The Twilight Citadel: Empire of Magic

by Pyrestrike

Rating: mature
Tags: Tragedy, Twilight Sparkle, Profanity, Gore, Violence, My Little Pony: Friendship is Magic, Dark, Death, Alternate Universe, Main 6, Applejack, Original Character, Rainbow Dash, Adventure
Length: 4710

With the fall of the kingdom of Equestria and its Princesses as a result of the Changeling Invasion, Ponykind now faces a fate worse than extinction. However, a new Kingdom to the North now challenges the onslaught of the Changeling Swarms.

During preparations before the much-anticipated wedding between Captain Shining Armor and "Princess Mi Amore Cadenza", Twilight Sparkle had vanished without a trace. Ignoring her warnings and proceeding with the occasion without her, the rest of Twilight's friends were powerless to watch as Queen Chrysalis and her waiting Changeling invasion force swept in and devastated Canterlot. With the capital gone and Celestia apparently under their control, the Kingdom of Equestria fell in a matter of weeks. Forced to choose between abandoning their homeland or face lifelong enslavement, Applejack and the rest of the Mane Five have managed to flee to the North with a large group of refugees from parts all over the ruined nation and establish a settlement to escape the emotion-feeding parasites.

A decade has passed since then, and things seemed to have calmed until the discovery of their refuge is made apparent by a survivor originating from what perhaps is the only source of salvation for Ponykind: The Crystal Empire

And its mysterious, but faithful Queen.

This is meant to be a rewrite of my previous story The Twilight Citadel, aspects of the old story can be found in this new one, but most of the structure and character development has changed significantly.

Cover Art not owned by me, I only added a few effects to it.

Published 2020-05-21 12:20:01 UTC
Last updated 2020-05-21 12:20:01 UTC

Remembrance

Author's Note

My god, it's been literal years since I've been able to update or post anything on this. College just completely screwed over my time and scheduling. But hey, I'm back in some capacity and I figured I'd finally finish writing this re-write. Thanks to anyone who was patient in waiting for this. :twilightsheepish:

Remembrance

"Honestly. The Bride herself? Evil? Out of all the outrageous things she's done today."

"Why would Twilight do such a thing? Calling Princess Cadence those awfully mean things..."

"I like telling jokes and all! But she went waaaay too far with this one, and it wasn't even funny to begin with."

"I know she's an Egghead, but come on! That's not how you're supposed to treat somepony who's about to get married, and to your own brother nonetheless!"

"Come on ya'll, let's go check on the Princess."

Applejack could only frown as she remembered the last words she and the rest of the girls said to Twilight before she disappeared. Cursing to herself as she remembered the hurt look on her friend's face as they turned and left her in the hallway after the argument between Shining Armor and her. Before she could dwell any deeper into the horrible events of that day a gust of frigid wind reminded the former farmmare where she was before she began to lament. The cold wind lashed against her covered face as the blizzard around her continued to howl.

This was her home now, and every shiver she felt rush through her body gave her a solid reminder that it was.

Sitting up from the stone she was taking a rest upon, Applejack adjusted her saddlebags and shook off the snow which had gathered on the brim of her stetson. The piece of headwear had seen some rough patches ever since the Changelings took Equestria, with cuts, holes, and other markings from past battles marring the material in ways the mare never thought it would have to endure. But endure it did, and so did she.

The condition of Applejack's stetson, of course, said nothing about the mare herself. Years of having to live on the run with the risk of losing everything at a single wrong move had hardened mare. To say nothing of the sub-zero conditions which forced her to abandon her family's trade of Apple farming. Scars from several close encounters with Changeling soldiers were peppered along her body, though most notably around her legs and forelimbs. Either from the lack of sunlight or the depressing fact that her very way of life was gone, her once bright orange coat now resembled her look under Discord's spell, albeit with rough and uneven patches thanks to the impacts of combat spells which burned quite painfully when they made contact.

Needless to say, life was rough for the former Element of Honesty. The Tundra that she was forced to make her home in only added salt to the wound.

"Applejack! Where'd ya go!"

