frustration.

"Princess Celestia! My top soldiers and I will get all the remaining citizens in Canterlot and defeat Discord!," exclaimed Shining Armor, his team coming to attention behind him..

His wife, Princess Cadance shook her head "No, Shining Armor, it's too dangerous for you all to do even for Celestia and Luna."

Shining Armor smacked his hand on the table.-------- "But Canterlot is under attack by Discord and we left a bunch of citizens out there! Now they're just puppets being controlled by Discord like it's a sick game!"

"We had no choice Captain Armor, other than that force field you put around Canterlot, we couldn't get more citizens to evacuate because we couldn't risk Discord spreading chaos all over Equestria. We cannot let anyone go, even sister and I; Discord stole the Elements Of Harmony," said Princess Luna.

Princess Celestia had a cross look on her face. "I still don't know how he got them or how he escaped his stone prison! That chamber that holds the elements can only be opened by a spell I can do! Without the elements we are powerless against him."

Lady Sunset Shimmer spoke up, "Our first priority should not be defeating Discord; It should be saving the ponies of Canterlot!"

"Exactly!" shouted Celestia. After she said that she bit her lip and looked down to the ground. "Cadance, is the prison holding those six criminals still in The Crystal Mountains?"

Cadance looked lost for words "Yes, wh-why do you ask? I thought you never wanted to speak about them ever again?"

All the ponies in the room in Crystal Empire castle were silent, all looking to one another very nervously.

Celestia took a deep breath "I want to assemble a task force of the six most dangerous ponies Equestria has ever seen."

"WHAT!" everypony in the whole room shouted in shock.

Luna looked like she had seen a ghost. "Sister, have you gone completely mad!?"

Celestia shook her head. "I don't think so Luna, but just hear me out on this, please?"

All the ponies in the room whispered to one another and then nodded agreeing to listen to Celestia.

"I think those six mares can do some good, they all have extraordinary powers that nopony else has. It is much too dangerous for anypony including me to go into Canterlot, but those six can. They have the power to evacuate the ponies in Canterlot and take down Discord."

"Well," said Sunset Shimmer, "nopony thought of me doing anything good, but I came back to Equestria reformed because I discovered friendship by making friends with five girls in the alternate world I went to. Also, I helped us win the war with Saddle Arabia against Yakyakistan and Griffonstone. I don't see why we shouldn't give them a chance".

Shining Armor gulped, "What if they don't cooperate with us?"

Celestia bit the inside of her cheek, "Well, they already have microchips in their heads to shock them if they get out of hand, but I have a feeling that won't intimidate them enough, so we'll just have to replace them with explosive ones"

Cadance's head jerked to the side in shock,. "Wait, we won't really blow off their heads, right?!"

"Of course not! It'll just be a bluff." Celestia quickly replied.

"We can't just let them go alone!"

"I'll go with them!," Sunset Shimmer cut into the conversation.

"No Sunset–" Celestia was cut off by Sunset before she could finish.

"I can take care of myself, remember, I helped us win the war. Plus, somepony needs to keep them in line." Sunset continued.

Luna put a hand on Celestia's shoulder, "she can go Celestia, somepony needs to keep those six in check. After all she did save us a lot during the war"

Celestia exhaled, "Please be safe"

Sunset Shimmer bowed to her teacher "I will, Princess, and I will do our mission"

"I just hope I did the right thing," mumbled Celestia.

Author's Note

Okay just to clear some things up. One yes there was a war it started before the events of season one. Two yes the rainboom Rainbow did as a filly never happened,but Twilight did have an uncontrollable surge of power still when trying hatch Spike in this universe and she came Celestia's student. Three the war against Yakyakistan and GriffonStone happened about 2 years before the events of season one. This is set two years after the war ended. The war
happened because of corrupted leaders. I will get more into it in the next chapters. Four Rainbow Dash did do the Sonic Rainboom to help Equestria. Five that scene in the begining of the chapter started it all for Rainbow Dash once again I'll get more into it,plus they're might be more to the picture. I love writing alternate universes for Equestria. Six yes all the mane six are bad guys once again I'll get into it by the next chapter. Seven this story is kinda inspired by DC comics and their Suicide Squad comics. I'M SO EXCITED FOR THE SUICIDE SQUAD MOVIE! Sorry I'm a fangirl. Eight Sunset Shimmer did come back for the war and eventually stayed in Equestria. She got reformed by the humane five. Nine yes Discord is the main villian he is like the Joker in DC comics I'll get more into him in the next chapters. I really like these alternate universe stories. Please tell me if there is any errors in the story. Well that is all folks stay tuned for the next chapter!:raritywink:

Chapter 2 (edited)

Author's Note

This chapter is now edited. Sorry Grammar Nazis for the unedited draft.

