A Blackened Equestria

by NightLord

Rating: teen
Tags: Bon-Bon, Adventure, Lyra, Cake Twins, Gore, My Little Pony: Friendship is Magic, Dark, Alternate Universe, Other, Original Character
Length: 4541

Set in the alternate universe where Queen Chrysalis is not defeated, this is a story about a group of survivors, banded together to fight back against the changelings. But as the changelings begin to infiltrate the resistance, who can be trusted?

Set in the alternate universe where Queen Chrysalis is not defeated by the Mane 6, this is a story about a group of survivors, banded together to fight back against the changelings.
When Lyra Heartstrings has her life turned upside down, she must learn how to survive in an Equestria turned cruel.

Cover art by Alyssa Hartwick

Credit for the title goes to Quillian Inkheart. Original title was 'Trust No One'.

Published 2016-03-23 20:00:02 UTC
Last updated 2016-06-04 13:40:17 UTC

Chapter 1

Lyra cautiously peeked through her window into the barren streets of Ponyville. Almost two weeks ago, Changelings invaded Canterlot. There had been many rumors spread that the forces in Canterlot were unable to contain the invasion, and that the apocalypse was nigh. Of course, there was no official news to back this up, and she did not believe a word of it. She was one of the only ponies who had not fled into the forest, following that crazy zebra. She remained in Ponyville, along with the mayor and a handful of other level-headed ponies. She was determined to stay here and wait for her friend to return. It had been one week since Bon Bon had left for Canterlot to help the cause, and she had not received any news. Although she knew her friend would be safe, she had to admit that the lack of any communication from Canterlot was unsettling.

A blaring noise interrupted her thoughts. As far as she could tell, it was coming from outside. Hesitantly, she walked to her door and slowly opened it.

“EVACUATE, NOW! THIS IS NOT A DRILL! THE CHANGELINGS ARE HERE! RUN FOR-”
Lyra immediately recognized it to be the mayor's voice, amplified by a loudspeaker. Suddenly, it was cut off with a splat. Lyra could hear her heart threatening to burst from her chest. The Changelings had spread from Canterlot. They were here now, in Ponyville. And they had just killed the mayor. Just then, Lyra realized that everything had gotten darker. She looked to the skies, and was horrified to see that the swarm of Changelings that were swiftly descending on Ponyville had blotted out the Sun. At that moment, she knew she must make a choice. She could either stay in the temporary protection of her home, allowing her a few extra moments of life, or she could take her chances in the streets with the goal of escaping this nightmare.

After a few seconds of thought, she chose the latter. She swiftly burst open her door and sped into a full run. As she galloped through the streets, she could see the ruins of what used to be so familiar. It was worse than she possibly could have imagined. In the distance, she could see huge clouds of smoke rising from Sweet Apple Acres. As she passed by Town Hall, she saw Mayor Mare's lifeless body lying on the ground, confirming her suspicions. She was speeding past Sugarcube Corner, which had already been reduced to rubble, when she spotted Mr. Cake, causing her to stop in her tracks. He was valiantly fighting off two Changelings with a rolling pin, his wife standing behind him, cradling their children.

Without thinking, Lyra rushed to help. She was too late. As she rushed to tackle the Changeling closest to the family, blood spattered onto her face. An ebony blade was protruding from Mr. Cake's back. She pummeled the Changeling at fault until it was still, and the other quickly fled, but that could not undo what already occurred. Ms. Cake was frozen in shock, tears streaming down her face.
“Hello? Mrs. Cake, I know this is hard, but I need you to listen. We have to get out of here.”
The blue mare was unresponsive. Already, another group of the bugs had taken notice of them.
“Please, I'm begging you. Do it for your kids!” Lyra pleaded. It was no use.
Lyra then made a decision, one that would haunt her for the rest of her life. She grabbed the foals from their mother's arms and placed them on her back. Mrs. Cake did not react at all. Lyra gave the mare one last, sorrowful look and ran. She didn't look back, but she could still hear the screaming, and the sickening sound of blade meeting flesh. It was the only option. Ms. Cake would not have been mobile in time, and Lyra was not about to let these innocent children be slaughtered.

She kept running. The edge of the Everfree was now in sight, and Lyra let out a sigh of relief. Almost there. She glanced behind her back, just to be sure. Nothing. The group that had noticed them must have been too occupied with Mrs. Cake to notice their departure. All of the gore she had just witnessed flashed back into her mind, causing her to vomit. She noticed that both of the children were now crying very loudly, and would soon give away their location.

