Fallout Equestria: Hidden Legacy

by RuinQueenofOblivion

Rating: mature
Tags: Main 6, Drama, Original Character, My Little Pony: Friendship is Magic, Other, Adventure, Wind Rider, Science Fiction, Crossover
Length: 4973

In the still recovering wasteland of Equestria, a legacy left behind by the Ponies of old has awoken. What will it mean for Equestria?

10 years after the events of Fallout: Equestria, in the lands surrounding New Pegasus, Stable 112 has been opened to the outside world for almost half a century. Most ponies ignore it though, a few raiders have tried to loot it, but most just vanish. The rest come out with horror stories of killer robots that try to kill all intruders.

Left behind in Stable 112 was Project Legacy, a secret Stable-tec project built to build a new generation of ponies from genetic material. Now, Rain Runner, a survivor of the project must strike out on her own, and find her own place in the Post-Apocalyptic world and find the others created by Project Legacy.

Listen to it here: Hidden Legacy Reading

Published 2016-03-21 11:10:02 UTC
Last updated 2020-01-11 03:15:37 UTC

Prologue: Legacy

War… war never changes.

Honestly, I don’t know how it all came to this. Equestria was once at the height of its golden age, most of us remember it, but now everything has gone wrong. We’ve all had to make difficult decisions in order to survive, and the war with the Zebras is showing no sign of ending anytime soon.

So that’s how I got stuck in this situation. Scootaloo and Apple Bloom hired me to work for Stable-Tec in order to put together a new project. I created Project Legacy as an effort to create a way that would help save Equestria if the worst happened. That was our mission as part of Stable-Tec after all…

But now I honestly don’t know what to do anymore. With everything that is looming on us, I sometimes wonder if there really is a way to preserve Equestria, maybe we should all just be wiped clean. A clean slate where the future will belong to those who are absolved of the sins that we’ve created.

So, here I am underground waiting for everything to be ready as I decide what I’m going to do next. Project Legacy is on the verge of completion, and we all know that the day may come soon that it will be necessary to activate it. So, what am I going to do now?

I honestly don’t know. I guess I’m going to have to fulfill my duty to Equestria… or maybe I’ll just run as far as I can and get out of the country. I’ve heard the Crystal Empire is taking in ponies that don’t want to get involved with the war effort, or as best as they can at least. I don’t even know what’s going on in Las Pegasus, I’ve heard Robronco is buying up most of the territory and set up a Stable there too.

Maybe I should just go home. But the war is going to reach there eventually too, if it already hasn’t. So, here I am like I said, just doing my job working in Stable 112 on Project Legacy. There’s nowhere left that the war hasn’t touched at this point…

And War… War never changes…

00000

A stallion finished writing in a journal as he looked over at six strangely designed pods with ponies inside. He took a deep breath as he took down notes, going over the readings on several devices to make sure that everything was in working order.

He leaned back and adjusted his glasses for a moment as he looked at one of the readings for a nearby foal. This was Project Legacy, the product of several years of work by Stable-Tec, and things were at least looking up. The project itself was complete, so that meant their work itself was done. So, what were they going to do now?

There wasn’t much they could do at this point. He leaned over and turned on the radio as he sat back in his chair and listened to the music as it started to play, enjoying the moment for as long as he could.

“The Battle ends tonight,
It’s time to fight our fight.
Hoping somehow we’ll have the courage to be the
Light in the darkest hour,
When things are turning sour.”

As his mind started to drift with the music, he almost didn’t notice that the door to the lab opened up. His eyes finally opened when he felt a pair of hooves rubbing his shoulders and he smiled up at the face of a Unicorn mare with a white coat and a light blue mane. She was dressed in Stable barding with the number 112 on the collar.

“Hey Eureka,” she said as she smiled down at him gently. “What’s the latest word on the big project?”

