The Civil War Of Equestria

by BronyNinja209

Rating: teen
Tags: Other, Adventure, Gilda, Tragedy, Dark, Alternate Universe, Anthro, Main 6, Gore, Original Character, My Little Pony: Friendship is Magic, Comedy
Length: 1876

The mane 6 go undercover to try and stop the war, that Manehattan started

Equestria faces dark times as war breaks out between Canterlot and Manehattan. Cloudsdale, Ponyville and The crystal Empire Faces a new threat from Manehattan, and the rest of Equestria. No pony knows why Manehattan is attacking, so it is up to Twilight Sparkle and the rest of the mane 6 to go in and find their leaders, and put a stop to them using any means nessessary.

Tagged other for every other pony in the story.

I don't really like to write anthrio so this WILL be the only one that i will write.
Looking for an editor.

Published 2014-07-12 23:50:03 UTC
Last updated 2014-07-12 23:50:03 UTC

Prologue

Prologue

The Civil War Of Equestria
By BronyNinja209

“Princess Luna, has Flash got your soldiers ready for battle?” Princess Celestia asked, looking down at the map of Equestria.

“Yes my sister, is shining Armour’s soldiers ready?” Luna replied.

“Yes, he is outside the main gates with his men.”

“Sister, do you know who is the current leader of Manehattan?” Luna asked taking her sword in her hand.

“As far as i am aware they haven’t got a leader, so I don’t know why they decided to attack”

Meanwhile in the Ponyville castle, Twilight and the rest of the girls were getting geared up. Each of them armed to the teeth.

Rainbow had a belt of six throwing knives, a short sword, a dagger and a hidden wrist blade for a stealth attack.

Fluttershy had a dagger, a bow and twenty arrows, a small cross bow with twenty bolts and a wrist blade.

Each of the six ponies had wrist blades so they were never without a weapon. Rarity had the same weapons as Fluttershy, and so did Twilight. The only difference was that Twilight also had a short sword aswell.

Applejack and Pinkie was armed with two daggers to duel wield, with four throwing knives, and a short sword.

Each of the girls was wearing iron breastplates and iron leggings underneath their black hooded robes for protection.

“It’s time to go to Canterlot castle to see the Princesses.” Twilight said. “Are you girls ready?”

“Yes ma’am!” the rest all said in unison.

“You know, just because we are at war and i am a Princess, doesn’t mean you have to address me formally, right?

They all nodded and with that a purple glow of aura started to form around Twilight’s horn, within a few seconds they found themselves in the war room of Canterlot castle.
The war room took up half of the basement of the castle. It had a big square table in the centre of the room with a holographic map of Equestria, each City marked with a small blue flag or a small red flag to indicate where they stand in the war. On one side of the room was a coffee machine and a kettle so the troops would be able to get a drink during meetings. On the other side was a white screen with a projector pointing at it and chairs facing in that direction for meetings and battle tactics.

“Ah girls, we have been expecting you.” Princess Luna said whilst arming herself for the upcoming battle.

“Princess Luna, Princess Celestia. It’s good to see you!” Twilight said as she hugged the both of them.

“It is a shame that the circumstances are as they are, or it would be better.” Luna said flatly but returned the hug.

“As you maybe aware, the enemy have outnumbered us. We only have Canterlot, Cloudsdale, Ponyville, and The Crystal Empire. Whereas all of the other Cities of Equestria are standing by Manehattan.” Celestia explained.

“So what will you have us do?” Rainbow Dash asked.

“We will be splitting you into pairs and you will be going into enemy territory and finding out information on our enemy. And if possible, bring them in using any means necessary, so we will once again have peace in Equestria.” Luna instructed. “Go and get some rest you will be setting off shortly.”

Luna and Celestia discussed the best plan, and who to send where. while they spoke they received a letter from The Crystal Empire. The two Princesses set it on the table and began to read it.

Princess Celestia,

I regret to inform you that the Empire has been

taken over and they are right outside my private quarters

I fear that by the time you get this letter I will most likely be killed or

tourchored by the enemy.

I am sorry, I have failed you aunt, I love you.

“No!” Celestia said under her breath, tears started to stream down her eyes. Luna put a hand on her shoulder in reassurance that everything would be fine, but that did little to help. Luna’s ears perked up at the sound of Twilight Sparkle walking in the room.

“Twilight, can i speak with you a moment please?” Luna asked.

“Sure Princess, is everything alright?”

“No, not really you and Fluttershy will go to the Crystal Empire and retrieve Princess Mi Amore Cadenza. we have information that she is in immediate danger. Bring her back dead or alive however you find her. I only hope that she is still alive.” Luna instructed.

“Yes ma’am” Twilight said with a nod. She looked calm on the outside but fear was eating at her from inside. The thought of losing her new sister nearly drove her to tears, but she wanted to look tough for the Princesses.

Twilight walked into the barracks where her friends were. “Fluttershy, grab your things we’re leaving!” She instructed. The others looked at her in confusion but Fluttershy did as she was told.

“Where in the hay do you think your going?” Rainbow asked stomping a hoof on the ground.