She turned quickly in the direction of the source of the voice, squinting her eyes to get a better view through the blizzard. A few feet in front of her she could make out the shape of a pony, trudging through the snow towards her. Unsure of the identity of her contact, she stood her ground and waited for them to move closer.

"Jeez Applejack, the least you could do ya know is to meet a mare in the middle! I may be the fastest flier in the area, but I'm still a pony!" Rainbow Dash complained. Rainbow Dash was in a similar state to Applejack, with the past decade of living in the tundra having a negative effect on her physical appearance. The color of her coat and mane seemed faded, and she bore scars the same as her friend, though with more emphasis on the area near her wings and body rather than her legs.

"And how exactly do ah know it's really you 'Rainbow Dash'?" She couldn't take any more risks, especially after what happened to Bon Bon. Her tragic incident was among the many times they failed to be cautious of newcomers, and what was meant to be a warm hug from her missing friend Lyra was instead the cruel knives of a Changeling assassin.

Never again she promised.

Reaching with her right hoof, she unbuttoned the top of the holster which held her trusty hatchet. She once swore an oath to use such a deadly tool only for building and betterment. Needless to say, however, she quickly renounced that oath the moment Changeling soldiers tried to put their hooves on Granny Smith. Hooves which ended up on the floor after a single savage swipe.

Seeing what she was doing, Rainbow Dash stepped back in a defensive posture. "Whoa, whoa! Hold up! It's me, really!"

Rainbow was right to be terrified. Fear wasn't enough to describe the sheer terror of Applejack when she brought her hatchet into the mix. The farmmare began a long streak of straight-up decapitating any Changeling that was unlucky enough to meet the edge of her axe, and the dozens of heads she saw rolling the last time she took it out in anger only reinforced that terror into her.

"Alright then partner, Ah'm givin you just ten seconds to prove you're the real deal ya hear? And if ya don't manage to convince me that you're really Rainbow Ah'm gonna split your skull like a watermelon."

Rainbow stammered to give a response, running multiple answers and scenarios through her head to prevent the short sharp shock she'd face if she didn't give a clear enough response. Desperate, she thought back to the time she and Applejack participated in the Running of the Leaves. Thinking she could prove her innocence with that, she opened her mouth to shout her answer.

"Time's up!"

"Wait, what!" Rainbow's heart skipped a beat as in a flash, Applejack pounced onto her unfortunate victim and held the axe in her mouth in a position ready to strike down the poor pegasus.

"T-That's not fair! That wasn't even ten seconds!"

"Can it Changeling. If ya really were Rainbow Dash, ya could clear the sky over Ponyville in ten seconds flat, and considering how you didn't give me a straight answer in that ten seconds Ah reckon you're a fraud." Applejack stated darkly.

As much as Rainbow struggled, she couldn't escape the grip her friend had on her. Years of restraining and putting down Changeling scouts which managed to sniff them out had refined her already impressive strength to allow her to pin the cyan mare easily.

"You're being ridiculous! I'm not a Changeling! Let me go!"

"Ya know, that's exactly what a Changeling'd say in these kinds of circumstances."

"What about the Running in the Leaves! We both tied for last remember!"

"Ah know me and Rainbow did, ya'll coulda just looked it up in one of the old record books in Golden Oak Library in Ponyville. Provided of course that ya'll didn't burn it with the rest of the town. Anyway, it was nice meeting ya 'Rainbow Dash' I hope ya have fun in Tartarus." Rainbow Dash watched helplessly as her friend raised her axe to deliver the blow that'd turn everything black. Inhaling deeply, Rainbow shut her eyes and gave a defiant scream to the heavens as if to summon help from Faust herself.

"AAAAAAAAAAAAAAAAAAAAAAAAAAHHHHHHHHHHHHHHHHH!!!!! *gasp* AAAAAAAAAHHHHHHHHHHH—!"

"Ya done yet pardner?"

Rainbow Dash's eyes shot open as she realized she wasn't headless, nor was she pinned by Applejack anymore. Rapidly getting to her hooves, she quickly shook off the snow that was on her back and glared at her assailant. After a few seconds, Applejack started to chuckle and eventually it devolved into a mix of cackling and wheezing at her friend's expense. Rainbow looked to the spot where she was pinned and saw that Applejack's axe was several good inches to the right of where her neck was in the outline. Realizing she'd been played, Rainbow stomped up to her friend to give her a piece of her mind.

