The Reign of a Queen

by SonicRPika

Rating: mature
Tags: Tragedy, Dark, Alternate Universe
Length: 4168

As the war against the changlings continue, a new threat arises. When it does, nothing looks bright for anypony...

Life in Equestria is boken down. There are no elements of Harmony, or Alicorns. The fate of ponykind rely on one event, one terrible event.

I only made it a mature rating because of one certain scene. Just a forewarning.

Please let me know how I can improve, it helps a lot :pinkiehappy:

Published 1970-01-01 00:00:00 UTC
Last updated 2015-12-11 00:20:02 UTC

The Prophecy of the End

"If Nightmare Moon is to return, a group of 6 ponies will go and stop her. But a darker theat looms for all Equestria. Soon, nopony will be able to live here.

"If the bearer of the Sun is to die, then the bearer of the moon will take over both duties. But then there will be no way to save ponykind. A series of events will sort that out.

"The root of the problem lies with one pony. An Unicorn with coat of Pink. She will have power greater than an Alicorn. Her destiny will drive the existance of us all to nothing, all on a revenge plot. If she isn't stopped, there may be no fix...

"First a swarm of copies will come to end life. A unicorn of red will come next. Next, a reign of chaos will come about, while an evil soul takes everypony's talent. The end comes with a wasteland, so barren all life has died. This is Equestria's fate if the sun bearer dies."

(Prophecy from a thousand moons ago, given to Princess Celestria after banishing Nightmare Moon)

<><

A huge croud came to see the execution of Princess Luna, even though many of them were captued ponies. Some looked unharmed, mainly because they were just recently captured. Others were hevaly cut and bruised, tired from countless hours of tourture for only bits of informaion they were able to give. Among them was Applejack, who was captured during the fighting in Ponyville. She didn't want to see what was going to hapen, but knew it would.

So far, her hair was sevearly messy, filled with blood from the many attacks from Queen Chrysalis in a vain attempt to get any new information. Several wounds were present, many of which would never heal due to some magic Queen Chrysalis had used. The left side of her muzzle was slashed, and blood drip eternally from it. It was a  miracle she was alive.

However, Applejack couldn't help but notice somepony among the changlings. Somepony she had known for as long as she could remember. Apple Bloom. At first, Applejack thought it as a trick, but as time went by, the chance of it being Apple Bloom got bigger and bigger. There was only one problem: this Applebloom had no cutie mark. Applejack could've sworn that her sister had now gotten her cutie mark, however so much time had passed that Applejack couldn't remember.

At last, Luna was brought onto the stage that was in front of everypony. Her wings were torn off, and her horn had some spell put onto them to prevent Luna from casting any spells. Queen Chrysalis followed, and began to speak.

"Today marks the day that the last alicorn, Ex-Princess Luna, is to be executed." Chrysalis began, as meniacly as ever. "Do you have any last words?" Luna, by this point, was now chained to the stage. The night sky, alongside the various torches lit around them, made this look more like a sacrafice than an execution.

"Only that you will not rule Equestria for long!" Luna was weak, but her voice strong. There was no hesitation in her voice. Luna did not shake, nor did she flinch when she saw the blade that would surely end her life. Applejack was unable to watch. While she suspected Luna of being evil, this was proof of how innocent the alicorn was, and now is.

The blade hovered close to Luna's heart, being controlled by the magic Queen Chrysalis possessed. With one lunge, the blade went into the flesh of Luna's body. Poison from the tip rushed into her blood, and withing minutes, the last alicorn was slain.

"This marks the end of ALL alicorns!" Queen Chrysalis's voice rang loud. Many changlings cheered, and all Applejack could do was mourn Luna's cruel death...

A Blast of the Past

It had been a long day for Rainbow Dash. Her flank was hurting more than ever, no thanks to the rogue changling that atacked her. She landed near the edge of Canterlot, and listened out for the cheers from many changlings, letting her know that Luna was now dead.

A group of fillies, mainly Earth ponies, were cowering in the corner near where Rainbow Dash had landed. After considering leaving them in case of an ambush while she slept, she trotted over to them, and applied some cream to show them she was really who she was. Some cream from her last bottle. She then proceded to apply the same cream onto the fillies, comferming that they were actually ponies. The fillies were no longer shaking, as they knew Rainbow Dash from the many tales, explaining her deeds. In light of all the events in place, the cyan pegasus was like a beacon of hope for all Equestria.