“Hush!” Lyra insisted. She had never been very good with children. They ignored her, and continued their wailing. She kept them both on her back, and continued running. Soon, she was well into the forest. Both children had fallen asleep at some point during their ride, and she realized just how tired she was. Lyra collapsed to the ground, barely mustering the energy to remove the foals from her back and place them on the soft ground. Although she was physically exhausted, she realized after a few hours that it would be impossible to sleep. Staring up at the sky, she then noticed something very peculiar. When she first left her house, it had been sunset. Now, as far as she could tell, several hours had passed, and it was still sunset. She felt a sinking feeling in her stomach, for she knew who was always responsible for raising the Moon and Sun. Could it be? Are the princesses... She pushed the thought away as soon as it had appeared. Of course they weren't. The day-night cycle had been just fine for the last week, even after Canterlot was first attacked. Why would something have happened to the Ruling Sisters just now? And why, Lyra wondered, was she thinking about something as small and trivial as this right now? It was probably a defense mechanism of her mind, blocking what had happened today from her thoughts for the the time being. After another uneventful hour or two, sleep didn't see so impossible. She closed her eyes, and everything faded to black.

Author's Note

So, first real chapter, first story. What do you all think? (Be honest, I can take criticism.)

Chapter 2

Lyra awoke with a start. She jolted up and scanned her surroundings. She was in a very different place than she had been when she fell asleep. There was a roof of some kind over her head, with large patches of light gleaming through. She reached up to touch it, and realized that it was an assortment of large leaves commonly found in the Everfree. Lyra searched for the walls of whatever construct she was inhabiting, and noticed that there were not any walls, at least not in the sense she was accustomed to. Instead, there were multiple branches and small logs arranged in such a way to support the roof of the shelter. She noticed a small opening on one side, just barely large enough for an average pony, and proceeded to squeeze through the threshold. What she saw then shocked her. She was still in the forest, but all around her makeshift shelters dotted the landscape. Some were simply a few twigs jammed into the soft forest soil with a blanket thrown on top, while others were slightly more complex. In the center of the area, a massive tree house rose above the rest of the huts. The exterior design seemed a bit eerie to Lyra, and she immediately guessed that this must be where the zebra resided. There were several ponies milling about, carrying out various duties. She saw some gathering firewood, others tending wounds, and even a few crafting meals. At the sight of the cooking ponies, her stomach grumbled, and Lyra realized how hungry she was. The last meal she had consumed must have been around noon, the day before.

“Excuse me, ma'am?” Startled, Lyra turned to see where the voice had come from. It was a stallion. He was a white unicorn, with brown and black hair, and a splash of blue on his muzzle. And on his back were two fillies. A sense of guilt welled up inside her. How could she have forgotten about these two already?

“Do these two belong to you?” the stallion inquired.
Lyra shook her head.

“It's a long story. I was leaving Ponyville, and their parents were...” Her voice trailed off, cut off by tears.
“I tried to help... It was the only option... I had no other choice... I couldn't just leave them there.”
The stallion nodded sympathetically.

“I'm not sure that I understand what you're saying completely, but it sounds like you saved the lives of these two young ponies.” He gestured to the fillies for emphasis.

“Yeah, I guess,” Lyra replied. The guilt that tugged at her heart was even stronger now that this guy was treating her like some kind of hero. She didn't deserve that kind of treatment, not after she had just let those fillies witness the deaths of their parents.

“So, would you be willing to watch them? All of the other ponies have their hooves full, either with their own children or with other jobs.”

“I'll help with whatever I can,” Lyra answered truthfully.

“Great. So let me give you a quick overview of how everything works. The center of this whole place is that creepy looking tree house. That's where Zecora lives. She's in charge around here. Your tent is here, in the center circle. This is the most well-protected area, and where the families are housed. The next section, surrounding this, is the main circle. This is where the ponies without children live, and is where most of the work is done. Finally, there is the outer circle. This is where the guards, scouts, and hunters reside. The job of guards is to, well, guard this...”
The stallion paused, gesturing all around them. “I'm actually not really sure what we're calling this place. For now, I guess I'll just call it 'The Compound'. That sounds cool, right? Anyway, that's what the guards are for, obviously. The job of the hunters is to go out into the Everfree to secure food for the compound. Then there are the scouts. These guys do the hardest work. Their job is to find other survivors and bring them back here. Most of them don't come back.”
Lyra shuddered at the thought of ponies willingly subjecting themselves to that nightmare. She could not imagine mustering up enough courage to ever go back out there, especially after what she had seen. Still, she would do whatever she could to help, as long as it was inside the confines of this place.