“Well, it’s pretty much done,” Eureka said as he adjusted his neck a little for a moment. He smiled as he leaned forward a little bit and kissed the mare on the nose. “The readings are holding stable and we’ve managed to set up the rest of the equipment elsewhere in the Stable. How about your side of things, Holly? How’s everything going up top?”

“Good, we’ve got the Stable all set up for if, you know, the worst happens,” Holly answered as she stroked his mane gently. “So, how about you and me head up to the Saloon together? I’m sure your aides can take care of anything that’s left down here or call you if you’re needed.”

“Yeah, that sounds good,” Eureka replied with a smile as Holly released him and he got up. The two of them started out the door and down the hall. They made their way to an elevator and started up into the main Stable itself.

Holly smiled as the two of them headed down the hallway of the Stable itself. There were a few ponies in security and scientist gear. A few of them nodded to the couple as they went past with a smile.

“So, what do you think?” Holly asked. “I think it’s coming along pretty nicely.”

“Yeah, Stable-Tec did a good job,” Eureka answered with a shrug. “Did Sweetie Belle talk to you the other day? She swung by the lab.”

“Yeah, it sounds like things aren’t going well topside,” Holly answered. “She wanted to run another drill. We’re obviously not set up for that right now, and I told her as much. That kind of thing requires extra preparation given the nature of our work here.”

“If we’re going to make the Project work, we’re going to need to make sure the ponies in the Stable are unaware of it,” Eureka agreed. “Sweetie should know this. But still, we’re almost ready… right?”

“Right,” Holly answered as she shook her head a moment. “I don’t like this, Eureka. We’re stuck in the middle of a bad war and this is our only way to save Equestria? Why only the ponies that was picked for the list?”

“We picked the list for the best ponies for the project,” Eureka reminded her. “And we only have so much room in the Stable so we can’t take in more ponies than are on the list. I don’t like it either, but we did what we could to save ponies that were needed.”

“Yeah… I guess,” Holly said as she leaned over and nuzzled her husband gently. They reached the saloon and opened the door as they headed in together and took a seat at one of the booths. “So, what are we going to do in the meantime? I mean, we don’t know how long it’s going to be until we’re actually going to… you know… wind up staying here…”

Eureka paused a moment as he looked down at his hooves for a moment. He reached over and gently placed his hooves on his wife’s and gave her a smile. “Listen, Holly… I, uh…”

“What is it?” Holly asked with a tilt of her head. “Is everything okay? What’s wrong?”

“Nothing’s wrong, more like, something is very right,” Eureka said as he held his wife’s hooves in his own for a long moment and tears started to well up in his eyes. “It worked, I finally got it to work…”

“You got what to…” Holly started to ask before her eyes went wide in realization. “Wait, you mean you figured out how to let us have a foal together? After all this time?”

“Yeah, I had to figure out how to work around the genetic damage, but I figured it out,” Eureka said with a smile. The two of them had always wanted to have foals of their own, but they had problems conceiving along with problems keeping them from just using the conception spell. “If you’re willing to do it I mean… I want to start a family, even if it’s down here.”

“I’d like that,” Holly said as she brushed her mane back for a moment. “What do we have to do in order to do it?”

“It took me some doing to figure out the magic, but after that we just need to do it the old fashioned way,” Eureka replied. He leaned in and kissed Holly deeply for a long moment, the couple enjoying the moment before breaking the kiss. “I love you Holly.”

“I love you too, Eureka,” Holly said as she pulled Eureka in close. The two enjoyed a moment together as the pony running the saloon walked over them to get their orders.

00000

Eureka fell back onto the bed next to Holly, breathing heavily as he did. The mare giggled as she leaned over and kissed him before resting her head gently on his chest, snuggling against his body gently.

“That was amazing…” she said softly as she closed her eyes. “It feels like it’s been years since we last did that…”

“Only a few months,” Eureka said as he stroked his wife’s mane gently. “Maybe it isn’t so bad here. Just you, me, and next year a little filly or colt… even if it’s underground, I’m glad we’re together.”

