The Uncharted Federation: The Discovery

by Dragonface

Rating: mature
Tags: Death, Alternate Universe, Human, Narcotics, Sad, Anthro, Main 6, Princess Luna, Drama, Gore, Original Character, My Little Pony: Friendship is Magic, Sex, Fetish, Science Fiction, Bon-Bon, Suicide / Self Harm, Profanity, Non-consensual, Violence, Princess Celestia
Length: 4617

Equestria is at peace, till they discover something in the stars. How long have these unknown creatures been coming to Equess?

Equestria has discovered they are not alone in the Universe. Problem is, what are their intentions? are they friend or are they foe? Are they makers of peace, or Gods of War?
(This is the first story in hopefully a long series of stories)
Be warned this story deals with very dark subjects as well such as PTSD, Child Abuse, and more though these are not the focus of the story

PS. I make no claim of ownership on any pictures, videos, songs, etc. that are used in the story, I usually find these things randomly on YouTube or Google. If you are the artist or know who the artist is then please type it down in the comments so people can go and check these people out.

Published 2020-07-29 22:10:01 UTC
Last updated 2021-01-17 02:14:45 UTC

Chapter 1: The Moon

POV Luna

I let out a deep sigh, tonight had been full of meetings with nobles and trying to reintegrate the Thestral population into Pony Society, I am quite proud of my children of the night for hiding so well but it was so frustrating to find them. My muscles are still tense from what Prince Blueblood said, the insults he had so casually thrown at my children of the night. The hallways are echoing with the sounds of my hoof falls in tune with the flow of my midnight blue dress as I wander the castle trying to desperately ease my muscles of that striking intensity. My mind slowly drifts to parts old and best left forgotten, parts full of blood, fire, and the same damn intensity in my muscles.

*BUMP*

"Ow what the....?"

I look up at what had just brought me out of my calming emptiness, it was a door, a door I was all to familiar with. The castle had many doors, some that led nowhere, others that hadn't been opened under my sisters orders, but this one was opened to all but lead to my favorite room. The Observatory. I smirk a bit at this and mutter to myself "Perhaps a look at my night sky will sooth my thoughts and ease my nerves."

As I enter the room I take a deep breath, while the room didn't have a particularly interesting smell, in fact it smelled like nothing, just that empty smell was comforting to me. That combined with the wide open room with the map of the stars covering the dome shaped ceiling and a telescope just outside on the balcony, could no one ask for anything better. I had grown to enjoy solitude like this over what I used to love to do in my past, after all in times of peace no one had any use for a sword. I walk to the telescope to look at my all to familiar stars and see if I could notice any differences in them. As I look through the telescope I see it had been set to look at my moon, I shudder a bit as I stare at it, my old prison where I was alone with nothing but my madness.

As I look to the moon I notice something odd, something just a bit of ways passed it, what could be their? I slowly adjust the telescope to its max setting, and with it I can just barely make out what I see.

"By all the stars in my night...."

I see a fortress, floating in the great empty of space. A fortress made of steel and glowed with faint magical lights, all around it were smaller metallic things that kinda resembled bugs if I was to be honest. I quickly move away from the telescope and rush out of the Observatory, I must inform my sister of what I had discovered.

POV Celestia.

"I'm gonna get you my sweet! And your delicious Todo too!" I cackle as I fly after the delicious vanilla cake.

The cake ran with its éclair in hand, the aforementioned éclair barking at me as the cake ran. Suddenly I feel a rumbling all around me and slowly my dream fades away.

"NOOOOOO!!! MY PRECIOUS!!!" I cry out as slowly the cake fades into nothing and slips through my grasp when I reach for it.

I am awakened to the sight of my sister, who looks rather panicked, shaking me in my bed. I grumble a little and look outside, seeing it is still night outside.

"Lulu" I grumble out "What is the matter? It's still night out and I know for a fact it isn't time to raise the sun."

My sister suddenly grabs my hand in hers and says "No time, gotta show you now!" and drags me out of my bed, despite all I had on was my favorite banana patterned nightgown.

As we rush past halls and doorways, climbing stairways and going down stairways, we eventually burst through the observatory door.