Yet Rainbow Dash felt glum in all of this. Being this far away from Ponyville meant being this far away from Fluttershy. Before the attacks, they were living quite happily in the cottage near the Everfree forest. Their time in flight camp made them great friends, and eventualy found they liked each other. Rainbow Dash missed waking up to the smell of the allotment Fluttershy kept, and the lovely muffins that she baked. Becides Pinkie Pie, Fluttershy's muffins were generally the best.

While it was hard, Rainbow Dash finally found sleep.

<><

A dim light luminated in the room. Stenches of blood and decay could be smelt from the moment anypony entered the room. And at the back, tied up to the wall, was Rainbow Dash. Weak from constant torture, as changling after changling tried to get information out of her. Many cuts and gashes covered the one cyan pegasus, now a red-blue mix. Her mane remained as messy as ever, but instead of being rainbow-coloured, it was purely red from blood.

Thoughts were in the pegasus' mind. Thoughts of escape. But then what? Her right wing was broken, although it had been healing by itself quite fine. If, by some miracle, Rainbow Dash did escape, there was the task of getting help. Help that didn't exist anymore. Not to her, at least.

Then, a hooded figure came into the room. Rainbow Dash was used to this: many changlings would be cloaked to try to confuse the pegasus, but this one was diferent. A green glow came from where the horn would be, a sign for Rainbow Dash to get ready for whatever this changling had in store. However, no pain came. Instead, the magic was used to remove the bounds that kept the pegasus to the wall. Then, the magic changed. Rainbow Dash felt her wings heal to full strength, something that felt unusual given the past state of them.

"You better leave, before Chrysalis comes!" The voice was low, quite hoarse, but sounded nothing like anypony Rainbow Dash knew. As the pegasus went to leave, she felt a sharp pain where her cutie mark was. Chrysalis had just appeared in the doorway, and attemped to take Rainbow Dash out. She was met by a blast of green light from the hooded figure. A blast that uncovered the hood. A changling was under the hood, which wasn't what Rainbow Dash was expecting. Grounded by the magic Queen Chrysalis posessed, Rainbow Dash was unable to move. At least two of her legs had broken from the impact, and there nothing she could do...

<><

"AAAAAAAAAAHHHHHHHHHH!"

Rainbow Dash woke with a start. It had been a while since she had that nightmare. Looking around, the pegasus saw she was still where she was before her slumber, which worried her a bit. What worried her more was the nightmare.

The nightmare was a constant reminder of when she, Rainbow Dash, was captured. it was drove her to help everypony, not just the ones in Ponyville. It allowed her to become the beacon of hope she had now become. If it wasn't for that changling, if it was a changling. The thought of a pony disguised as a changling made a cold feeling rush around her, making her wonder how many ponies she had killed that was disguised as a changling.

"A...are you alright?" One of the fillies Rainbow Dash had met hours ago had come up next to her. Rainbow Dash could tell that the filly meant well.

"Yeah. Just a nightmare. That's all," Rainbow Dash told the filly. While she told her companion about the nightmare, it only frightened the filly more. Seeing this, Rainbow Dash quickly changed the subject, and began to comfort the filly. One thing was wrong: the cream was no longer on the filly's face. Rainbow Dash knew this could've been a changling, so reached for the cream. One touch of the cream transformed the filly into the one thing Rainbow Dash feared. A changling. Rainbow Dash reacted by kicking the changling, eventually breaking its skull. The pegasus, breathing heavily from the fight, took off. The changling left as a warning for anypony or changling not to mess with her.

Kindness, Laughter and Loyalty

The battle of Ponyville had taken its toll for everypony. Many lives were taken. Big Mac, Rarity, Lyra and Bon Bon were among the only few who were confermed dead. It was hard to tell who had died, who was simply captured, and who went AWOL mid-battle.

While Zecora was in charge of the camp inside the Everfree forest, she didn't like being called that. Instead, she insisted two other ponies rule with her. Two ponies that helped her build the camp. Fluttershy and Pinkie Pie.

