Artificial Codex: Fallout Equestria

by BioQuillFiction

Rating: mature
Tags: Adventure, Dark, Alternate Universe
Length: 4850

In the war times of Equestria history tells one side of the story and most ponies believed that as the one truth, but as they say behind the velvet curtains are the ones who are really in control of the world. (The squeal to Pre-war Nobodies)

History is supposedly set in stone yet not all of the details are written. The great war, not even history can tell exactly what happened. Only the ones who have been behind the velvet curtain can tell of the missing events that lead to the great war, along with who caused it and who wanted it.

Now fifteen years after the Equestrian wasteland has started to heal the old world secrets are rising from deep below the earth and falling form the stars above, ready to write the final bloody chapter in pony history.

This story follows the lore and settings set after Fallout Equestria only. Characters making appearances belong to Kkat and this was done with her permission. I asked before I used. All inspired by Kkat's Fallout Equestria.

Link to original story.
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Published 1970-01-01 00:00:00 UTC
Last updated 2015-07-19 15:53:27 UTC

The Prologue to Another Bloody Chapter in Pony History

Change, something’s move with it, others try and fight it, and some are forgotten by it entirely. Over two-hundred years ago the magical land of Equestria changed from a land of peace, tranquility and harmony into a savage, radioactive wasteland. But this change, this Armageddon was not as some would have predicted the end of the world. Instead the apocalypse was just the prologue to another bloody chapter in pony history.

But rarely does the prologue to a chapter require a prologue.

Long before the war began beings from the stars discovered Equestria and were threatened by its magic, a force they could not understand or harness. As a final resort at the attempt to understand the world better they sent four of their own disguised as ponies.

Mecca, a mad man obsessed with immorality and building the ultimate weapon, in the end he got what he wanted but not quite as expected.

Genetic, never before have the building blocks of life been altered in such a way by anything other than nature until she discovered their secrets.

Flux, son of one of the leaders of the species, he devoted his life to creating sub-life forms that would serve their creators with unquestioned loyalty and devotion.

Replica, a master at metal crafting and programming he created artificial life forms that were fully capable of emotions, learning, independent thought, and could even feel pain and reproduce.

These were the four Gods that were sent to Equestria years before the war, a thousand years before the war to be precise. Each one out done and killed off by the very weapons they created to destroy the land of Equestria. But even with their creators gone they still had a hand in the destruction of the old world.

In the end the weapons were locked up willingly in the depths of Tartarus where they would be guarded from any chance of escape from outside forces, both within and outside Tartarus’s gates. At least that’s what they wish the story could end on.

For in the magical land of Equestria, after nearly ten complete years of sunlit peace brought upon by its young heroin fifteen years ago, found itself in yet another bloody war against two fronts; one from above the clouds, above the planet, and beyond the sun; the other seemed to rise from the ground itself. Now five years later pony kind is at the brink of extinction and only the pre-war weapons of the Gods stand a chance at turning the tides of war.

The only chance Equestria has at survival lay within a sex addicted symbiot, an AI that wishes to be flesh and blood, a clone put together from DNA of the old world element bearers, and an immortal the wishes to die. In the end everything changes, for better or worse.

Chapter 1: Old World Secrets

Fifteen ago Equestria had found its long missing peace, nearly all trade routes had no worries of raiders or gang. Food and clean water was plentiful once again and everyone pony or not could get along without discrimination. Sometimes.

For those new to the experience it was an adjustment but for Fluttershy, who was around back when this was common, it was like a blast from the past. Back on the day the mega spells fell her friend Rarity teleported her to an area near Zecora’s hut in the Everfree forest. However Fluttershy was transported to a clearing where killing joke was growing and she, rather than killed off by the evil plant was instead tortured and transformed into a tree, still able to see, see as the world she loved and tried to save kill itself before her very eyes.

Fifteen years ago she was saved from her curse by one young Velvet Remedy who idolized the shy Pegasus to the point it could be called an addiction. As a result a whole group calling themselves the Followers of the Apocalypse sprouted up, following the timid mares example of peace. Fluttershy did not want this, she was glad to see her ideals being realized but after the war and spending two-hundred years as a tree she didn’t want to be in a position of leadership but she accepted and vowed to do better to avoid her previous mistakes.

