Equestrian Civil War - An Alternate Universe

by twotonedearly


At the Crystal Empire. Luna's Revelation. Evil revealed!

“Oh man, what the heck is going on here??” Rainbow Dash asked.

“This could be that omen Zecora told Fluttershy about.” Applejack answered as she could see the thick smoke rising from Canterlot's direction.

“Mayor, get everypony ready for evacuation. Whatever is going on in Canterlot might come over here. And we need to be ready.” Rainbow Dash told Mayor Mare, the Mayor nods as she rushed out to warn the citizens of Ponyville about the impending attack.

“Ah hope Twilight is alright.” Applejack continued to look toward the smoke as she and the other element bearers rushed off to help with the evacuation plans.

Meanwhile in Canterlot the attacks began to worsen as the royal guards battled the soldiers of Unicornia. Magic blasts were traded between the two factions as the war waged on. At the castle Princess Celestia watched the on going fight from the window as Twilight and her family figured out what to do. “Mom, Dad, you'll be safer in the Crystal Empire with Cadence and Shining Armor.” Twilight told her parents.

“Twiley's right, the Empire's defenses are fortified. We won't have any problems there.” Shining Armor told his parents.

“It'll be good to see our granddaughter too.” Twilight Velvet said, Twilight blinked hearing this.

“Wait, granddaughter??” Twilight Sparkle looked at her mother.

“Oh yeah, I forgot to tell you Twilight. Cadence and I had a daughter.” Shining Armor told Twilight, the alicorn couldn't believe it, not only did she have a new sister but now a niece too.

“I was gone for a long time. I missed the births of both my sister and my niece.” Twilight felt angry. So much was robbed from her by the nobles and Amadeus Blueblood. “Amadeus Blueblood has a lot to pay for!” she growled.

“Twilight, I don't understand why they hate you so much. I learned about how you saved Equestria from a lot of evils. I thought everypony respected their heroes.” Twinkle spoke up, Twilight shook her head hearing her sister.

“Not all ponies are satisfied, especially those low down nobles.” Twilight told her sibling.

“Twilight honey, we hope you'll come to the Crystal Empire. It'll be more safer for you to be there.” Nightlight told Twilight.

“I know dad, but there's somethings I need to take care of in Ponyville, one I need to make sure everypony there is evacuated safely. Second I need to rally my friends, and third I need to find Spike.” Twilight told her father.

“I see.” Nightlight told Twilight.

“Twilight, I want to go with you to Ponyville and meet your friends.” Twinklestar spoke up.

“Twinkle, it's dangerous though I know you won't take no for an answer. Just be careful and stay close to me. Our family's suffered enough as it is.” Twilight told her sister. Soon after exchanging goodbyes with their parents and elder brother and sister in law, Twilight began to plan her own trip back to Ponyville.

“Heading back to Ponyville I see?” Discord appeared as he looked at Twilight.

“Yeah, I need to check in on my friends. I hope they found Spike.” Twilight told Discord with a worried tone.

“Don't worry Twilight. I'm sure he'll find his way home.” Twinklestar told her big sister.

“Yeah, right now my concern is to warn my friends.” Twilight's horn lit up.

“We'll hold out as long as we can here. I'm not certain how much longer we can hold out.” Princess Celestia told Twilight.

“As much as I dislike destructive chaos, I'll have to help as well. Besides this is as much my home too you know. And besides nobody can cause chaos like me.” Discord spoke up.

“Princess, I'll defend you to the end.” Gladius Strife added in as he stood at the ready with the other guards.

“Then we'll begin as soon as possible.” Princess Celestia told Gladius. Twilight nodded as she and Twinklestar were engulfed by magic as they teleported away. Celestia turned to Luna, Discord, and Gladius. “This may very well be the fight of our lives.” She warned them.

“They used my brother to break his vow of friendship to Prince Shining Armor and to Princess Twilight Sparkle. I will take revenge on them.” Gladius responded to Princess Celestia as the four of them headed out into the heat of battle.

Meanwhile in Ponyville Twilight and Twinklestar arrived in the library just as the elements arrived as well.