"You son of a whorse! You nearly gave me a bucking heart attack right there!"

Still snickering, Applejack responded, "Oh don't get yer mane rustled, Ah knew it was you the moment ya opened yer big mouth and bragged about being 'fastest flier'. The thing about Changelings is that while they can get the look down, they can never truly mimic that bonafide attitude of yours."

"Still! You didn't have to pull your hatchet out and go psycho on me! I was this close to knocking you out right then and there!"

Applejack rolled her eyes, "Suuuure. Ah bet you really coulda knocked me out cold from where you were lying."

Rainbow sighed. "Look, we don't have time for this conversation right now. I came looking for you because Rarity told me to find you and bring you back to camp."

That sobered the mood. "What for? There ain't an emergency is there?"

"Nah, something else apparently. She won't tell me or the others until everyone's gathered in the Meeting Area."

Raising her brow, the former farmmare trotted over to her half-buried blade and jerked it from the snow before gingerly holstering it back next to her saddlebag. She hoped she wouldn't have to use it again soon.

"If Rarity's keepin her mouth shut about it, then it's gotta be important. Lead on Rainbow."

Rainbow Dash started trotting ahead before she turned back to Applejack with a smirk, "... Just for the record, I totally could've beaten you back there."

"Ya'll go ahead and keep tellin yourself that."

"Seriously though, my attitude is what convinced you?"

Applejack chuckled, "Course it did, little details in the personality is all ya gotta notice."

"Then why didn't we notice at the wedding?"

Applejack froze. She whipped around to see Rainbow glaring at the ground. The confident and unbeatable vigor she always exuded was gone.

"If it's that simple, why didn't we believe her?"

"Rainbow, we couldn't have known that—"

"Why didn't we just stop a moment and actually listen to what she was trying to tell us, and why didn't we side with her when that bug bitch manipulated her brother like that! Why didn't we try and help her when she needed us the most! Why didn't we—!"

"AH DON'T KNOW!"

The blizzard around them had already calmed. Hot tears were pouring down both mare's cheeks as silence had overtaken the tundra. Rainbow fell to her haunches as Applejack continued to stare at the ground with a storm of emotions replacing the blizzard that had ceased around them. Both of them said nothing as they lamented their past mistakes.

"...What's the point?"

Applejack looked up again to see the anguish in her friend's eyes, the guilt and regret that had built up over the years clearly present in her pink irises.

"She's probably dead because of us."

"Now hold up there Rainbow! We don't know that she's gone yet!"

"You saw what they did to Ponyville. What they've done to everypony that tries to fight back. You saw what they did to Spi—"

The farmmare didn't let her finish as she embraced her friend in a tight hug. The memories of a certain baby dragon's sacrifice were already bringing tears to their eyes.

"It's my fault... He's gone because of me Applejack... I could've saved him..."

"C'mon! We need to get outta here now!"

"Ah'm with ya Rainbow! But these guys are everywhere!"

The group was currently galloping towards the train station, Rainbow Dash was following from the air while Rarity and Pinkie were blasting Changelings left and right with their magic and Party Cannon respectively. Applejack was leading from the front with Spike on her back breathing fire into the faces of Changelings who got too close. The dresses and gowns they wore for the wedding ceremony were in tatters, with Rainbow and Applejack forgoing them completely for the sake of maneuverability. Spike's comically large top-hat was gone and the small suit he wore was dirtied with dust and ash from the destruction around them.

"Does anyone know how far the train station is! We can't outrun them when they're everywhere!" Spike caught sight of a Changeling soldier about to dive in and attack. Before it could get the chance however, he inhaled deeply and spewed a stream of emerald fire into its attack path. The invader let out a small scream trying to shield itself with its forelegs and barely missed the pair as it crashed behind them.