“So, what can I do to help? Other than watching these guys I mean?” As she asked this question, she removed the fillies from the white unicorn's back, placing them on the soft ground.

“I can't think of anything right now,” he answered, “We usually give ponies 24 hours before they have to start working, and you still have 12 of those left. There's not really a defined time to rest yet, mainly because it's been sunset since yesterday, so there are ponies working at all hours.”
Lyra looked up to the sky to see that he was right. She was mainly relieved that it wasn't her imagination.
“So after your 12 hours are up, find me or one of the other organizers and tell us which shift you would like to work. Nice meeting you.” He nodded to Lyra, and began to leave.

So he was an organizer, whatever that meant. He was the first pony she had met here, and he was actually pleasant and welcoming, not at all how she would imagine the ponies in a place like this to be. She would look forward to meeting him again, this...

“Hey!” She called back to him, as he was already ten yards away, and she had to shout to be heard. He wheeled around, facing her. “What was your name again?” She continued.

“Azure. Azure Haze. What's yours?”

“Lyra Heartstrings. Good to meet you, Haze.”
She knew that Haze was his last name, but it was way easier to pronounce than his first one, so she was going to call him Haze.

“Likewise, Lyra.”
And then he was gone, disappeared into the crowd.

The next 12 hours were relatively uneventful. Lyra spent the majority of this time resting with the fillies, who were unusually quiet. During this time, she thought. It was the first time she had really gone into thought, deep thought, since her escape the day before. Even for the many hours that she had lain in the forest immediately after fleeing Ponyville, she had been in shock, and had temporarily lost the ability to process things. But now that the shock was fading, everything began to sink in. Just two weeks before, she had been leading a carefree life in Ponyville, delighting in every ordinary day that she had shared with her closest friend, Bon Bon.

Bon Bon.

Her heart dropped as she thought of her friend. From what she had gathered in the few conversations she had taken part in that day, the forces in Canterlot had been utterly destroyed. Yet Lyra still tried to to hope, to imagine different scenarios in which Bon Bon could have survived. Maybe she had escaped Canterlot, just as Lyra had escaped Ponyville. Maybe she had gone undercover, imitating Changeling behavior. That wouldn't work, though, Lyra remembered. Changelings excreted pheromones that allowed them to recognize each other, no matter what form they were in. Lyra shook her head as tears streamed down her face. As much as she didn't want to, she had to accept the fact that her friend would probably not be coming back. And neither would the Cakes. Or the mayor. She had not thought about the mayor much, not because she didn't like her, but because she didn't really know her. It wasn't the mayor's blood on her hooves, either. No matter how hard she tried, she couldn't stop reliving that moment. She had been so close. Had she been given a single moment more, she could have saved Carrot. As a result his wife, Cup Cake, could have been saved as well. She wouldn't have spent her last moment watching her husband live his. Thinking about these ponies who sacrificed themselves so that she could live, she knew that the least she could do was care for their offspring. Lyra's parents had always been right there by her side, guiding her through childhood. Pound and Pumpkin would never know what any of that was like. With that, something completely strange occurred to her. She did not know how much longer life in Equestria was going to be like this, or if it would ever even go back to how it was. If everything continued this way, she would most likely become the guardian of the Cakes. Just the thought of it seemed so bizarre, so surreal. In the past two days, she had probably gained more experience with kids than she had in her entire life prior. Even when she was a filly herself, she was an only child, and mostly hung around ponies a couple years older than herself. Besides, even if she did have a basic understanding of how to care for infants, these weren't just some ordinary earth ponies. Pumpkin, the girl, would be the easier of the two, as she was a unicorn like Lyra. But the boy, Pound, was a pegasus. Lyra was going to have to find someone to help care for him, preferably a pegasus, but really anyone who knew what they were doing would be an improvement. All of her worries, both about the past and future, overwhelmed her. She lay down next to the foals, who were embracing each other in their deep slumber. The sight of these twins, the future of Equestria, so serene and warm, calmed Lyra, allowing her to gather herself and prepare for the work that lay ahead of her.