Chapter 2 (edited)

The Mane Six: Chapter Two

Chapter 2 Recap: Rainbow Dash, the leader of the mercenary group, The Nightmarebolts, is having dreams of her part in killing her old group, The Wonderbolts. Rainbow Dash is deeply confused on why her past is haunting her. While this is happening, Discord, The Spirit Of Chaos, has broken free of his stone prison and has stolen The Elements Of Harmony for unknown reasons. Princess Celestia had called an emergency meeting in The Crystal Empire to save the capital of Equestria, Canterlot from Discord. They only evacuated a couple of citizens and had to put a magical force field to keep Discord from spreading his chaos all around Equestria, leaving ponies trapped inside who were held hostage by Discord. Celestia thought of a plan to employ the six most dangerous ponies in Equestria who are currently incarcerated to save Canterlot.

“So...what do you think?” said Princess Celestia.

"So...you're going to have Pinkamena go back to her abuser!" screamed Limestone Pie who then flung the table to the window shattering the bullet and magic proof glass, scaring the guards near the window. The guards in the room rushed in to restrain her.

Cloudy Quartz looked as if she saw a ghost. she scolded, "Limestone!” –she turned to the royals– “I'm sorry, Princesses, she never acts like this!"

"Limestone, calm down," said Maud in her usual emotionless tone. "But Limestone is right. I'm sorry Princess, I don't agree with your plan.”

In the room was Princess Celestia, Luna, and Cadance with Lady Sunset Shimmer who were telling the Pie family about their wanting to have their second youngest daughter, Pinkamena to be in a task force to save Canterlot.

Sunset moved over to Celestia and whispered into her ear, "I just knew this family wouldn't like this.”

Igneous Rock Pie sighed, "I'm sorry, your majesties, but we can't agree with your plan and and we refuse to let Pinkamena go to Canterlot".

Limestone clenched her fists "I thought you guys were going to cure her, not put her in even more danger! SHE DOES NOT NEED MORE ABUSE!"

"We just want Pinkamena back your majesties," said Marble Pie in a very quiet voice.

Princess Luna took a deep breath. "We know your family is going through a hard time, but we need Pinkamena. She has the power to save Equestria.”

Princess Cadance spoke up, "Mr. And Mrs. Pie, we won't abuse or mistreat your daughter as we are still treating her. There are hundreds of ponies still being held hostage by Discord and Pinkamena can help."

"You..y-you promise?" said Marble.

"We promise to Faust herself that we will try to make sure Pinkamena will have no harm done to her," said Princess Celestia.

Igneous exhaled "Fine."

Limestone looked shocked and glared at their father. "Dad-"

Cloudy Quartz chimed in, cutting Limestone off. "I'll let my baby go too."

"I'll allow it," added Maud.

"Me...too," cracked Marble in a louder voice.

All of the ponies in the room looked at the remaining family member.

"Fine...but you better be telling the truth!" Limestone said, disgruntled.

Princess Celestia had a small smile on her face. "I'm glad we could reach an agreement. Now... would you like to see Pinkamena?" All of the Pie family's ears perked up at what Princess Celestia said.

Maud changed her emotionless expression to a small grin "We would like that, Princess Celestia."

The princesses and Sunset Shimmer exited the room. Princess Cadance's horn glowed and restored the window back to it's original form.

A crystal guard came up to the four. "Shall we charge the mare, Your Highness?".

"No...let her be," said Cadance, dismissing the guard.

Princess Luna had a confused look plastered on her face. "How did she break that glass?"

Sunset replied "Well, she's a Pie, don't question it."

"True."

Applejack sighed as she plopped down to her bed. She had grown bored of everyday prison life. She had been out of her cell to interrogate prisoners of war from Yakyakistan and Griffonstone sometimes. She was friendly, but when that failed she used violence. She did the same things when she was a changeling and general of Chrysalis's army. But that was years ago.

She understood why Griffonstone and Yakyakistan were against Equestria welcoming changelings as citizens and why that was a big reason they declared war on them. Changelings are bugs, and when you come across a bug you exterminate them.