"The other streets are too overrun! We have to get to Fluttershy and the rest of our folks before the train leaves!" For once in her life, Rarity couldn't care less about her physical appearance. The safety of her little sister was her top and only priority. While still wearing a portion of her gown the majority of it was torn off to allow freedom of movement for her, she also stuck several pins, needles, scissors and other sharp tools into the fabric for quick use against anyone that got in her way. The group had stopped at a fork in the road and ducked into the veranda of a nearby cafe to get some cover from anyone watching from above. The next move was to find the fastest and safest route to their destination.

"Alright, I propose we take this street on the right towards Restaurant Row and cut across the alleyways to the station!" Rarity pointed with her hoof towards the street in question to make her point.

"Uh, no Rarity! That area's probably swarming with Changelings. We should stick to the path we're on and it's a straight shot to the station. We can "

Rarity's face scrunched up in frustration. "Yes for a pegasus, but as you can see we clearly lack the appendages to do so without becoming food for these monsters!"

"Hey! Hey! This ain't the time for fighting ourselves. Besides, we're not done yet girls. We've still got a chance if we just get these safely outta the city!" Applejack motioned towards the saddlebag on her side, a metallic clang gave away the knowledge that the Elements of Harmony were tucked safely away for future use.

"After we get outta here, we've gotta find Twilight. Once we find her we can blast that Queen and her swarm right off the face of Equestria like flies on a Zap Apple Tree!"

Both Rainbow Dash and Rarity looked downtrodden. The last words they spoke about their friend not being the kindest... Spike also had a hard look in his eyes, his fists clenched and eyes closed in regret. Pinkie Pie then popped up from between them all and pulled them into a tight hug.

"Hey! I know we didn't believe her over this whole messy mess! But I'm sure that once we apologize we can get things back to the way they were!" Pinky cheered, pulling her friends even tighter against herself and nuzzling into them. The moment was ruined however when Pinkie's tail twitched. She opened a single eye and noticed a shadow on the canopy of the veranda. Not wasting a second she pulled her party cannon and trained it in Rainbow's direction much to her friend's shock.

"Rainbow duck! And not the animal kind!"

The mare of the hour had only a second to do so before a blast of party supplies ripped a hole right though the fabric of the canopy. A Changeling trying to get the jump on them ended up eating a face-full of hot confetti before crashing into the adjacent building.

"We'll go with Restaurant Row then, the alleyways will make it easier to avoid these guys." Rainbow took to the air a few feet and looked around for anymore drones. After the all clear sign from her the rest of the group followed her as she took the lead.

Canterlot was a war zone now. Hundreds of Changelings were swooping in from the air and attacking swiftly with both melee and magic. Much of the pristine ivory towers and elegant architecture of the city was reduced to rubble, with magical flames causing fires to spread throughout the city. Many of the citizens tried to flee from the oncoming threat, but ended up becoming cornered quickly. Some tried to fight back as much as they could, joining the hopelessly outnumbered Royal Guard in trying to defend their precious capital. Yet while their actions were valiant, it was mostly futile against the almost endless swarm and were quickly overrun. The train station wasn't too far ahead now, and the group had just about enough of this nightmare.

"We're almost there! Just a few more blocks and-" Rainbow Dash couldn't finish as a drone managed to knock her out of the air with a tackle from above. The two of them skid several feet ahead and the drone was the first to get back on its hooves. Rainbow was also quick to get up but a strike from the Changeling's magic knocked her into the side of a building, the impact leaving cracks on the surface.

"RAINBOW!"

The rest of the group could only watch in horror as the drone swiftly maneuvered itself behind their friend. The next few seconds felt as if time stopped. With a mad cackle, the drone enveloped Rainbow in its magic and held her still, before bringing its forelegs up and crashing his hooves over the one thing all Pegasi considered unforgivable to damage in a fight...

Her wings.

A sickening crunch and then a long scream from Rainbow could be heard. The Changeling's work was cruel and clear. One of the appendages was twisted outwards with a dark purple spot marking the area where the drone had smashed. Several cyan feathers were still stuck to its hooves as it prepared to repeat its gruesome act on her other wing.

"GET OFF OF HER!"

The Changeling glanced up in time to see Spike lunging from Applejack's back with a furious glare. The baby dragon managed to grasp onto its horn and pivot around so he was on its back. With another shout, Spike began to angrily claw the face of his enemy with one hand while gripping its horn tightly with the other. With yelps and shrieks of pain, the green aura over the wounded Pegasi dissipated as the drone tried his hardest to shake Spike off.