I look around briefly and ask "Ok sister what am I suppose to be seeing?"

''Look through the telescope, it should show you everything you should need to see."

I decide to comply with my sisters wish and look through the telescope, what I see is a large fortress like construction made entirely out of metal. My jaw drops in shock at this, I had heard of some old griffin named Hawking who predicted that extraterrestrial life had to exist beyond our own stars. I had wrote him off as a crackpot, oh how that old bird is probably rolling in his grave laughing his head off, granted that could happen since by now he probably is only bones. I shiver at this thought and look to my sister who looked deeply worried. I could only guess what she was thinking but I probably was having the same thoughts as her, 'Were these alien friends? Were they our enemies? What were their plans? What were all those other metallic objects up their? Were those ships? were they preparing a invasion?'

I take a deep breath and say with as much as I could muster "We need to contact Twilight and Cadence, have them come here so we can show them and quietly discuss our next course of action."

Luna nods and says "I will go and inform the Night Secretary to prepare a letter for you to send to them first thing in the morning sister....if you would like I could use a spell to send you back to sleep.'

''I would deeply appreciate that sister, thank you"

Me and my sister head back to my bedroom where I slip underneath the covers. As I do I look up to my younger sister as she prepares the spell and say "Goodnight Lulu..."

She smiles warmly and says "Good night Tia, sweet dreams." and just as horn releases the spell I drift back to sleep, chasing my cake and her éclair again.

Author's Note

Hey everyone hope you enjoy this story, this is my first time writing so any advice would be awesome :twilightsmile:

Just to note I may switch between first person and third person between chapter's.

Chapter 2: Good Morning, Meeting

3rd POV (Focused on Twilight)

Twilight rushes into Canterlot Castle, having teleported just outside the castles gates. She having just received a urgent message from the Princesses moments ago. The letter was pretty vague but had told her to come to the throne room immediately. Twilight, after a bit of navigation, bursts into the throne room but oddly sees none of the Princesses were their, instead was Celestias assistant a dark gray unicorn she knew by the name Raven Ink.

'Ummm excuse me Raven, but where is Princess Luna and Princess Celestia?"

"Oh your just in time, please follow me Princess Twilight, they and Princess Cadence have just about started the meeting."

Twilight follows Raven Ink through a door that was hidden off to the side, the room had no windows and was dimly lit with a square table in the middle. The princesses were all seated and seemingly having been in the middle of chatting about something, but stopped when the door was opened. Celestia smiles upon seeing her student and says "Twilight so glad you could make it, you were cutting it a bit close their to being late."

With a blush of embarrassment Twilight hurriedly apologizes with "Sorry Princess, when Spike had gotten your letter I was with the Crusaders, they needing some advice for how to break the news to a young dragon that they cannot get a cutiemark."

Luna "Perfectly understandable, though I believe that since Twilight is here now sister, we should explain to them the urgent news."

Cadence, taking this opportunity to speak up, says "I would like to know that as well, after all if it requires all of us present it must be serious."

Celestia "Quite so Cadence, you see last night my sister had discovered something that could change the world as we know it, for better or for worst. That thing we discovered is that we are not alone in the Universe."

Twilight lets out a excited gasp and says "You mean Silver Hawking was right! I knew he had to be, after all space is just so expansive that their just got to be other life out their. It was quite sad though how the scientific community just wrote him off as some crack pot who didn't know anything.''

Luna gives her sister a knowing grin, and whispers "Your so lucky that old bird isn't alive right now, or else he would have been laughing at the entire world for thinking he was wrong," Celestia was lightly blushing by this point.

Cadence, brows furrowed in deep thought, asks "Do we know their intentions? What they look like even for that matter?"

Luna "That we do not, we have only seen their space fortress and their fleets, and though we do not wish to jump to conclusions.....you don't have a fleet for no reason so their intentions could be just as harmful as they could be helpful."