Author's Note

Well, I was hoping that this chapter could be longer, but I am also currently working on a story to enter in the "Twist of Fate" contest on Deviantart, which ends it's submission period on the 7th (I'm starting a bit late). Fortunately, that story is definitely going to be pony-related, so I'll be able to post it here as well.

Chapter 3

Lyra was just finishing her first work shift when the meeting began. As Lyra had not attended one of these yet either, she did not know what to expect. Joining the crowd of ponies surrounding Zecora's home, Lyra noted that 'meeting' was not an accurate term. Assembly would have been more fitting. She had been told that a gathering like this took place every week, and simply functioned as a way for everypony to get up to speed on current events. Seconds after the crowd had gathered, Zecora appeared outside the doorway of her hut. Mounting a large boulder that Lyra had never noticed before, Zecora began to speak.

“I bring news. The great city of Canterlot has fallen. This has been rumored for some time, but we now have confirmation, thanks to a survivor of the massacre. Details on this pony are confidential, at least until we know who can be trusted.”

There was a stunned silence, followed by futile shouts of protest and muffled whimpers among the throng of ponies. Lyra knew that many of the ponies standing there had someone they knew, perhaps loved, in Canterlot. Whether that had been a family member, a close friend, or even just someone they knew in passing, the sense of loss weighed heavily on the entire assembly. Zecora had halted her speech, presumably waiting for the noise to die down.

As Lyra went over the words Zecora had just uttered, a spark of hope was ignited in Lyra. She realized that this pony, this Canterlot survivor, could be Bon Bon. Yes, the odds were entirely against it, but Lyra could not give up hope, lest she fall back into despair. Her mood significantly brighter, she listened to Zecora as she continued, noting the lack of poetry and rhyme in her words.

“There is more.”
The somber tone of Zecora's voice silenced the crowd. The feeling of dread was palpable.

“We are in need of new scouts. Because there are no volunteers, we have no choice but to enact a draft. Only fillies and the elderly will be excluded. If you are chosen, we will notify you.”

The following outburst was nothing short of a miniature riot. Lyra distanced herself from the main cluster of ponies, not wanting to be caught in any crossfire. While a draft seemed outrageous at first, Lyra could not think of a better alternative. After all, they could not all remain in this one camp forever. Inevitably, the Changelings would discover this place, and it would all be gone. Scouts were a necessity, the only way to contact the outside world. Maybe a draft wasn't such a bad idea. Never mind that now, though. There were more pressing matters at hoof. Despite what Zecora had said, Lyra was determined to learn the identity of the Canterlot survivor. If there was any chance, however minuscule, that Bon Bon was among the living, it would not matter how much trouble Lyra got into. It would all be worth it.

Later that day, Lyra had thought up a plan, one that she considered to be fairly decent, and was determined to go through with it. Now, it was time for the first step. She inhaled deeply, preparing herself. It was the time that would usually be night, and a significant portion of the ponies were fast asleep. The timing was an integral part of her scheme, as she wanted as few potential witnesses as possible. Nearing the entrance to Zecora's hut, she attempted to turn the doorknob. To her relief, the door had no lock, swinging open swiftly and a bit more noisily than Lyra would have liked. Directly above her, voices were emanating from a loft area that looked to have been a recent addition. Luckily, the wood separating herself from the other ponies was thick enough to absorb most sound. Though it was muffled, she could make out the voice of Zecora, as well as at least three others she did not recognize. Lyra could only hear bits of dialogue here and there, but it was clear that they were discussing the survivor.

The survivor. That was why she was here. Lyra quickly ruled out the possibility of this pony being upstairs, as the way they talked about the survivor would not be fitting with the pony present. This meant that the only option was the first floor, unless there was a basement Lyra was unaware of. This floor was really just one big room, with walls separating it into segments. Within seconds Lyra had found the pony. Or rather, a lump under the blankets that adorned the bed. A lump that was shaped very much like a pony. Lyra approached, waking it. A head peeked out from under the covers. Lyra felt her heart shatter. The head belonged to a complete stranger. The first thing she noticed was the horn, protruding from the long, tan mane. As the pony sat up, Lyra realized that this pony could not be more different from Bon Bon. She could see now that an ivory stallion faced her, an incredulous look across his face.