"Scaled Savage! Ahh!!!" Spike held on for life as the Changeling took to the air in a panic. Rarity screamed and tried to pull Spike back with her magic, to no avail as he was too far away.

"SPIKEY-WIKEY! NO!"

Rainbow Dash was slowly taking to her hooves, with Applejack rushing over and helping her up. The cyan mare looked back to see the damage done to her left wing with despair. That despair then turned to rage as she returned her gaze to where Spike and the drone had flown off. Painstakingly folding her wing into a more compact position, she let out a painful scream through clenched teeth before she finished.

"That Bug is gonna pay for this..." Rainbow said nothing else as she took off with a gallop in Spike's direction. Hot tears flooded her eyes as the pain fueled her to seek vengeance.

"Rainbow! Wait up!" Applejack called to her friend. The words fell on deaf ears as the mare bolted around the corner.

"Dammit, we've got to get em back!" Applejack untied the saddlebags and quickly trotted to where Rarity was shaking with anguish.

"Rarity, you've got to get these to the train station. Pinkie, Ah want you to go with her and back her up."

"WHAT!? ABSOLUTELY NOT! THEY HAVE MY SPIKEY-WIKEY!" Rarity was now in hysterics, her mascara was running freely down her face in a most unladylike fashion.

"Yeah! We can't just leave Spike and Rainbow like that! We've gotta go and rescue them!"

"Ah know, but someone has to make sure that these are safely on the train. Ah'll go and get em back, but ya'll need to make sure that these Elements and our families are safe!" Applejack dropped the bags onto Rarity's back and pulled the belt to secure them tightly.

"Ah'll get them back before we depart. Ya need to trust me on this alright?" Applejack readjusted her stetson before looking expectantly at her two friends for an answer. Rarity was trying her best to wipe her ruined mascara off with another rag she tore from her dress. Pinkie looked worried, watching the skies for any Changelings that might have noticed them in the fighting.

Pinkie looked back into Applejack's eyes and nodded before picking Rarity up in a display of strength not seen from her in a while. The farmmare looked in surprise at the sudden action from her fellow Earth Pony.

"What in the-? Pinkie! PUT ME DOWN!" Pinkie paid her no heed as she tossed her onto her own back before turning to face Applejack.

"Applejack, go save our friends. I'll make sure the Elements and the rest of our folks are safely onboard the Friendship Express. Just promise me one thing."

"Sure, what is it?"

Pinkie moved trotted forward and enveloped Applejack into a hug before speaking softly. "Please come back. I can't afford to lose any more friends."

Rarity resigned to her position and craned her neck to talk to Applejack. "Applejack, please bring them back safe. We all need to leave this terrible place."

Applejack nodded. "I Pinkie Promise." The farmmare prepared to perform the gesture but Pinkie put her hoof over hers and shook her head.

"No time for that! Get going!" Pinkie pointed with her hoof down the street Spike and Rainbow went. Applejack galloped away as Pinkie started galloping quickly with her passenger on her back.

"I can still walk you know!" Rarity complained.

Both Spike and the Changeling continued their awkward fight down the abandoned streets. As much as the Changeling tried to throw him off, Spike continued to hold on tight. Before they knew it they were in an alley, away from the main sources of battle in the city and isolated from any who could try and help. The drone now flew himself against the walls to scrape Spike off. Each attempt scraping and scratching the both of them yet neither had a clear chance of victory.

"You'll! Pay! For! That!!!" Spike punctuated his words with a punch to the back of the Changeling's head with his free arm. The drone growled and tried flipping to get its unwanted passenger off. In response, Spike wrapped his arms around the drone's neck tightly and held on for dear life. Unfortunately the lack of interference on the drone's horn meant it was free to use its magic. Realizing it's won it let out a choked laugh, the drone lit its horn and levitated the dragon off its back and in front of it so as to get a better look at its enemy.

"You're a brave one dragon, one has to ponder why a creature such as you would be living amongst such lesser beings..." The Changeling's voice was cold, yet dripping with enthusiasm of a dark nature. Different from the language it cursed Spike in earlier, the drone smiled as it waited to see how his quarry would respond.