Twilight goes to speak when suddenly they hear the door open, and in steps a Thestral stallion follow by two others and a large one winged peguses in chains. The Thestral had dark grey fur with graying black mane and tail he wore casual looking brown pant with a plain white shirt, his wings tucked into his sides, while the Guards wore some advanced looking armor. The peguses, beyond his one wing looked to have been horribly beaten recently and had several scars some fresher than others, what's more the Peguses had a very tan coat and blonde mane and tail, though his mane was so long it covered his eyes and his clothes were so torn they practically didn't count as clothes, last thing to note was his size, he easily stood a fully head and shoulder above Bulky Biceps.

Celestia and Luna were pissed at this sight, but before either could speak the Thestral stallion in casual clothes says "Greetings Princesses, we have been waiting some time to meet with you."

Luna, grinding her teeth at the show of complete disrespect, shouts "Who are you, and what have you done to this stallion!?!?"

Twilight and Cadence, covered their ears as to not go deaf, though the Thestrals made no such move which could not have been good, cause if what Twilight knew about Thestrals was true then Thestral hearing was three times as sensitive than a ponies.

"To answer your first question, we are the Guardians of the Stars, a organization founded long before ponies came to Equestria even existed, and it has been our duty to protect all of Equess from these aliens. As for your second question this is actually a alien spy who came to this world about 7 or so years ago, and up till now he has refused to say anything to us except that "His people are watching" "He's a Alien Operative meant to simply observe us and report our behaviors", but when we had received word of this meeting he said he wanted to cut a deal with you and us."

Celestia frowns at this and says "So you have spies amongst our staff then."

The Thestral waves his hand in a dismissive attitude "Purely a formality, we have spies amongst all Governments and Kingdoms, safe for the Changelings though and that is purely do to their Hive Mind."

At this moment the Stallion chuckles and says "Yea we had that problem too, but we found a few work arounds, wasn't perfect by any means but it served it's purpose." this stallions voice was quite rough, like the kind you get from someone who spends most of their life screaming.

The lead Thestral looked ticked but held his tongue, all the while the Stallion raised his head giving the Thestral a smug grin with his dark yellow, plaque covered teeth, his eyes were bloodshot but held a odd warm brown color. Twilight felt worried for this stallion, more so because he is a alien spy. All it could take for these aliens to come and bring the end of their very existence with a single word from this spy.

Suddenly the Stallion turns his eyes to Celestia and says "Now then lets get down to brass tax."

Chapter 3: Questions and Deals

POV Celestia

I take a deep breath, everything about this situation was stressful, but this also provided a golden opportunity. I look at the stallion and say with as much calm as I could "Very well then let's talk, would you like a seat?"

The alien smiles to me and responds with "Yes, that would be lovely, preferable with a cushion on it for my blisters, but I'm not to picky."

In this moment I just ignore everyone else, instead my eyes are focused squarely on this alien, I need to know what I am dealing with. While he may be a alien he was in a ponies body and I have mastered over the years to read the slightest of gestures on someone to see their thoughts. I notice that my former student goes to get up to give this alien her seat but I simply just summon a chair for him. The Alien looks at the chair with a critical eye, as if he was searching for something, what is it he could be looking for I wonder? Seemingly satisfied with whatever he was looking for her sits down in the chair and lets out a content sigh.

Luna suddenly speaks up "What is your name?"

The Alien lets a grin grace his lips and says "I have many names, as I have been a operative almost all my life but you may call me by my pony name Thunder Wave."

Twilight speaks up with a quizzical look "How does one become a Operative amongst your people? What kind of training involved?"

Thunder says a bit smugly "That little princesses, is classified information."

I glance over at Cadence noticing that she is looking at Thunder with a frown, I was aware she could somewhat sense others emotions, was she detecting something worrying about Thunder? Or was it that she can't detect anything from him. I clear my throat gaining everyone's attention and say "What is it you want Thunder."

The heavily scarred stallion grins and says "I want my freedom, a simple inconsequential thing really, that's all I want."

I frown at this, I honestly suspected more, then again he was a Alien and he could do a lot with that freedom. Whats more he seemed genuine with this desire and I could not detect any malicious intent, perhaps he had none or I was just not detecting anything cause he is just that good of a liar. I briefly consider my words then reply "What is it you offer in return?"