Today is a day like many others for her now, after reading a chapter or two of The Book of Littlepip to the young ones and aiding with whatever care is needed of patients at the clinic. Now however she has finished her reading and the clinic is starting to receive less and less patients that needed care. Fluttershy has nothing to do.

Oh dear there must be something to do. The mare thought to herself, when suddenly a small crowd of ponies started to quickly make their way to the gates of the town, the caravans have returned. Oh I hope everypony's accounted for. Despite the fact that caravans haven’t lost a life within the two years since the reign of new peace started Fluttershy still worries over their departure and return. The elderly mare works her wings, pulling her into the air just a few feet above ground and heads towards the gates. She was never a strong flyer but spending two.hundred years as a tree didn't help this fact.

Upon reaching the gate what she sees stops her in mid flight, letting herself drop to the hard dirt ground with wide eyes, pupils dilated in complete and utter terror. Only one pony has returned, a rust colored cyber Pegasus, Calamity; covered in cuts, bruises and blood. The first to emerge from the crowd is a charcoal black unicorn with a white mane holding streams of color, Velvet Remedy. Calamity’s wife.

“Calamity what happened?!” Velvet screamed, wiping the blood from his mane.

“I… I’m not so sure. We was flying by the spot where we killed that last raider group and there was this pony down there, he just walked by the corpses and then they got back up.”

“What?” Velvet asks, removing a small piece of flesh from her husband's’ mane.

“They just… g… got back up and started shooting at us. I shot one of ‘em’ at least twelve times before he finally dropped dead again. Then… then there was this light behind me and the others were screaming and, and when I turned they were gone, wh… when I looked up it was raining body parts.”

Velvet placed her hoof to her mouth in shock. That can’t be real! It must have been something else Something that makes sense! Velvet mentally argues, not daring to speak out loud, the look on Calamity’s face screams of truth and fear.

“Calamity it’ll be alright we just got to…” Just then the sky above begins to emanate with a bright unearthly blue light. “What’s…?”

“Get back!” Calamity screams, grabbing his wife and running into the nearest building, taking her under the cover of a rusted metal table. The sounds of screams litter the air for several seconds before it is replaced with the sounds of raining ‘water’ and thuds. “It’s the same light, it happened again.” The cyber pony mutters, curled up in fear under the table gripping Velvet’s hoof like a baby foal.

Velvet slowly removes herself from her husband's grip and made her way outside. The ground before her eyes is littered with puddles of blood and chunks of flesh unable to be recognized for what part of the pony they were, or who they were. Ponies scream in terror and Velvet gallops over to the nearest waste basket and empties her stomach contents into it. When she looks back up she spots Fluttershy sitting in the middle of the road, staring into the sky, blood staining her mane and coat. Velvet gallops with all her might to the yellow Pegasus.

“Fluttershy!” She yells out to the mare and when she is unresponsive she shakes her a bit. “Fluttershy it’s… it’s, I’m not sure but we can get through this. Now I need you…”

“Oh goddess…” Fluttershy mutters. “How? Why are they back?!”

Velvet is shocked by the mares response. “F… Fluttershy do… do you know what that light was, who’s behind it?!”

The yellow Pegasus looks Velvet straight into her eyes. “The Gods have returned.”

“The… the what?”

“The Gods… Come on!” Fluttershy grabs Velvet’s hoof and pulls her back into the building where Calamity is still hiding under his table. When to two reach said table Fluttershy pulls Calamity from under it and seats him next to Velvet.

“Calamity calm down!” Fluttershy barked. Calamity obeys, not from the order itself but from the fact that she yelled. Fluttershy has rarely raised her voice above a whisper, a shout caught him off guard.

“A… alright I’m a bit better now.”

“Good. Now then there’s something I didn’t tell you, and you’re gonna have to take my word for it cause it’s not in any recorded data.” Calamity and Velvet nodded in agreement. In the back of their minds; Calamity is still surprised from her shout, and Velvet is thinking Fluttershy might be having a nervous breakdown.