"Those lesser beings are my friends!" Spike tried throwing more punches towards the drone but failed to do anything in its aura. It's eyes glowed a bright blue as it studied Spike further.

"Friends? How sweet! A bunch of sweet little ponies being friends to a savage dragon! I can certainly feel the power of friendship between you all..." Sarcasm was obvious from its tone.

Before the drone could continue there was a shout as it was tackled to the ground. Rainbow Dash was already over it, pummeling it with her forelimbs. Each punch making a resounding thud as it echoed off the walls of the alley.

"THIS. IS. FOR. MY. BUCKING. WING!" Rainbow was about to bring both of her hooves down on its face until the drone lit its horn again.

Rainbow was flung towards the wall with telekinesis as the Changeling got up slowly. Spike rushed over to help Rainbow up as he kept an eye on their enemy. It's face appeared to be horribly bruised and swollen, but after seconds it began to morph and shift back to its original status. The Changeling cracked its neck and turned to the pair looking unamused.

"Some power of Friendship... Seems to be more along the lines of being the power of incredible violence and rainbows..."

Rainbow scoffed and Spike scowled. "What do you know about friendship? You're just some parasite taking things that don't belong to you and hurting people that don't deserve it!"

"But Spike, you do deserve it." Spike had gone pale. With a flash of green flames the Changeling before the two of them was now his best friend and caretaker.

"You left me alone... I tried to warn you all but none of you listened..."

"No... No I didn't mean to... I didn't mean to!" A green flash had overtaken Spike's eyes. Rainbow kept looking between "Twilight" and Spike as her mind continued to readjust from her impact.

"You all turned your backs on me... You all left me to die..."

"D-Die? Twilight no you're not dead!"

"Spike... It's not her... Get ahold of yourself..." Rainbow started to shake Spike in an attempt to break him out of his stupor. She wanted to move and combat the fake, but the pain was too great.

"Why Spike? Why?! You left me! You left me! YOu LeFt mE!!!" The illusion had grown demonic now. "Twilight's" body began to melt, with bits of her skull being displayed in a nightmarish way. Rainbow was horrified and did her best to keep herself from getting sick from the sight.

"Twilight! NO! TWILIGHT!" Spike was sobbing now, the vision breaking him emotionally.

"LEAVE EM ALONE!" Rainbow turned to see Applejack come barreling into the Changeling. Spike was released from its magical grip and came to his senses.

"W-What? Where's Twilight?" Spike rubbed his eyes and saw both the drone and Applejack wrestling. Neither seemed to have the advantage until the Changeling's horn lit up again. A bright flash had enveloped the alley and before anyone could react it had its hooves around Spike.

"Spike!" Both Applejack and Rainbow Dash made a leap to intercept, but they were too slow. The Changeling encased Spike within its magic and shot above the alleyway until the two of them were well above the rooftops. Spike continued to struggle against its magical grip like he did before, but the drone only laughed as they continued to ascend. Spike could see the entire city now. The magnificent capital of Equestria was now burning, smoke rising from almost every portion of the once great metropolis.

"Do you see now dragon? How far your friendship has gotten you?" The drone turned him around into the direction of the castle, now swarming with Changeling soldiers and banners of the Changeling insignia were being flown across every spire and wall which was still standing.

"If anything, you are friends with food at best. Food that deserves nothing more than to be either consumed, or burned." Spike could see groups of captured ponies being forced into lines and being led into cages. Rich or poor, young or old, it did not matter as a life of servitude was what awaited them now.

"So dragon... any last words?" The Changeling was smirking now. Victory was surely his as he turned Spike to face him. The defeated dragon clenched his fists and knew this was his only choice.

Spike breathed deeply. "If I'm gonna burn, then you're burning with me."

A magnificent torrent of orange fire escaped his mouth. The Changeling screamed in agony as he was consumed in the intense flames. His source of flight gone, Spike now plummeted to the ground. Yet he didn't scream nor did he flail. He opened his eyes... and admired the twilight.

"Hey Twilight... I'm coming home.