“Twi! Glad you made it back in one piece. We got worried when we saw the smoke over in Canterlot.” Rainbow Dash was the first to break the silence.

“Unicornia started the invasion. We haven't much time to lose. Where's Spike?” Twilight asked.

“Ah'm sorry Twilight, we searched everywhere and no pony has seen Spike anywhere. It's like he vanished off the face of Equestria.” Applejack told Twilight. The Alicorn frowned although she was worried sick about Spike and now the war beginning.

“Darling don't worry. We ran into Starlight Glimmer, she's gone to search for Spike.” Rarity told Twilight. The Alicorn perked at the mention of her student's name.

“Starlight, I'm glad to hear she's okay.” Twilight said in a relieved tone to hear about her student.

“I'm sure Starlight will find Spike. Right now we gotta stop Unicornia from taking over Equestria.” Rainbow Dash spoke up.

“We need to make sure everypony here is safe. Then we can concentrate on stopping the invasion. And I know who's at the center of all this too.” Twilight said to her friends.

“Yeah, ah bet it's them nobles who hated yer reforms.” Applejack said too as she remembered everything that happened, that led up to the attempt on Twilight's life.

“You got that right Applejack, it was the nobles and their leader Amadeus Blueblood.” Twilight explained all she knew to her friends.

“Prince Blueblood's own father?? I can't believe it!” Rarity said in shock.

“Same here, that low down snake in the grass sold his own kin out fer power.” Applejack said in disgust.

“Yeah and for what nopony knows.” Rainbow Dash added in as she too felt disgust hearing the news from Twilight.

“My brother also knows why Gallant Heart tried to kill me. He was blackmailed with the threat of his younger brother's life over his head.” Twilight said as her friends reacted.

“Shiny said that?” Twinkle asked her sister as Twilight nodded her head.

“Hey Twi, sorry if i'm changing the subject but who's that pony who came with ya?” Rainbow Dash asked Twilight.

“Oh, I'm sorry guys. I forgot. This is my little sister Twinklestar Sparkle.” Twilight introduced her sister. The younger unicorn stepped up to Twilight's friends.

“I didn't know you had a sister Twilight, if I did I would have thrown her a biiiiig party! Well if we weren't still sad thinking you were gone and all.” Pinkie Pie said.

“Oh it's okay. I know of you guys and how your friendship with my big sister helped Equestria time and time again.” Twinklestar told the element bearers.

“Hey Pinkie you better save the party till after we stop Amadeus Blueblood.” Rainbow Dash told Pinkie Pie.

“Right, first thing we need to do is get everypony to safety. The Crystal Empire is our best bet.” Twilight told her friends whom all nodded. Mayor Mare suddenly rushed back inside.

“Everypony is ready to.... Oh my heavens! Princess Twilight?? Is that really you?!” Mayor Mare froze in her hooves seeing Twilight alive and well.

“It's a long story Mayor, right now we need to get everypony over to the Crystal Empire.” Twilight told the Mayor, she nods as she heads outside to get everypony prepared to leave to the Empire.

Soon every family and every citizen in Ponyville gathered to leave via trains to the Crystal Empire. Some felt remorse for leaving, others afraid of the looming threat. Applejack stood with her family as they prepared to leave. “Applejack?” Applebloom looked at her older sister. “Why is everypony leavin Ponyville?” She asked.

“Cause, them nobles started war. Ah don't want you or any of mah kin being harmed.” Applejack told Applebloom whom nods.

“Okay everypony. We need you all to board each train.” Mayor Mare's voice cut through the air as the ponies boarded the trains. Once on board the ponies all waited to move out. Ms.Cheerilee looked out the window of the train seeing the school house a distance away as she sighed.

“If only Twilight Sparkle were here, she'd be able to stop this madness.” Ms.Cheerilee said. She wasn't the only one who felt the same way as many other ponies shared the same settiments.

In one car the element bearers and their families were seated in. Twilight happened to sneak onboard with her hood on as Twinklestar came alongside her. She got noticable looks from many of the ponies on board. “Hey, Ah wonder who that can be?” Big Macintosh asked Applejack.