Pinkie Pie tried to cheer everypony up all the time. She held parties, played with the young, and generally looked after the camp. Fluttershy wasn't the weak pegasus everypony knew. She was a stronger flyer, and led all counterattacks that were needed. Zecora was left to make any potions they needed. All three met up daily to talk about ways of strengthening security, and making life easier.

Whenever Rainbow Dash came around, often every moon at most, she brought information about others around Equestria. Some good. Some bad. The pegasus was able to sneak around due to her speed, making her an ideal spy for the pony rebels. Zecora told Rainbow Dash to come infrequently, and to avoid comming if she suspects being watched. This caused Fluttershy to grow uneasy with every passing day.

You couldn't blame Fluttershy, really. Fluttershy and Rainbow Dash had lived together most of their life, and Fluttershy had some feelings for her pegasus friend. Zecora tried using this to make Fluttershy a better fighter, making her believe she was fighting for herself and Rainbow Dash.

<><

It had been a fornight since Rainbow Dash's last visit. Her visit was a relief for Fluttershy, who was fearing Rainbow Dash being dead. But still...

A woosh went past where Fluttershy was. This meant one thing, as a changling could never go that fast. Rainbow Dash had returned.

Fluttershy abandoned her post to meet her pegasus friend. Pinkie Pie and Zecora were aleady there, chatting with Rainbow Dash as if it was only yesterday she had left.

"Rainbow Dash, so glad you could come! -" Fluttershy had come up close to the cyan pegasus, and began hugging her. "- Any news?"

"Just the one..." There was a faulter in Rainbow Dash's voice. Zecora knew at once what had happened.

"If Luna has been killed, then an army we must build." Zecora's voice was strong, although she was stunned by the news.

"True, but something is wrong with the map. It seems black crystals are sprouting in North Equestria." Fluttershy had seen the map only hours ago, and noticed the change, however only considered it as a minor detail.

"Does this mean..." Pinkie Pie started to speak, but found it hard to finish. Both Zecora and Rainbow Dah knew what she meant, and meerly nodded their head.

"Like a china shop with a bull, problems will come from this war triangle." Zecora was sure of what they had to do. "Go and find out more, Rainbow Dash, but be sure to not be rash."

"Sure thing Zecora!" Rainbow Dash was ready and rearing to leave, but agreed to stay for the night, as she was tired fro her flight.

An Apple Tradegy

Applejack grew wearier and wearier as time went by. Often, Queen Chrysalis would enter the dungeon where she was, and begin torturing her for information. Had the orange pony been able to move, then Queen Chrysalis would most likely be dead. However, a tight band over each leg kept her bound to a large plank of wood. A chain was tightly fastened around her neck with the other end hungon the ceiling, in case she was able to escape. Several cuts covered Applejack's body, all of which were a direct cause of Queen Chrysalis.

There was no strength left in Applejack. Instead, she spent her time thinking to herself. Thought of whether Apple Bloom was ok. Thoughs of a better Equestria. Thoughts of being with her friends one more. The first thought, she hoped was true. As for the other two...

"Thing will work out soon," Applejack sighed, lying to herself about being able to see her friends again. Or anypony for that matter. What felt like months being tortured was actually weeks, but Applejack didn't care. All that mattered to her now was not telling Chrysalis anything that would give her an advantage.

At that point, three changling guards had entered the room.

"We have orders from the Queen to bring you to prisoner one!" Barked the middle one. His helmet was diferent to the others, making him look like the leader.

"Y...you mean Rainbow Dash?" Applejack was releaved she was heading to another pony.

"No, she isn't prisoner one. Which reminds me," the left changling didn't sound as strict, but was demanding nonetheless, "if you try to esape, we have orders to kill you. Understand?"

Applejack gave a small nod.While the changlings undid the ties, the leader grabbed the chain that was around Applejack's neck. Without another word, Applejack followed the guards. The walk was slow and painful, mainly due to the cuts all over her body. But other ponies were able to see her duing the walk. Other captured ponies. Applejack looked in each one, and found none of them had Rainbow Dash in. There was a scream. A scream that could only belong to one pony.

<><

Apple Bloom awoke slowly. Through dreary eyes, the filly saw the face of Queen Chrysalis. Panicking, Apple Bloom screamed as loudly as she could.