“Okay then, well you know those zebra tales about evil beings from beyond the stars that only wish the worse for us?” They nod again. “Well they’re not stories, they’re real.”

There is an awkward pause amongst the three before Calamity barks. “Now hold up, how exactly do you know this?”

“I had family before the war that was dealing with them in secret. Ever wonder who made those Star Blasters Homage and Autumn had? They built them and they have more. Not many but still, and other weapons that make the bail fire bombs look like grenades.”

“But you said they ‘returned’ when did they leave?”

“They didn’t exactly. One by one the four that were on Equestria were killed off my uncle and a few others, I know they all died my uncle showed me the things they used to look like ponies. Then they sent the rest of them out there a false report stating that Equestria was destroyed and there wasn’t enough time for their evacuation.”

“But that don’t explain why when one of ‘em’ walked passed corpses they got back up.” Calamity barked.

“Yes it does, either that God carried parasites that took control over the body or nanobots that can make necessary repairs to the host up to a certain point before they burn out.

“But… now if what you’re say’en is true then did your uncle leave any kind of gear behind or something that we can use to fight them cause it’s pretty clear that bullets ain’t that effective.”

“Yes, the Gods that were sent to Equestria each built a weapon to use and destroy Equestria but they were instead used to destroy them.”

“Then where are they?” Velvet asked.

“Well… that’s the tricky part, I know where they are but with what’s going on now and what’s there when we get there, it will in no way be safe or easy.”

“If those weapons are our only hope then we don’t have any other choice, where are they?”

Fluttershy took a deep breath. “In the deepest pit of Tartarus.”

Calamity and Velvet both sat in an impregnable silence. Tartarus was the ultimate prison guarded by a three headed dog. Within its depth lay imprisoned beings of immeasurable evil and horror. And their only hope against the Gods lay within its deepest pit.

Calamity gulped. “Well…. Well then where’s the gate?”

“About a mile or so out into the badlands, its actually pretty easy to find just look for the big stone door in the middle of nowhere… There were two ponies I knew that were assigned to guard the weapons, one was to guard them within Tartarus, and the other was supposed to guard the gate.”

“Wait, I thought that entrance was guarded by Cerberus?” Velvet questioned.

“It is, was, I’m not sure anymore. Not even sure if my friends there are still alive, probably not.” Fluttershy felt a pinch of gilt strike her heart, she hadn’t thought about those old friends in a long time, too long a time. “How long until we can leave.”

“We, no, no, no, no, no, Fluttershy I’m going, you and Velvet are staying put.” Calamity asserted.

“Note likely Calamity. If my friends or Cerberus are still there then you won’t get close to the gate, let alone get in. I’m coming.”

“I’m coming to.” Velvet spoke. “I kind of miss venturing out into danger like the old days.”

Calamity muttered a rather sexist comment under his breath before speaking. “Fine, so Shy how many of those fancy light shows do you think they’re gonna rain down on us, I’m pretty sure we’d be encountering them a lot on this journey.”

“Well my uncle told me that those things were only used against large populations so they might not use it on us but towns and such are likely targets.”

“Then what are we going to do? Have towns ponies say inside?” Velvet questions.

“Well I got one idea but ya’ll not gonna like it Velvet.” Calamity said. A slight terror expression across his muzzle.

Velvet’s eyes widen in anger. “NO! We all fought to live under the sun and out of those stables! If we send ponies back into them then all that blood shed was for nothing!”

“I ain’t saying we keep them down there for hundreds of years. Just until this shit dies down.”

“And how long will that take! My stable wasn’t supposed to open, ever! What if ponies start getting that idea in their heads!? I’m not sending them into those cages!”

“Velvet!” Fluttershy’s bark stopped Velvet dead. “I know you don’t like the idea and frankly I’m not that supportive of it either but it’s the only way to save ponies from that death ray they have. Think about it how many other towns do you think have been obliterated while we’ve been sitting here!” Velvet sits herself back down, tears forming in her eyes. “Personal feelings aside, when the bombs fell the stables saved most ponies and now ponies will have to occupy them again, but this time they will all be saved. But it’s not permanent and I promise Velvet when we get those weapons ponies will be living under the sun again.”