“Don't worry Big Mac, you'll know soon enough.” Applejack replied. The trains soon departed from Ponyville, the town was soon completely abandoned as the last train left. Back in the mane 6's car Twilight stood up to face everypony in the car.

“Everypony, I think I owe you an explaination.” Twilight began.

“Yeah, it's already breakin mah heart ta leave the farm as is.” Granny Smith spoke up. “ah hope the nobles rot in Tartarus once this war is over.” she said.

“Hey Rainbow Dash, that hooded pony sounds familiar..” Scootaloo said to Rainbow Dash.

“I understand that, but rest assured the nobles and Amadeus Blueblood will be stopped before they can corrupt Equestria under their banner of hate.” Twilight answered Granny Smith.

“Land sakes, your so wise, just like Twilight Sparkle was.” Granny Smith said amazed unaware she was talking to Twilight.

“Well to be frank, i'm that wise because..” Twilight took her hood off as she revealed herself. “I'm still alive.” she said.

“Oh my faust! Twilight is that really you??” Granny smith asked shocked to see her, Big Macintosh was shocked to see Twilight too.

“Whoa! Twilight's alive!” Scootaloo said in shock.

“Oh yeah, we were going to tell you Scootaloo.” Sweetie Belle told Scootaloo.

“So that means.. Button Mash, Featherweight, and Pipsqueak saw you in the library and thought you were a ghost!” Scootaloo couldn't believe what she heard.

“Yeah, sorry I kept myself hidden. I didn't want Amadeus Blueblood's spies knowing I'm alive and well.” Twilight told Scootaloo. She noticed Sweetie Belle and Applebloom not looking surprised.

“Hey sorry Twi but we kinda knew you were alive still. Applejack told me.” Applebloom told Twilight.

“Yeah and Rarity told me too.” Sweetie Belle added on.

“I understand.” Twilight said as she and Twinklestar took their seats.

“Hey Twilight, um who's your friend there.” Applebloom asked Twilight.

“She's my sister Twinklestar.” Twilight answered Applebloom's question.

“Nice ta meet ya. Ah'm Applebloom and these are my friends Scootaloo and Sweetie Belle.” Applebloom introduced herself to Twinklestar and her friends too.

“Yeah, we are part of a club called the Cutie Mark Crusaders. We used to do a lot of stuff trying to get our cutie marks till we got them. Now we help other ponies understand the meanings of their cutiemarks.” Scootaloo told Twinklestar about the CMCs.

“Wow, that does sound cool.” Twinklestar said amazed.

“Yeah it is.” Sweetie Belle said next. “Hey, can you use magic like Twilight can?” Sweetie Belle asked.

“Not yet, my BSBFF is going to teach me how though.” Twinklestar said. Twilight looked at Twinklestar.

“BSBFF huh?” Twilight asked.

“Yeah, since Shiny is our BBBFF you can be my BSBFF, my big sister best friend forever.” Twinklestar told Twilight with a smile.

“Wow, never thought I'd hear that.” Twilight said to her sister. Now Twilight was determined to teach Twinklestar magic.

“Twilight once we get to the Empire what do we do next?' Rainbow Dash asked.

“First we need to tell Shiny and Cadence the situation, next I need to find a way to communicate with Starlight Glimmer and let her know the situation at hoof, and third I hope we can search for Spike.” Twilight told her friends and their families and friends.

“Sounds like a big plan Twilight.” Rainbow Dash said to Twilight.

“I know. For now we can only wait.” Twilight responded to Rainbow Dash. As the ride continued into the late hours Twilight tried to rest though she was worried about Spike and more so what was happening with Princess Celestia, Princess Luna, Discord, and Gladius Stride. She hoped they were okay as she finally succumbed to slumber. Hours passed into days before the trains all arrived at the Empire. The ponies all disembarked as Twilight and her friends stepped off the train as they were greeted by the royal family.

“Twiley, Twinkle, you made it. And I see you brought all of Ponyville with you.” Shining Armor greeted his sisters.