The door which kept Applejack in the magical glass cell that weakened her abilities, opened. Applejack got off her bed as the two guards came into the cell and put Applejack in handcuffs. They led her out of her cell, but not before putting a neck brace on on her which had the same spell the cell had.

"Y'all gonna use me for dirty work again?" asked Applejack.

"Quiet!" one of the guards told Applejack sternly.

The guards escorted her to the visiting room with a table and two chairs on one side and another one on the other side. In the two chairs was her little sister, Apple Bloom and her big brother, Lieutenant General Big Macintosh.

Apple Bloom had a faint smile. Applejack still couldn't believe that her family could forgive her for her sins. "Howdy AJ, Sorry fer not visiting y'all in a while, or writin' to ya’ in some time.

"That's fine. RaRa visited me a lot so ah wasn't alone," replied Applejack.

Apple Bloom bit her lip and sniffled. "You know Granny hadn't been feelin’ so well. Sh-She died a few days ago."

Applejack stared down to her feet, her mane covering her eyes. "Ah knew this would happen some time. She's lived over three generations. Ah hope she's happy with Ma and Pa. Ah'm not gonna see them in the afterlife, of course."

"Jus to let you know, she died peacefully like she was just going to sleep," said Big Macintosh.

Applejack nodded "So...you gonna tell me what y'all gonna do to me."

Big Macintosh bit his lip. "Discord is back."

"How did that happen?" responded Applejack.

"We don't know. But like when you did yer interrogation techniques to shorten your life sentence fer first degree murder, to forty-seven years, this is your chance to do it again. Discord took over Canterlot. You and five other prisoners will go to Canterlot to defeat Discord and save the Equestrians held captive by Discord. Though be careful, the five mares are corrupted by magic."

"So y'all gonna shorten my sentence, but what bout' the others?" questioned Applejack to her brother.

"They will likely be locked up ferever unless the dark magic is ridden from them. Your sentence of forty-seven years will be shaven down a bit to thirty-four years. The others will be forced to cooperate."

"Like when y'all tried to force me. Nice try, but that didn't work."

"It didn't work because ya overheard us," rebutted Big Macintosh.

Applejack thought of bucking Sweet Apple Acres apple trees. Her thirst to get out into the open world was relentless. "When will ah go?"

"You will go in five hours. Remember this, AJ" Big Mac got off his chair and walked to his sister and got close to her face. "Do not. I repeat, do not kill anypony innocent or kill anypony guilty on purpose."

"Yes sir," said Applejack resentfully.

"May I get some information on those six?" asked Sunset Shimmer to one prison guard.

"Yes, Lady Sunset," said the guards-mare and exited the room.

Sunset opened up her bag and pulled out a pencil and a brown journal with her cutie mark on it. She then opened the magical journal and began writing.

Dear my friends,

Discord still has Canterlot under his rule, sadly. But Princess Celestia has come up with a plan. This plan has the evil pony version of you five and Celestia's former student coming together as a task force. Those six have the power to take down Discord since the elements were stolen by Discord. Princess Celestia thinks that they can do some good still. I mean, I did so once. I think they can too. Princess Celestia made me the leader. I just hope I'll be able to control them! Wish me luck you guys! I really miss you. I'll try to visit you soon, I love you all.

Sincerely, Your friend Sunset Shimmer

Sunset Shimmer closed the journal and put it back in her bag with her pencil as the guards mare re-entered the room. She had six files in her hands and threw them onto the table Sunset was standing near to.

"I hope this is of some use to you, Lady Sunset. in the files are medical and prison reports," said the guards-mare.

"Thank you ma'am." Sunset held up one of files and looked for the prison.

Sunset scanned through the prison reports. Five of the mares were imprisoned for crimes they weren't technically guilty of because of dark magic corruption. And those five ponies she was very close friends with. They would be released if the dark magic was rid from their bodies. Applejack well was the odd one of the bunch. Applejack was once a changeling and even the general of Queen Chrysalis's army.

She wasn't born a changeling, she was turned into one as a filly. She went to Manehattan and stayed with her aunt and uncle. When she wanted to come back to her home, Sweet Apple Acres she went alone and got lost in The Everfree Forest. She stumbled upon a changeling base and was turned into a changeling.

When Queen Chrysalis and her changeling army’s invasion of Canterlot failed, Lieutenant General Big Macintosh, the big brother of Applejack apprehended Applejack. Even as a changeling he instantly recognized her. Through magic Applejack was returned to her regular self. But when she got turned back into a pony she retained the powers of a changeling.