Twilight frowns at me, I could tell she didn't like the idea of us keeping any creature in the hands of these ponies, but in this moment I couldn't take any risks. My sister seemed to agree with this line of thinking what with how relaxed she seemed to get when I had asked for what he would give in return. Cadence oddly gave nothing away, I would need to talk to her after this.

The Stallion seemed ready for my question though "Simple you don't know what your up against, I do but I am not allowed to give away much. However, other races have been coming to this planet for many many years, and have left behind lots of goodies. So what I offer is that in return for my freedom I tell you where these sights are and you all go their to get those goodies, which honestly is mostly information. We all win in the end, you get information I get freedom."

I frown at this and look to my sister, it looked like she was having the same line of thought as I was. I say "Me and the others will discuss on this, I shall put a barrier around you so you can't hear what we have to say, just incase you try to influence our decision."

Thunder frowns a bit but says "Please make the dome spacious I hate small spaces."

I nod and create the barrier, being sure to give him a decent amount of space, despite this he still seemed uncomfortable in it. I then look over to my fellow Princesses and say firmly "I would like to hear your thoughts on this."

Twilight spoke up first "It seems like as good as a deal were going to get from him, and I personally don't like the idea of him going back to where ever they came from" gestures to the Thestrals, the leader of whom was still present and keeping silent, just watching Thunder.

I took Twilights words into consideration and in truth had plans that even if she couldn't negotiate a better deal to not let Thunder go back to whatever Tartarus awaited him with the Guardians of the stars. I then turn my attention to Cadence and say "What about you Cadence."

Cadence replied with a simple "We can't let him go back, I can sense his desperation to get away from them, his entire body aches and he is currently afraid while in that dome aunty."

I nod at that moment my sister speaks up "While I agree we shouldn't let him go back we need to at least negotiate better deal for ourselves. After all this is potentially the decision that will decide the entire fate of our planet and it's inhabitants."

I need and after briefly thinking of everything I look to Twilight and say "Would you and your be able to accompany him to these locations?"

Twilight scrunches up her eyebrows in thought then says "It is possible, I will have to ask them first and get some things set up first but I do believe It can be done."

I nod and say "Unless their are any objections to this I will be dropping the barrier."

After briefly looking around I see no objections, I lower the barrier not missing how relieved Thunder seemed with it now gone. I clear my throat a little to get his attention and says "We have a counter proposal, in return for you accompanying our ponies to these sights, to act as security and guide, you shall be given your freedom."

Thunder frowns a bit but says "Doesn't seem like I got much of a choice, but under two conditions."

Luna says in a annoyed tone "And those are?"

Thunder "No chains, manacles, anything that shows subservience for one, and for two I want compensation for this beyond just simple freedom."

After a brief moment of thought I say "This seems fair, for now I will leave you in the care of my servants to clean you up while Twilight and her friends get their affairs in order."

Thunder frowns, looks to Twilight and says "Really? You got to be joking, no offense but I expected certified scientists and soldiers not a prissy royal and her friends."

Twilight puffs up at this and says "While I understand your hesitance me and my friends are quite capable of handling what is thrown at us, after all we have handled lots of things in the past and saved Equestria too."

"Things from this world that is." Thunder counters.

Luna "That is why you are going with them, to make sure they can handle what is thrown at them.'

Thunder sighs and says "Where all gonna die, all well get me out of these damn chains and into a shower.'

Chapter 4: Order of Affairs Part 1.

Author's Note

I am horribly sorry for how overdo this update was everyone, some stuff happened that I personally don't want to get into, but it led to me being unable to update this story for some time.

Also I am horrible with accents which is why I didn't do a southern accent for AJ or the rest of her family and don't plan to sorry

also I am splitting this into two parts cause of how over do this is and I want to just let everyone know that no, this story isn't dead, just a lot has happened and has made me put this on the back burner.

Chapter 4: Order of Affairs Part 1.

3rd POV (It shall vary on focus later on)

Twilight heads to Sugar Cube corner where her friends were waiting for her, having sent a letter ahead of time to them. She honestly was a bit nervous, after all how would they react to everything? As she steps into the shop she can see her friends gathered at their usual table, chatting to themselves about their day. Twilight stops for a second, takes a deep breath and walks forward.