“Yeah, hope this won't be of an inconviniance Shiny.” Twilight told her brother whom nods. “Where's mom and dad at?” Twilight asked.

“Back in the castle with Flurry Heart.” Shining Armor answered.

“So that's her name, I hope my niece will know me as family.” Twilight said to her brother as he motioned for his crystal guards to help the citizens of ponyville to their designated area. The mane 6 along with Twinklestar and Shining Armor headed to the palace where Princess Cadence was waiting at. Once there Twilight and Twinklestar greeted their sister in law and parents. Twilight noticed the bundle Cadence was holding and approached.

“That bundle, is that Flurry Heart?” Twilight asked as Cadence nodded.

“Yeah, I know how much it meant for you to be here when she was born, but those blasted monsters...” Cadence began before Twilight stopped her.

“We'll stop Amadeus Blueblood and his ilk in Unicornia. I promise.” Twilight told Cadence as she looked at Princess Flurry Heart. “She's beautiful.” Twilight said to Cadence before she saw the infant's wings stretch out, she looked both surprised and amazed at her wing span. “She's an alicorn??” Twilight looked surprised.

“Yeah, she surprised Princess Celestia and Princess Luna when she was born.” Shining Armor added in. “Though we had no idea one of those lowly bastards from Equestria's First tried to kidnap her from the nursery. Luckily I was able to stop him with help from Gladius and the royal guards whom were there.” Shining said with a growl. Twilight gasped when she heard this as did her friends.

“Why them twisted monsters! Bad enough they attacked Princess Celestia's school now they tried ta kidnap your baby too??” Applejack said infuriated.

“Man that's the lowest anypony could go! I say we take the war to Unicornia!” Rainbow Dash shouted looking angry.

“I know, those monsters targeted Flurry cause of her connection to me.” Twilight growled.

“That would be kidnapper refused to talk before he used his own magic to snap his own throat.” Shining Armor said with a glare in his eyes.

“Those rotten monsters have it our for our family that's what I'm getting.” Nightlight said to his son.

“They didn't even try it when I had Twinklestar. Why go after Flurry Heart? She's just a baby.” Twilight Velvet said looking at her granddaughter as she used her magic to wave a rattle infront of Flurry heart as the foal giggles and coos reaching for it.

“All because of my plans for reform..” Twilight sighed and lowered her head.

“Twi, you had no idea those jerks were going to try to kill you. If anything those creeps should be sent to the sun or moon.” Rainbow Dash said with a huff.

“No, that would be too good for scum like Amadeus Blueblood.” Twilight lifted her head. “I hope to find a way to communicate with Princess Celestia in Canterlot. I hope she's alright.” Twilight said thinking of her mentor who stood by to battle the unicornian army. “mom, I think the reason might be, is because of what Flurry is, what I am, an alicorn.” Twilight told her mother.

“That would make sense Twilight dear.” Twilight Velvet watched as Flurry Heart started to suck on her rattle.

“It's just guess work.” Twilight told her mother. Twinklestar went over to Flurry heart and played with her too. Twilight excused herself as she grabbed a familiar journal and started to write in it. “I'm sure Sunset will be happy to see this.” Twilight said to herself as she wrote in it. “Sunset, it's me Twilight. I know your going to want to know how I survived, it was Princess Celestia who healed me though it took along time due to the Orichalcum those devils stabbed me with. Sunset, if anything happens or if the Unicornians tried to invade Canterlot High with the portal get all our counterparts together and prevent them from taking Canterlot High. Signed your friend Twilight Sparkle.” Twilight finished as she sets the journal down. “I hope she gets the message.” she said.

Meanwhile in an alternate universe a flaming haired girl was reading from a journal and sighs. Sunset Shimmer was about to close the book when she noticed it glow. “What?? Can it be??” Sunset opened the journal as she read the words that appeared, her eyes widened as tears welled up in them. “Twilight.. You're alive!” she exclaimed before she further read her warning. “Unicornia?! It can't be!” she realized Twilight wouldn't lie about this if it wasn't serious. She knew what she had to do as she shut the journal and went to get her friends, the human counterparts of the mane 6.