Velvet looks at Fluttershy with red tear filled eyes. “Alright. I’m gonna go find a courier pony to deliver this news to Littlepip and Celestia.” Velvet got up and left the room, still crying.

“I’ve only seen her that made one other time.” Calamity gives a heavy sigh remembering the event. “So Shy, do any of our normal weapons have a chance to take them out without waiting ammo?”

“My uncle told me that magical energy weapons deal more damage than bullets against them, also if those… corpses have nanobots in them then EMP weapons should be extremely effective.”

“Alright then, I’ll go stock up.” Calamity tips his hat and fly’s off.

Fluttershy is left alone now, only her uncle is on her mind. I’m sorry uncle but it looks like you're gonna have to fight again. I’m so sorry! She begins to cry, guilt filling her heart.

Tartarus. A prison like no other. Existing in a plane between life and death, a form of purgatory if you will. The landscape is nothing more than jagged stone and poison air. The exception to the alien landscape being the holding cells. Each crafted to suit their prisoner. Beings from as early as the dawn of time are imprisoned in thick magical chains, doomed to stay there for the rest of eternity.

Tartarus's deepest pit is not as some would think it to be. In legends Tartarus's deepest pit is said to be made of a monster's flesh, and the blood of all its prisoners victims will drown them for all eternity. In actuality it appears no different than the rest of the landscape. The prisons built the hold the weapons of the Gods were made from a magical crystal, only the one who built them or the blood of a family member can release them.

There are four crystal prisons. Within them are four ponies;  a metallic grey Pegasus stallion, same color mane and tail with a mirror cutie mark. A Thestral stallion with a black mane and tail, a cutie mark showing a crimson eye. A mare with patches of coat, mane, and tail that resemble a mismatch of the old world element bearers, unique in her appearance for resembling an Alicorn, her cutie mark is covered by the black suit she wears.  And last a red stallion, same color mane and tail, his cutie mark is a book with the old symbol for magic.

Sitting just a few meters in front of the prisoners is a maroon mare with a dark purple mane and tail, her cutie mark is a large number eighty seven. Without warning she jumps up, alert for anything.

"That... That can't be right. I must finally be losing it. Took long enough, now at least I won't be all that bored." She chuckles. "No, wait is it even possible for me to go mad?"

She shakes her head and regains a serious composure. "Well then, if somepony is coming here then they won't leave here. Flash, if you are still alive out there don't let anything get passed you."

***

Tartarus's gates. Visually they appear as a set of massive stone doors, decorated in ancient ruins whose meaning has been lost to time. After the great war time finally started taking its toll on the ancient stone, almost as if the material itself acknowledges the fact that the world came to an end all those years ago. Resting beside the stone bearing heavy chains rests the long decayed corpse of Cerberus, the gates guardian. Where time failed, radiation finally ended the mighty beasts eternal guardianship.

However camped out next to the large corpse is a ghoul Pegasus, dressed in solar guard armor. All of the hair on his body has been replaced by half rotten flesh. He lays deep in sleep until his ears perk up and he jumps, ready for anything, clutching a rusty spear in his teeth.

"... Something is coming. But, what is it. Definitely not the Gods, they would have been here by now." The Pegasus ghoul exhales a large held breath. "Must be one of those damn caravans again. They're getting to close in search for water for the ghouls in Equestria."

The ghoul drops his spear and returns to his makeshift bedding of dry weeds and leather. "If it was anypony else I'd have left years ago. That and I pretty much threw myself into this, wanted to know the truth, well I got it and then some... and now I'm talking to myself again."

An hour passed by before Velvet, Calamity, and Fluttershy were finally air born.

Velvet sent a letter via courier to better explain the situation and what they are doing about it to Littlepip and Celestia at The Single Pegasus Project. She had no doubt in her mind that they saw the blast that hit the town but an explanation was appropriate to give.