“Me too,” Holly said as she closed her eyes. “With everything that’s going on today, it sometimes feels weird to think about bringing foals into the world, you know? Are you sure we’re ready for this?”

“As sure as I’ve ever been,” Eureka replied as he leaned down and kissed her gently. The two of them laid there for a long moment, starting to drift off to sleep before the lights suddenly started flashing red as an alarm went off. “What the…”

“Dear Celestia… it happened…” Holly said as the two of them struggled to get up and get their clothing back on. “I need to get to the entrance… there’s so much to do… so much to do…”

“Calm down, it’ll be okay,” Eureka said as he straightened his lab coat out. He had his own duties to attend to, and he hated having to leave Holly alone to deal with things up top. He pulled her in close and gave her a long kiss for a moment. “It’s going to be okay, we’ll get through this together, okay?”

“Okay,” Holly said, she was still breathing heavily as she finished putting on her stable barding. “I’ll see you once everything settles down, okay?”

Eureka nodded as they headed out of the Overmare’s quarters together. They exchanged one last look as Eureka opened the door to secret elevator that went down to the secret labs. He got stopped by a Unicorn as he made his way out of the elevator who looked scared.

“Doctor, what’s going on?” The Unicorn stallion asked. “Is it true? Did the bombs really fall? It’s not just another drill is it?”

“I don’t think it is, no,” Eureka replied as he looked up at the main lab for a moment. “I need to get in contact with Stable-Tec to make sure. Is the open line to headquarters still working?”

“No, it was cut off,” the scientist replied which made Eureka flinch. “We’re completely on our own down here. What are your orders, Doctor?”

Eureka paused a moment as the scientists around him stopped to look at him. Eureka had to admit that he wasn’t sure what to say. They had always known this day could come, but he had hoped that there would be some sort of contact with the outside world. If they couldn’t get word to Fillydelphia, then it meant that they were going to have to make sure everything went through themselves.

And it was his responsibility to make sure of it.

“Get everything together,” he said finally. “Get the foals into the Stasis Pods. Make sure that the genetic library is still up and running. Project Legacy is not going to fall apart now if we’re going to make sure that our duty to Equestria is done. This isn’t going to be easy for all of us, some of us have families up in the Stable that we want to go see. But this is our duty to Equestria, and we’re going to do it. I promise you all that you will get to see your families, we’re all going to be just fine, our families are going to be fine. Let’s make a future for Equestria right here, right now.”

The scientists still looked a little nervous but nodded as they went back to their work. Eureka took a deep breath and headed into the main lab where the pods were being kept. He took a seat at a large terminal and entered commands into it.

The screen turned on and showed an image of an orange Pegasus mare with a purple mane dressed in a suit. She took a deep breath and started to speak on the recording.

“To the project leader of Stable-Tec Experiment 112-A, codename Project Legacy, I’m not going to bother giving you the usual spiel, you know who I am and what I’m doing here,” the mare, Scootaloo said. “If you’re playing this recording it’s because the worst has happened and Equestria is no more. You’ve set up everything in order to make sure that Project Legacy is ready, and we thank you for your service to Equestria. I wish I could tell you that everything was going to be easy from this point forward, but you’re going to have to make difficult decisions. The ponies above are your primary research subjects until everything is ready to leave the Stable. I’m sorry that things aren’t going to be easy for you and that you have your families in the Stable, but this is for the future of Equestria. Your purpose will be to maintain population and create a new generation of ponies that can survive out in the new world from the population of Stable 112. It’s your choice however, but everything we know says this is the best chance for Equestria’s future. You are Equestria’s future now, I hope you’ll make it, for all our sakes.”

Eureka leaned back a moment as the message ended and took a deep breath. He had been the one to give the original pitch for Project Legacy and knew what it entailed. The rest of the scientists only knew some of the details, and it was now up to him to decide how to proceed. The rest of them deserved to know after all.