Meanwile back in Equestria Twilight was looking at the crystal heart as it shined. Twinklestar joined her sister as she looked at the crystal heart. “Hey twinklestar.” Twilight greeted her sister.

“I know it's late but when will we start the magic lesson?” Twinklestar asked

“Tomorrow, right now it's late.” Twilight told her sibling. Twinkle noticed Twilight looking at the crystal heart.

“it's beautiful huh?” Twinklestar asked.

“Yeah, Spike helped reforge it when the Empire was in danger from King Sombra.” Twilight told her sister as she reflected on how the Empire was in danger from King Sombra and how Spike was able to bring the Crystal Heart back in order to defeat Sombra.

“Guess that's why there's a statue of Spike in the garden. He really is a hero.” Twinklestar said.

“Yeah.” Twilight looked out toward the night sky as the stars illumninated the sky. “No moon, I hope Princess Luna is okay and Princess Celestia too.” Twilight said as she sighed.

“Oh no need to worry about moon butt and sun butt Princess.” Came a familiar voice. Twilight and Twinklestar turned around just in time to see Discord appear with Luna and Celesia, Gladius was with them though he had wounds all over his body.

“Princess Luna! Princess Celestia!” Twilight rushed to the two alicorns.

“No concern for me Twilight? I thought we were such good friends.” Discord huffed as he turned away.

“Sorry Discord, It's just I was so worried about what was happening in Canterlot.” Twilight said to Discord whom nods.

“We may have more to worry about.” Princess Celestia stood up weakly.

“I hope Discord's little trick will buy us time to formulate a plan to stop the unicornians before they take all of Equestria.” Princess Luna added in as she helped Celestia to her feet.

“What trick?” Twilight asked as she helped her mentor.

“Simple, remember when I made your friends act the total opposite?” Discord asked Twilight as he grinned.

“I remember.” Twilight said as she remembered how Discrd discorded the element barrers and herself. “Discord did you...?” Twilight asked.

“As a matter of fact I did. Let's see those invaders fight amongst themselves.” the draconequus cackled.

“The barrier around the castle is reinforced, no matter what happens the unicornians won't set hoof inside.” Gladius Stride told Twilight whom nodded.

“That's a relief.” Twilight said as she looked at Princess Celestia.

“For now, I fear the worst for Equestria.” Princess Celestia went out to view the night sky. Princess Luna followed her sister as she used her magic to raise the moon.

“As do I Tia.” Princess Luna told her sister. “Especially after what I've learned.” she said as Celestia looked at Luna. “I'm sorry Tia, there's so much I've held back but in these dark times they must be known.” Princess Luna said to her sister.

“More secrets moon butt?” Discord asked.

“Princess Luna what's going on?” Twilight asked the night princess as she approached her.

“I know why Amadeus Blueblood sacrificed his own son. I saw it in his dream.” Princess Luna told Twilight.

“I had assumed the nobles would have sealed their minds with that Dreamless Sleep Potion to keep you out, when they feared your alter ego Nightmare Moon.” Princess Celesta said to her sister.

“I read about that potion in my textbooks, they made it as a fail safe to keep Nightmare Moon from attacking them in their sleep.” Twilight spoke up next. Princess Luna nodded.

“Even though now I'm not Nightmare Moon they still fear me enough to use that potion. But as I said before I saw the reason for Amadeus's plans. His own daughter.” Princess Luna said to her sister and Twilight.

“He has a daughter??” Twilight asked in surprise not even knowing of this. “I had no idea Prince Blueblood had a sister.” Twilight said shaking her head in disbelief.

“Indeed. She's the focus of his plans. That monster sacrificed his own son and wife just to make sure his precious Majesty gains power.” Princess Luna growled.

“What?? I knew he was scum but this takes the cake.” Twilight spoke up.

“Indeed, he even taunted me with the knowledge I could have stopped the assassination or even told Tia and Cadence.” Princess Luna shut her eyes. “I could have warned you and your friends about the assassination but I failed to even do that.” Luna lowered her head.