The shapeshifting and immunity to toxins and poisons still remained. Applejack was angry at the changeling race and even angrier that they were welcomed into Equestria and made citizens. Like Yakyakistan and Griffonstone she had the racist idea changelings were all 'evil bugs'.

When Queen Chrysalis was apprehended and put into this very prison, Applejack snuck in and killed her. Applejack was given the sentence of life in prison. This wasn't Applejack first job for the government, though. She was the interrogator and spy for the army.

Her choice of interrogation techniques were unique. She treated the war prisoners with kindness and they opened up to her. The war prisoners didn't even notice they spilled secrets. Applejack's sentence was shortened to forty-seven years for her contributes to the war.

"SUNSET SHIMMER!" Sunset's head jerked and she accidentally dropped the files in her hands. What she saw made her gasp.

"S-Spike!?" Sunset hadn't seen the dragon since Discord had taken over Canterlot. Spike was now traveling around doing damage control. For a nineteen year old drake Sunset was quite impressed.

"Sir Spike? I thought you were in Vanhoover?" asked the guards-mare.

"I was, but I came here because of this idiotic plan including my MOTHER!"

Sunset cringed at Spike's outburst. Twilight Sparkle was the adopted mother of Spike. She was once a royal lady and personal student of Celestia like herself. Twilight also fell down the dark path like her, but she didn't realise her mistake.

During the war against Griffonstone and Yakyakistan, there was a surprise attack known as “The Battle Of Griffonstone”. Shining Armor was killed by rebel assassins, bitter of the lost of Griffonstone. Shining at first survived. But the doctors said it was likely he wasn't going to live long as he was shot in the head.

Twilight turned to dark magic to save her brother. So she had gotten the Alicorn Amulet. How she got it is still unknown. The Alicorn Amulet does have incredible power, but it corrupts its host. Shining Armor had died from his injuries, but Twilight brought her brother back to life with the amulet’s dark powers.

The amulet corrupted it's host and she became power hungry. It turned Twilight Sparkle into a demonic alicorn. She was eventually caught, but it was too late. The amulet was merged with Twilight Sparkle and it was too late to save her.

"Spike, we're desperate. Twilight and those five mares can save Equestria," defended Sunset.

Spike clenched his fists. "You know damn well none of those mares are mentally sane including my mom, Sunset."

"We're trying, Spike."

"YOU'RE NOT TRYING ENOUGH!"

Sunset cringed even more. "Spike... this is our last attempt. All of our other attempts have failed."

Spike exhaled “Sunset...Please make sure Twilight is not harmed."

Sunset had a small smile "Yes... I will try with all my might."

Shining Armor and Cadance looked nervously to one another. In the anti-magic glass cell was a disheveled mulberry colored alicorn. Her mane was messy and the feathers on her wings looked like they weren't preaned in forever. The alicorn mare was in a sitting position facing away from the two royals.

The mare smugly grinned. "Hello, my brother and sister in law." The mare then glanced at Princess Cadence's pregnant belly. "Aren't you due in a two months?"

"Yes, Twilight," replied Princess Cadence.

Twilight Sparkle laughed quietly. "Can't wait to be an aunt, but you're probably not going to let her see me on the account that I'm a monster. I wonder if she's going to be an alicorn."

Shining Armor glared at Twilight. "You're not a monster, Twily. We will save you."

"I saved you. You were a dead stallion and I saved you. Yet I'm deemed a monster. Me being saved is what you said two years ago. I'm still here, B.B.B.F.F," replied Twilight Sparkle. She then turned around showing her face to her brother and sister in law.

"Twilight something is going to happen to you soon," said Shining Armor.

Twilight raised an eyebrow. "What? You're gonna execute me? Don't blame you."

Shining Armor and Princess Cadence eye's widened and both stepped back in shock.

"TWILIGHT! WE WOULD NEVER DO THAT!" scolded Shining Armor. He couldn't believe his sister would think he would let her be executed.

Twilight sighed. "Of course you wouldn't. Ponies are so weak minded. I have no reason to live, I'm not going to commit suicide, that's what cowards do, but why bother living if ponies think I'm a monster. I don't care if I live or if I die."

Shining Armor and Cadence looked as if they were to slap Twilight's face, but calmed down.

"Whatever is going to happen to me, I'm ready," Twilight said.

Shining Armor looked at his satchel and in it was books upon books. Shining Armor's horn glew and the satchel was no longer on him and now in Twilight's cell.

Twilight smiled. "Thanks, B.B.B.F.F."

Chapter 3

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