He turned back to the pods and looked at the tech for a moment. There were six fillies that had been growing in artificial wombs. They were the primary focus of Project Legacy really, as they would be the ones that left the Stable even if it took generations.

Or he could just hit the button and let them go. They could be raised like normal ponies in the Stable and the rest of the experiment could continue normally. Was it really his right to take away the truth from them?

No, as hard as it was for him, they deserve to have some happiness before it was time. It wasn’t easy to make the choice, but he activated the devices as the pods activated. The foals were carefully moved into the pods as they turned on, everything was reading green.

“I’m sorry… all of you…” He said to himself. “You don’t know what kind of world you’re going to wake up to. But it’s better for you…”

He closed his eyes as his hoof slid off the pod’s cover and he sat down by the terminal once more. He closed his eyes and removed his glasses for a moment as he started to cry. Equestria was gone, and they were now faced with an uncertain future in the Stable.

He just had to hope that everything really was going to be okay.

00000

A year later, Holly let out a cry and after a moment a new cry joined her as the Stable Doctor took the small pony into her forelegs. She looked up at Holly and Eureka and gave them a smile as she held the newborn foal.

“Congratulations you two, it’s a filly,” the Doctor said as she gently placed the filly in Holly’s forelegs.

“She’s beautiful,” Holly said as she looked down at the small pony resting in her forelegs. She smiled up at Eureka as he looked at his daughter. “She has your eyes, honey.”

Eureka smiled as he leaned down and kissed his wife gently. “She’s beautiful, just like her mother,” he said as he looked at their daughter. She had a blue coat with a light grey tuft of mane. “So, what should we name her?”

Holly smiled as she looked down at the filly for a long moment. She thought about the ideas for what she might be named, a few ideas went through her head, before she finally thought of one that she decided was perfect for the newborn filly.

“Inspired Light,” she said as she nuzzled her filly gently. “She’ll be our inspiration from now on as we move forward in the Stable, right?”

“Right,” Eureka said as the Doctor carefully took some blood. This was pretty much standard in the Stable now to check for any genetic problems the filly might have. She trotted over to the computer terminal and ran the blood through it, suddenly frowning a little at the results. “Doctor, what’s wrong?”

“Overmare, Doctor Eureka…” The Doctor said as she rubbed her temples lightly for a moment. They could hear the pain in her voice as she tried to figure out how she was going to actually say this. “I’m sorry that I can’t give you better news. Your daughter has a rare heart condition, she’s likely not to make it to the age of 5…”
“But... “ Holly said as she looked down at her daughter for a long moment. “Is there anything we can do to save her? There has to be a medicine or spell or… something!”

“I’m afraid not, at least not right now, there were some ponies working on it during the war but a lot of things started taking priority,” the Doctor answered. “I’m sorry, both of you. If there was something I could do I would.”

“So, what do you think we should do?” Holly asked as she looked up at Eureka worriedly. “There has to be something that we can do to help her…”

Eureka looked down at his daughter for a moment. With everything he had pledged to do for Equestria, there had to be some way to fix this. They had access to some of the most advanced medical equipment in the world, and yet they were unable to actually do anything? So, now he just had to think of something.

Maybe if they could find the notes from the ponies who had been studying it they could continue the work and find a cure. Now it was just a matter of figuring out exactly how they were going to do that.

“If there’s not a known cure, then we’re going to find it ourselves,” he finally said. “We have the best medical equipment in Equestria here. Do we have the notes from the previous work on a cure in the system?”

“Uh, yes we should,” the Doctor answered. “Are you sure you’re going to be able to figure it out?”

“We’ll figure it out,” Eureka said as he looked down at Holly and Inspired. “She’s going to live a long full life, I promise. Even if we have to spend the rest of our lives trying.”