While there wasn't a scratch on Apple Bloom, all four legs were bound together with chains, the cuffs having spikes that penetrated her flesh. Blood trickled down the legs, and a puddle of blood was forming around her.

"I'm so glad we have you here, pony." Chrysalis was strolling towards the filly, the use of the word 'pony' to make Apple Bloom feel left out. While Chrysalis waited for a responce, but none came. Chrysalis took this as a que to keep talking.

"Had you been Zecora, I would've had her executed. She is too...dangerous for my good. In fact, I'm ot sure if she is still alive. None of my minions have reported her death, so I don't know.

"As for you, pony. You were Zecora's student. You know the potions she does, with the innocence of a filly. I know you ponies are hiding somewhere close to that town, so I want  you to tell me where it is."

"Why would I want to betrey my friends?" Apple Bloom's voice was strong. Giving up the location of the base would mean allowing the changlings to take over, and she wasn't about to let that happen.

"Because," Chrysalis was ready for that responce. She had some guards fetch Applejack moments ago, "if you don't want your sister dead, you'll co-operate." With that, the guards entered. Applejack followed, a chain still around her neck.

"Applejack?" Apple Bloom was surprised to see her sister again, as the last time they had seen eah other was in the battle for Ponyville.

"Apple Bloom?" came Applejack's responce. The orange pony found the strength to run over to her sister, and gave what looked like a sort of hug. Chrysalis gave a signal, and Applejack was pulled off her sister. One of the guards had his spear pointed at Applejack's heart, ready and waiting to strike.

"Now you understand?" Chrysalis anticipated a no off of the filly, but was shocked to hear the faint yes comming from her.

"Good..." cackled the changling. While the guard with the spear hesitated, he put down his weapon.

"Ok..." Apple Bloom began, her voice trembling, "I guess I have no choice. We are hidden -"

"My queen!" In that moment, a changling disguised as Scootaloo had rushed in. Out of breath, she gave her message. "Terrible news...Crystal Empire...returned...King Sombra...out to take over your kingdom" Scootaloo was now her changling self, still exhausted from the flight back.

"Very well. You have done well." Chrysalis had turned her attention to the changling spy. She then turned back to Apple Bloom. "I guess we will have to wait until later, pony. I have some business to take care of." As Chrysalis left, she whispered toone of the guards.

"Leave them in here. And watch the door."

Applejack's chain was hooked onto the wall, and all changlings proceded to meet the threat that was King Sombra. There was nothing either of them could do but wait. Wait and form a plan of escape, unless a cyan pegasus has anything to say...

Truths and lies

King Sombra had waited over one thousand years for this moment. And for all alicorn princesses to be dead, all the better. However, having a changling army being in charge wasn't the best. Not to mention the small threat of the pony rebels, but he'll deal with them later. They wern't that much of a threat after all. Were they?

Queen Chrysalis wasn't anticipating having to fight two wars either. Since King Sombra was a new threat, more resources were devouted to the fight againt him. She still fought the pony rebels, but wasn't too concerned about them. Something a pleased Rainbow Dash was all too happy to boast to Zecora the next time they met.

However, whether a next time would come relied on one factor. Because of the new threat, Chrysalis left Applejack and Apple Bloom alone in the room. It just so happened that Rainbow Dash flew in.

"Rainbow Dash? What in tarnation is going on?" Applejack spoke with a hushed voice, as to not alert any changling around.

"I'm not sure, but it seems we have another problem." Rainbow Dash too was speaking in hushed voices, so that only Aplejack and Apple Bloom could here. "C'mon. Let me help you two." With that, Applejack's chain was no longer around her neck, and Apple Bloom was no longer tied up.

"Hey. What's going on?" A changling heard the sound of the chains falling, and came to investigate. Suddenly, without any notice, Rainbow Dash charged at the changling, and kicked it. The kick connected with the head with enough force to decapitate the changling. The three then raced out of the room, trying to find a way out. Many changling guards went after them. Apple Bloom, being the slowest, was caught quite quickly. As one of the guards went to stamp on the filly's back, Applejack did something she didn't expect to do.

"Not my sister you bitch!" Applejack had lunged herself at Apple Bloom's attacker, and knocked her sister out of the way. In the nick of time too. However, the same couldn't be said for the orange pony, who had now been stomped on. A crack sound made Rainbow Dash turn around, and saw Applejack unable to move.