“Princess Luna, even if you did get the word out what would have stopped Amadeus from denying your claims and claim your trying to attack his credibility.” Gladius said to Princess Luna.

“True. He would speak with his forked tongue as usual. I didn't buy his crocodile tears he shed for his wife.” Princess Luna told Gladius, Celestia, Twilight, Discord, and Twinklestar.

“Princess Luna, what about this Majesty?” Twinklestar asked.

“She was a filly when I saw her last. By now she's probably grown up.” Princess Luna answered Twinklestar's question.

“Princess Luna what else did you learn from Amadeus's dream?” Twilight asked now wanting to know.

“Majesty is a alicorn.” Princess Luna told Twilight, she gasped as she was in shock.

“I can only wager Amadeus and the nobles covered up Majesty's birth to keep us from knowing that an alicorn foal was born.” Princess Celestia said as her horn lit up. “Thought Luna got the information out. Had we known where they were headed at the time we could have captured Amadeus and punish him for all the sins he's committed.” Princess Celestia said.

“Princess Celestia, this could explain why Equestria's First tried to kidnap Flurry Heart. She's an alicorn as well and those maniacs might have been sent by Amadeus when he learned about Flurry Heart's birth.” Twilight spoke up.

“it makes perfect sense to me.” Princess Celestia nodded to her student.

“I wish you all could have seen Amadeus's face when I mentioned Majesty.” Princess Luna smirked.

“Indeed, but what else is he planning?” Twilight asked.

“He intended to arrange a marriage between Majesty and Unicornia's King Dauphin's son Prince Silversteel. By now Majesty is Queen of Unicornia.” Princess Luna informed Twilight Sparkle.

“the pieces of the puzzle are falling in place. Amadeus is using the armies of Unicornia and Equestria's First to force his vision on Equestria. And he's using his own daughter to do it.” Twilight looked determined now to stop the mastermind of her would be assassination.

“We wiped out Equestria's First a long time ago after they bombed Princess Celestia's school. Save for Flurry Heart's would be kidnapper.” Gladius infomred Twilight whom nodded.

“Okay, guess we focus on the Unicornia invaders and eventually getting to Amadeus and Majesty.” Twilight looked to her sister and the princesses.

“Indeed.” Princess Celestia nods her head. Twilight noticed Princess Luna smirking about something.

“Princess Luna?” Twilight asked the night princess.

“Oh sorry Twilight. Just thinking of the torment I left Amadeus. I know I can't harm anybody in their dreams anymore so I left Amadeus a parting gift.” Princess Luna's grin grew wider.

“Princess what did you give him??” Twilight asked Princess Luna.

“The Tantabus. It's giving Amadeus Blueblood eternal night terrors. My way of warning him he'll fall with his precious Majesty.” Luna responded grinning.

“It does serve him right.” Twilight said to Princess Luna though Twilight wanted Amadeus to suffer like she did.

Meanwhile a long distance away a royal caravan arrives in Canterlot. Inside an alicorn in the shadows waited as her soldier reported the situation.

“Your highness. We were able to pacify the guards that turned traitor on us. We suspect it was work of Discord the spirit of chaos.” the guard told the alicorn, she growled.

“And Princess Luna?” Majesty Blueblood asked as she glared at the guard.

“Gone with her sister and Discord. The barrier they placed around the castle seems to be impregnable by all our magics.” the guard told Queen Majesty. She growled before blasting the guard away.

“Weakling fool.” Queen Majesty growled. “I want that barrier destroyed!” she ordered as her guards went to try to pierce the barrier. Majesty looked over at Amadeus Blueblood, the elder blueblood looked like he was dragged through Tartarus and back, his eyes were bloodshot and had many bags from endless nightterrors inflicted by the Tantabus. “Father, i'll make Princess Luna pay for what she did to you. As well as every other alicorn in Equestria till I'm the only one.” Majesty told her father.

“Yes, indeed.” Amadeus said though he looked out of it. Majesty sighed as she returned her focus to Canterlot Castle. “I will rule Equestria and bring it back to it's proper age. My age!” Majesty said with her own determination.