“We are going to do our jobs, you should get your assignments soon.” The young Alicorn answered.

Fluttershy and Twilight strapped their armour on and checked they had all of their weapons at reach.

Fluttershy strapped the sheathed dagger to her right leg, her crossbow bolts and arrows to her back with the bow and crossbow.

Twi did the same but with the short sword she sheathed and strapped it to the left side of her waist,

They said their goodbyes to the other girls and set off toward the Crystal Empire.

Unfortunately for Fluttershy and Twilight the trains were out of service due to the war so they had at least a days flight ahead of them, with the added weight of the gear maybe longer.

They had been flying for about five hours and still the hadn’t made any progress, they decided to camp out the rest of the night in a cave on the outskirt of Fillydelphia, and get up at dawn. They laid on the cold cave floor none of them had said a word since they left Canterlot apart from when Twilight suggested to sleep in the cave.

“Um, Twi?” Fluttershy asked. “What exactly do we have to do once we get there?”

“Save Princess Cadence or retrieve the corps.” She replied flatly.

“Oh, um ok!” She replied.

After a while they both fell asleep facing the opposite way to each other.

A Loss Of A Friend

Twilight awoke to the sound of screaming coming from next to her, she turned to face the source and saw Fluttershy being strangled.

“Get off her!” Twilight shouted as she ran up to him, jumped and stabbed him in the neck with the wrist blade. She pulled the body off of her friend and threw it aside.

“Fluttershy are you ok?” She asked. handing her a bottle of water.

“Mm hm” she said whilst taking a sip of water. “Yeah Twilight thanks”

“We should get out of here before more show up!” Twilight suggested as she picked up her gear. Fluttershy nodded in agreement. Twilight got a drink of water and then they both made for the cave entrance and took flight.

The morning sky was perfect for flying, not too windy. After they passed Fillydelphia they could see the Manehattan so they had to be extra cautious, they only wanted to bypass it so they could reach The Crystal Empire. As they flew over Manehattan Twilight looked around the streets below and noticed that no one was there. As she looked at the buildings she noticed a light flicker from one of the windows, then suddenly a wave of arrows and bolts went flying at them from windows of the City.

They both flew as fast as they could but they soon ran out of energy, luckily for them they was nearing the end of the City airspace. Once they reached safety Fluttershy spoke up and got Twi’s attention.

“Twilight we gotta land!” Fluttershy said through gritted teeth.

“Wha…what do you mean?” Twilight asked in a confused yet shocked tone of voice.

“I, um I’m hit” Fluttershy said now falling from the sky. Twilight swooped down and caught Fluttershy just in the nick of time. When she landed she put her friend down on the ground, “Twilight, just leave me!” Fluttershy said now crying through her pain. “I will only slow you down.”

“I will not leave you Fluttershy” Twilight exclaimed “I will try to pull the arrow from you and find a spell to ease the pain a little. are you ready for me to pull it out?” Fluttershy just nodded. “Ok here we go,” she said as she grasped the arrow firmly in her hand. “Fluttershy, this is going to hurt.” She explained. “ Again she just nodded and squeezed her eyes shut. “ Three. Two. One.” She counted down and then yanked the arrow out.

Fluttershy screamed in pain with tears rolling down both of her cheeks. Twilight’s eyes was also starting to fwell up with tears at seeing her friend in pain. “I’m sorry Fluttershy! I don’t like to see you like this.” She said through her own tears. After the arrow was removed Fluttershy’s screaming stopped and her eyes were no longer squeezed shut, but was shut gently as if she was sleeping.

“Fluttershy, are you ok?” Twilight asked.

No response.

“Oh no, Fluttershy?” she said again her voice barely a whisper. She looked down at her friend’s stomach to see if it looked like she was breathing, but it was not moving. She put her ear next to her friend’s nuzzle to double check she was right.

“Fluttershy please wake up. You can’t die on me, not now, not after all we have been through!” Twilight shouted.

After about half an hour of talking to Fluttershy’s dead body Twi took her arrows and bolts and attempted to teleport her friend back to Princess Celestia. After she thought of a spell that would work she decided to use her magic to contact Princess Luna. Her horn started to glow a light purple as concentrated her magic until she had hold of Luna.

“Princess, we have a problem!” Twilight said.

“Cadence is dead?” Luna asked.

“No, not that, well we haven’t made it to the Empire yet, but I have contacted you about fluttershy.” Twilight explained. “She’s…she’s dead Princess. She was killed by a marksman in a window.”

“I am sorry to hear that and I wish you the best of luck with your mission” Luna said sympathetically. “We shall have a proper memorial when this is all sorted out, I promise.”

“Thank you Princess, I am going to send the body now. I will report back when I find Cadence.” With that Twilight ended the transmission. Twilight then focused her magic again and in a poof of light Fluttershy’s body was teleported safely to Canterlot.

Author's Note

Ok a short chapter. I wasn't gonna have Flutters die untill they had got to the Crystal Empire but eh I decided to go with this instead.

Next chapter will be up sometime in the week.