Lyra froze. Before she could move, the stallion issued a cry for help. It was too late to run. Zecora was there in an instant, flanked by her council. A mare at Zecora's left was the first to speak.

“What is the meaning of this?”
Lyra began to answer, but no good explanation came to mind. Instead, she decided on the truth.

“The survivor, I thought it might be my friend. I didn't mean any harm, I promise. I-”

“We don't want to hear yer story, Changeling!”
Her eyes widened in surprise as the older stallion chimed in. Something mentally clicked. Of course they assumed she was a Changeling. Who else in their right mind would do what she had? It was much more reasonable to make that assumption than to think she meant no harm, and only wanted the chance to see her dearest friend. Nevertheless, she needed to focus on her present predicament. It seemed that the best course of action available to her was silence. Not that anything she could say would make a difference anyway. Zecora nodded to a younger unicorn by her side, who eagerly ignited his horn. Lyra began to scream as her body was struck with a beam of light, closing her eyes and preparing for the worst. However, when she opened them again, nothing had happened. Another nod from Zecora, and two of Zecora's bulkier associates approached Lyra, each taking hold of a foreleg, causing her hind legs to drag against the ground when they began to move towards the entrance of the hut. As she was escorted from the hut, she managed to overhear scattered bits of dialogue from the remaining ponies still inside.

“-Prince's life in danger-”

“Who is she?”

“-Blueblood is safe-”

The very second she reached the exterior with her captors, she was tossed carelessly a few feet from the entrance, and the two ponies retreated back inside. Standing back up, she walked towards the caretaker's hut, where she would pick up the twins. As she traveled past a row of shelters, she began to analyze the details of her encounter. The most puzzling thing was the unicorn. What kind of spell had he cast? She guessed it to be some kind of detection spell, mainly because if there was even a chance that Lyra was a Changeling, they would have never let her go. Somehow, the spell had told them that she was, in fact, a pony. She breathed a sigh of relief as she realized just how lucky she was. Had there been no way to prove her innocence, there was no telling what could have happened to her. And even with them knowing she was a pony, she was still surprised that there had been no punishment. Breaking into other ponies huts was still a crime, even if there was no malicious intent. It didn't matter now though, she had been let go and that was what mattered.

And then there was the pony she had found. This time, she did not need to speculate. She knew exactly who Prince Blueblood was. Although she was immensely let down that Bon Bon had not been under those bed sheets, knowing Blueblood was alive was still a relief. Although Lyra had never met him personally, she had heard of his extensive resources, and knew he could be a great asset to their struggling settlement. Nearing the caretaker's hut, she tried her best to get these thoughts out of her head. She had enough to stress about as it was.

Lyra had hardly reached their residence, and was just getting the twins settled into bed, when there came a knock at the door. Opening it, she found one of the ponies from Zecora's council, a grim look on her face. The mare's voice came clear and militant, though there was a suppressed hint of sympathy that became more evident when her eyes fell upon the already sleeping twins.

“You have been selected for Scout Unit Three. You are ordered to be present at the Scout center in 10 hours, where you will be given more details.”
The mare paused for a moment, and nodded towards the foals.

“My condolences.”

Prologue

Day 1
We have received word that Canterlot has been overtaken by Changelings. The Wonderbolts, along with any military forces neighboring cities can muster, have been sent to Canterlot to contain the problem. I feel that it is my duty to join them, although my lifelong friend, Lyra, has strongly encouraged me to stay in the relative safety of Ponyville.

Day 2
The dragons have joined our side, and are transporting groups of soldiers from cities such as ours to Canterlot. I have made up my mind. I am leaving for Canterlot with the next group.

Day 3
We are nearing the war-torn city. I am writing this while mounted on a magnificent obsidian-black dragon. She is not very talkative, and neither is anyone else. The whole group is very somber. I can see the spires of Canterlot in the distance. It won't be much longer now.

Day 4
Our group is pinned down in a doughnut shop, and we are vastly outnumbered. We only have one unicorn remaining, and are protecting him at all costs. Unfortunately, he is weakening, and his energy shield is the only thing keeping us alive. This may be my last entry.

Day 5
It's hopeless. How could we have believed for one second that we had the power to stop them? This is Special Agent Sweetie Drops, signing off for the last time.