00000

And try they did, as the years passed the scientists poured over as many notes as they had, trying to find a cure when they weren’t working on the main project. There wasn’t a lot that they could tell, and as the years passed Inspired grew into a young filly, but she was always sickly and unable to play like the others.

But just as the Doctor had said as they neared her fifth birthday she was getting worse. She was now in the secret underground part of the Stable where she was being monitored by her father and his staff.

“Daddy…” Inspired said weakly as she looked up at her father. Eureka’s heart broke at the scared look on her face. “Am I going to be okay, Daddy?”

“You’re going to be okay sweetie, I promise,” Eureka replied as he placed his hoof gently on his daughter’s. They had made some small progress on the cure, but there wasn’t a lot more they could do right now, and there wasn’t a lot of time left. He squeezed her hoof gently, tears falling down his face. “I promise that we’re going to do everything we can to save you.”

“Thanks Daddy…” She said weakly. Her eyes slowly started to close before the heart monitor slowed down and finally flatlined.

“Doctor, move!” The Doctors said as they started to work on resuscitating the filly. Eureka stepped back against the wall as Holly ran in having been on her way to check on Inspired when she heard the alarm.

“Oh Celestia… was I too late?” She asked, starting to cry as Eureka pulled her close. “Is she…”

“I don’t know, I hope not,” Eureka replied as a plan started to form in his mind. There was one way to save her, but only if they could revive her. “Holly… we may need to put her in stasis…”

“What?” Holly asked shocked.

“She’s not going to survive if we keep this up, we can place her in one of the extra pods that were built for the Project,” Eureka quickly said. “I know that it’s not going to be easy on us, but it’s the best option we have right now. I’m sorry that we have to do this, but it may be the only way to save her life…”

Holly looked at him and then at their daughter as the doctors tried to revive her. She knew that if they were going to have to make a decision, they were going to have to make it now. She finally nodded and looked at him.

“Are you sure it’ll work?”

“These pods were made to keep ponies alive, and it’ll give us time to find a cure,” Eureka said as the sound of the heart monitor suddenly continued as Inspired started to breathe again. “I’m positive it’ll work.”

“Then let’s do it,” Holly agreed with a pained tone of voice.

“Doctor Eureka, she’s stable for the moment, if you’re going to do something you might want to do it now,” the doctor said as she looked up at him. “What do you want us to do?”

“Get one of the back-up pods ready, we’re going to move her into it,” Eureka replied as they finished checking her over. “Hopefully everything will work perfectly. Get everything ready to move her.”

“Yeah,” Holly said softly as she looked down at her daughter and placed her hoof gently on her. “I’m sorry Inspired… I wish there was a better way to do this.”

“It’ll be fine, I promise,” Eureka said as he placed his hoof gently on Holly’s shoulder. “I swear it, we’re going to do everything we can to make sure that she’s going to be okay, even if it takes more generations.”

“Okay…” Holly said as they wheeled the bed out of the room and towards where the pods were being kept. There were six main pods and on the edge of the room there were several empty pods. Two of the scientists had finished securing one of them and opened the pod’s lid carefully.

“Doctor, Overmare, everything is set up, you just need to place her in it and activate it,” the scientist said.

“This is our last chance to change our mind,” Eureka said as she placed his hoof on Holly’s shoulder. “Are you sure that you want to do this?”

Holly looked down at her daughter for a moment. She hated the idea of leaving their daughter in the pod like that and not being able to see her, possibly forever. But at the same time, it was probably the best choice they had right now. She slowly nodded, brushing her tears from her eyes.

“Okay, let’s do this,” she said with a nod. “Let me do it…”

Eureka nodded as Holly gently picked up Inspired and set her gently in the pod. The two of them watched it as the pod closed as Eureka squeezed her lightly. “It’s okay… I’ll make sure she at least has us in the simulation…”

She nodded as the two stood there, crying together as they stood there staring at their daughter as she slept.