Calamity stocked up on EMP grenades and even got Velvet and Shy some magical energy weapons. For himself Calamity brought out his old Enclave weapon, outfitted to now work with his custom battle saddle.

Fluttershy placed Angle bunny in Ditzy's care while they were to be away. And with all this done the three set off for the Badlands outside Equestria's borders.

Hours of flying in a caravan wagon, flown by Calamity, had passed. All in silence. None of them wanted to be distracted and then get shot at.

"... So uhh, Fluttershy what was your uncle like? You didn't talk much about e'm." Calamity said, breaking the silence.

"I'm intrigued as well." Velvet commented.

"Oh... well my uncle..." Memories flooded back to the mare, causing a sting of pain and sorrow to take hold of her heart. "He always tried his best to put on a smile and say ''it's okay" even when deep down he was broken. If you could use one word to describe it would be sad. You could just tell he was always hurting."

"Hurting from what?" Velvet asked.

"Lots of things. But mostly it's his past that hurts him the most."

"Why? Did he do something bad?"

"No, it's what didn't happen in his past that's always pained him. The reason he hunted the Gods on Equestria down was because they took away a future that became an unlived past."

"Uh, sorry Shy but that don't make a lick a sense." Calamity said.

"When my uncle was young he was moving from Canterlot to a new settlement, Ponyville. On his way there one of the Gods took him and did awful thing to him. When he finally escaped Equestria had changed when he didn't. Most ponies he knew were either extremely old or dead."

"So what? They throw e'm into the future?"

"They kept him as a test subject Calamity." Velvet snipped at her husband.

"Oh... well what about these 'Gods' ponies?"

"They're not ponies..." Fluttershy's tone was overflowed with anger. "Those monsters make the mega spells and the war look like two foals arguing. They've enslaved whole planets, mined them for all their resources and then destroy them when they've run dry. Inhabitants and all."

Velvet and Calamity both felt chills run down their backs all the way to the tips of their tails.

"They came to Equestria to learn about it then mine it dry like the other planets they destroyed. The only reason they took longer to attempt invasion was because of what they saw."

"What did they see?" Velvet asked.

"The sun and moon moving around the planet. Celestia and Luna at work."

"Now how's that odd fer them ta see?" Calamity barked.

"Because every single other star, planet and moon they've seen the planet moves around the sun and the moon rotates around the planet like a satellite. Equestria's sun and moon both rotated around it even though they planet was smaller than the sun and moon.

"This puzzled the Gods, Equestria wasn't just unnatural we're an impossibility. We shouldn't exist."

"It was just magic, no big..."

"To the Gods it was." Fluttershy said, cutting Velvet's sentence. "Every single other star in the sky the invaded didn't have magic, it's unique to Equestria and Equestria alone."

"So we're special." Calamity deadpanned.

"Yes." Fluttershy chuckled. "My uncle made a joke about it. Saying "we're cosmic payback for the Gods" a world they can't understand."

"But you don't need to understand magic to know it works." Calamity commented.

"That's the whole foundation of the Gods existence, they live to understand how the universe works, every little detail of it."

"They have a funny way of going about it." Velvet deadpanned, causing Fluttershy and Calamity to chuckle.

"No kidding." Fluttershy said.

The next hour of the trip fell into the same silence as before. Calamity kept an eye on the ground while his wife Velvet kept an eye on the sky. Enclave resistance was still a problem but nothing too serious. Without their leaders the resistance usually gave in and started new lives somewhere but some ponies are more stubborn than others.

Fluttershy kept thinking about her uncle, and how guilty she felt about almost forgetting him. She silently proclaimed that this journey to find the fallen Gods weapons was her first step to redemption. Despite her uncle once telling her it was best if she did forget him. A new guilt suddenly flowed over her, almost snapping her heart in two at the thought.

Velvet took notice of Fluttershy's guilty expression.

"Uhh, Fluttershy are you alright?"

"No, I just remembered something bad."

"What?"

Fluttershy was extremely hesitant to answer. She knows Velvet is kind and understanding but how would she react when told something like this?