With no regard for any life, Rainbow Dash went ahead and knocked any changling foolish enough to chalenge her away from her fallen friend. When the deed was done, Rainbow Dash lifted Applejack onto her back, and flew off, Apple Bloom running behind.

<><

It was getting late before Raibow Dash slowed down, finally landing outside of Canterlot. Carefully, the cyan pegasus slipped Applejack off of her back, and made sure she was comfortable. Apple Bloom caught up quite quickly. After making sure they all were not changlings, Apple Bloo went to make a potion to help her sister, while Rainbow Dash kept watch.

"Y'no,  Rainbow Dash." Applejack's voice sounded tired, quite likely from the flight. "What do you will happen now?  With King Sombra fighting and all."

"Err...I don't know, Applejack." Rainbow Dash's mind wasn't on the future. Not that future anyway. On a futre had she not gone into the castle, or if she was captured.

"You sure you can keep watch all night?" Applejack asked. There had been an awkward silence between the two ponies.

"Heh, it's better than going to sleep and having that nightmare." Rainbow Dash tried to avoid sleep whenever possible, as every time she does, she got the same nightmare. Recently, at least.

"What ni-" Applejack went to question on, but saw the cyan pegasus look reluctant to answer, so dropped the question. "Never mind."

Eventually, the silence had to be broken. Confersations were awkward, but they managed to get a good one on their fillyhood. It seemed the only thing they could talk about. However, it passed the time long enough for Apple Bloom to return with what she needed. A potion in her mouth, which was poured immediatly onto Applejack's back. It acted slowly, but allowed Applejack to walk in the meantime, eventually getting the orange pony back to full strength. Applejack hugged her sister, something she couldn't do before having the potion.

That night was one of the worst for Apple Bloom. A nightmare where she was back in the castle, tied up and everything. Her sister was opposite her, or what she thought was her sister. Instead of Applejack having a spear pointed at her, it was Apple Bloom that was dancing with death. Badly. The changling, after a painful amount of time, finally struck the filly in the heart.

Apple Bloom woke with a start. Both Applejack and Rainbow Dash were still there. Her sister was still asleep, but Rainbow Dash stayed true to her word, and was still awake. Now she knew why the pegasus was fighting sleep: she was having a simular nightmare. Instead of falling asleep, Apple Bloom found herself going to Rainbow Dash, and having a confersation with her.

"At least staying awake with somepony else was better than alone!" concluded Apple Bloom

A War for Power...ish

When two leaders clash, a war is inevitable.

Queen Chrysalis thought confusing the Crystal army would be the best route. Her changlings were able to disguise themselves as anypony they so wish. Chrysalis herself chose to disguise as King Sombra, and allow herself to command this new army to their own death. A stratedgy she hoped would ensure victory.

Sombra, on the other hoof, felt that a full frontal attack on all of Equestria was the best plan. He protected his army in crystal-like armour, which weighed a lot, but was helped by the magic of the army. The pegasii were given mounts so that they could carry unicorns on their backs. The unicorns were trained in using their magic to kill and maim. As for the earth ponies in the army, they were like footponies, many fighting with some carrying unicorns or the injured.

As for the rebels...they didn't want Chrysalis to continue her reign, but being under the rule of King Sombra would mean a lifetime of slavery. They didn't want either, so decided to help and hinder both sides in the war. Something that only one pony had to do...

As the changlings and the Crystal Army came at each other, Chrysalis was determined her disguise plan would work. And Sombra was certain that the changlings were a pushover. However both were further from the truth. Sombra's army were easier to take on, going by the fact they didn't know if they were fighting a friend or foe. However, the changlings were shocked to find some of the ponies didn't have any armour on, so didn't know whether they were fighting a friend or foe. In the end, with both armies significantly smaller, they both retreated.

Eventually, all three groups went ahead and tried to hinder each other, in case another fight was to break out. However most of the sabotaging was done in favour of the rebels. Many rebels had moved to bigger camps, easier to protect with the drawback of more damage if caught. More and more ponies were doing what they could to stop both enermies.

This was a war triangle like none other. One that would only get bigger as time went by...