00000

“She’s coming to,” A voice echoed as Inspired’s eyes fluttered open. She looked around confused, the only thing she could see was blurry figures of ponies dressed in white lab coats and looking down at her. “Inspired, my name is Light Bulb, take it slow, you’ve been asleep for a long time.”

“What… what happened…” Inspired said as she looked at herself. She blinked in confusion, she was lying in some sort of weird pod instead of the bed she had sworn she had fallen asleep in. “Where am I? This doesn’t look like Stable 112...”

“You’re in the labs under Stable 112 for Project Legacy,” Light Bulb replied as she slowly helped Inspired up. “You were placed in stasis by your parents when you were a foal. You were dying of a rare heart defect, and it has taken a long time to find the cure. I’m sorry, but your parents are long dead...”

“But… I just saw my parents… they were alive…” Inspired said weakly as she looked around confused. There were more ponies that were dressed similar and they were worried as she looked over at the other things in the room. “What kind of place is this? What’s with all the pods?”

“It’s all part of Project Legacy, which was made to continue Ponykind after the apocalypse,” Light Bulb answered. “We can tell you all about it, but there’s something you should see first.”

She lead Inspired over to a large computer terminal. There were several PipBucks and other items lying around and she picked up one and slid it into the holotape slot on the terminal. The screen turned on and a video of Eureka and Holly appeared on the screen.

“Hello, Inspired, we’re glad that you finally were able to wake up, we’re sorry that we couldn’t be there for you,” Holly said as she placed her hoof gently on Eureka’s. “Our only hope is that you’re well enough.”

“The pod that you were placed in was provided to us by Stable-Tec and the Ministry of Awesome as part of Project Legacy, I’m sure whoever is with you can tell you about that,” Eureka continued as he smiled sadly. “I’m glad that you’re okay, and wherever we are now, we’re watching over you.”

“I know that this is all confusing for you, dear, but everything will make sense as you come to learn more about the Project,” Holly said. “But needless to say, the last few years of your life were a dream of sorts. I wish that we could’ve been there for real, but I’m glad you made it.”

“You’re not required to follow in our hoofsteps, perhaps the world above is better now, maybe you can find a place there,” Eureka told her. “Spend your life as you see fit. You’re our daughter, and that’s what matters to us.”

“Remember, Inspired, we love you very much,” Holly said as she gave the camera a nod. “Now, make us proud honey. We’ll always be your parents.”

And with that the video turned off. Inspired stood there in stunned silence for a moment as she looked at the screen as if hoping that something more would happen. Finally she just broke down crying as she realized that she was completely alone in this world.

00000

“You know you don’t have to leave,” Light Bulb commented as Inspired gathered up her packs and checked her PipBuck. “You have a place here, and you still have family in the Stable.”

“I know, but it’s not the same, I don’t know anypony here,” Inspired replied with a shake of her head. “I’m going out there to find my place in this world. I don’t think it’s in a Stable, but I don’t know where it is anymore.”

“Of course, I wish you the best of luck,” Light Bulb said as she held out an old book. “This belonged to your father, he kept it while working on the Project. Perhaps it’ll give you some sort of insight.”

Inspired nodded as she took the journal and opened it up for a moment as she flipped through the pages. There were a lot of notes in it on genetics and pony DNA, she stroked her chin thoughtfully, perhaps this would be of use.

She levitated it into the bags, and nodded to Light Bulb. The door to Stable 112 opened slowly and she took her first steps out into this unknown world.

Beneath the Stable however, it was almost time for Project Legacy’s purpose to come to fruition.

Inspired levitated up her earbuds and started listening to the radio as she stepped out into the desert beyond.

“We’re starting over,
Build something new.
We’ve been a long time a-waiting but we made it through.
We’re starting over,
Celestia white and Luna Blue.
It’s a brand new Equestrian Dream for me and you.”

Author's Note

A bit of a new take on the prologue, a lot to come, but the heart of the story is still the same.