"Well, uhhh..."

"Equestrian border approaching!" Calamity shouted, taking Velvet Remedy's attention. Fluttershy thanked Celestia for that.

"Fly past it Calamity! Tartarus's gates are further in!" Fluttershy ''yelled" at an indoor volume.

Calamity nodded and flew over the border and past the dirty water caravans. Thankfully his new cybernetic parts allowed him to fly for a much longer distance and time before resting.

The Single Pegasus Project, a prewar spectacle of technology and magic. A device that allows a single pony to control all of Equestria's weather. It was also the only real project the ministry of Awesome ever built.

For two hundred years after the bail fire scorched the land it's only resident has been princess Celestia. Terrified of death and mourning the loss of her sister she used the SPP's crusader mainframe to copy her mind then using dark magic she locked her soul within the computer. Trapping her there forever and just like Fluttershy, watched the world she loved and ruled over kill itself.

After some time Celestia stopped watching over pony kind. Unable to watch the bloodshed that now was daily routine.

However five years ago Celestia was shown hope once again, in the form of a small, slightly mutated mare named Littlepip. She left the safety of her underground home in search of a run away and ended up bringing sunlight back to ground. How a petty search and rescue effort turned into a war for the sky is still unclear, even though she lived through it and it's now written in books it's still rather... fuzzy to say the least.

After finding Celestia's lost hope for pony kind Littlepip placed herself into the SPP's control chamber, taking it as her responsibility alone to bear. It's kinda her thing to do stuff like that. She hasn't left the Single Pegasus Project since she entered fifteen years ago.

It hasn't been all that bad for her though, Celestia is an interesting conversationalist. Having over a thousand years of stories to tell. And.Littlepip's very special somepony Homage, aka DJPon3, moved in not several days after the war for the sky ended. The three mares have had fun living there: telling stories, singing songs, and participating in a rather confusing, odd, dirty, all around seemingly impossible sexual activities.

Now though through the SPP's special high end cameras Littlepip watches.as her two friends Velvet Remedy and Calamity and living legend Fluttershy fly passed Equestria's border and into the depths of the Badlands.

This stung Littlepip, she knew the reason, after the crazy blue lights of death hit the ground a courier pony delivered a letter with details about what was known about what was happening. That wasn't what bothered her though. What bothered Littlepip the most was that her friends were going on an adventure, without her. Littlepip can leave the SPP at any time but ponies aren't fully trusting of the Pegasi yet and leave the SPP could be disastrous for agriculture.

Celestia took notice of Littlepip's expression.

"Feeling a little envious?"

Littlepip turned to Celestia. Being that the Crusader mainframe and SPP are connected within the machine the two can see each other as clearly as if they were standing in front of one another.

"... Maybe."

Celestia chuckled. "I know you want to go, believe me I wish I could have the ability to leave as you do. But you choose not to leave, remember?"

"I know, I'm just scared for them. The letter Velvet sent was helpful but we're still in the dark here."

Celestia felt guilt come up into her mind. "Well... not as much as you think." The sun goddess admitted.

"What do you mean?"

"Well I know the same amount as Fluttershy does about this. And much like her I thought Equestria would never see these monsters again."

"Again? They've been on Equestria before?"

"Yes, they're the ones who built the Star Blasters."

"You mean those things Autumn Leaf and Homage had?!"

"Yes."

"... Are we screwed?"

Celestia laughed. "Only if our friends don't get the weapons in time. And time is our enemy since we.don't know how long we have."

"Have till what?"

"Till they stop playing with us and begin setting hoof on Equestrian soil. If we don't have the weapons on our side before then, well we are screwed."

"Right... wait, what do you mean have them on our side. Aren't they just weapons, like a gun you can pick up and shoot?"

A mischievous smile grew across the Alicorns muzzle. "I won't give too much away cause I want you to meet them in person without knowing them. It will be more fun that way. But I will tell you they are a perfect example of how far advanced Equestria can become, given a few million years."

Littlepip facehoofes. "You're not making sense again. Why do you enjoy being vague?"

"That's just me. It makes things more fun."