Suddenly a very familiar pink pony appears right in Twilights face making the bookworm leap back and fall on her ass, as said pink party pony shouts " TWILIGHT! WHATS GOING ON! WHY ARE YOU SO WORRIED LOOKING!"

Apple Jack speaks up from her place at the groups usual table, a dust cloud of the party pony to her left, "Pinkie pie calm down, Twi just got her from a long trip."

Pinkie Pie backs off giving Twilight a chance to collect herself, somehow managing to return to her spot without any sign she had left. Twilight takes a deep breath and sits in her usual spot and says "I'm glad you girls could make it, cause the Princesses need our help but it has to remain a secret."

The main 6 agree and Twilight quietly explains as much as she can, the fortress behind the moon, the ships, Thunder, everything. The girls are understandably skeptical at first but quickly come around, Twilight then says "Anyways girls, that's why the princesses made a deal with Thunder and the plan is he will take us to key locations with evidence of other alien activity and act as our guard as we gather all the information we can."

Rarity nods her head and says "Well I will have to call Fancy Pants and tell him his latest delivery is going to be late.'

Rainbow "Yea going to talk to Spitfire and see if i can't take some time off for this, which isn't so bad all we had planned for this month was training anyways."

With that, the group splits up to get all their affairs in order and pack up for the coming trip.

3rd Pov (Fluttershy focus)

Fluttershy, after returning home, makes sure to feed the animals and arranges for Dr. Fauna to take in the sick and injured animals till she comes back, as well as to have her parents to come by and check on Angel at least once a week. After all of that she begins to start packing up her saddle bags when a certain Lord of Chaos appears behind her and says "Oh Fluttershy!'

"EEP!" said shy peguses jumps a bit in fear and turns to look at Discord, taking a sigh of relief and says "Oh it's just you Discord, you scared me."

Discord sweeps his pony friend up into a hug and says "Oh Fluttershy I am so sorry for scaring you, but I was just stopping by to ask if we are still on for tea next week."

Fluttershy gives a sheepish smile and says "About that, we are going to have to reschedule, the Princess hasa mission for us and it's going to take sometime."

Discord frowns and whispers "Does this mission involve at all a certain by the name of Thunder?"

Fluttershy frowns at this and says "Actually yes, Discord were you eavesdropping on us?"

Discord laughs and says as he sets Fluttershy down "Oh my no no no, I was eavesdropping on Twilight during that interesting meeting though admittedly i kept zoning out so i didn't get all the details....but if you are going on this mission Fluttershy I want you to have this."

Discord removes of his horns and it turns into a small, golden bell with a oak handle, on the handle and bell itself were several odd symbols that seemed to change every few seconds. Fluttershy takes ahold of it and says "Thank you Discord but may i ask what does it do?"

Discord smiles and says "If your ever in a spot of trouble Flutters just give it a ring and I will come and help however I can, but their are some places it doesn't work like rooms that have lead lining the walls and such of the like."

Fluttershy smiles and puts it in her things she then flies up giving the Lord of Chaos a kiss on the cheek and says "Thanks, its quite sweet for you to worry." Discord blushes like a little schoold boy who just got his first kiss.

Discord, after a moment of composing himself helps Fluttershy pack, but once they are done he says "Promise me Fluttershy you will be careful....I won't claim to know everything about these creatures....but I can sense how powerful they are and they withhold the power to crush anyone that crosses them and unlike me they aren't bound the one world."

Fluttershy "Don't worry Discord we will do this quickly and make them our friends.....wait your bound to this world then what about your chaos dimension?"

Discord "Oh yes, me and several god like entities on this planet are bound it just like the Tree of Harmony, and my Chaos realm is technically just a pocket dimension that's connected to this world, so technical still on the planet."

Fluttershy takes a moment to process this information before going to the train station to meet up with her friends, before leaving though she gives Discord a hug and another kiss on the cheek, leaving the flustered Draconequess behind afterwards.

3rd Pov (Applejack focus)

Applejack heads home to her families farm, trying to come up with a believable excuse for her family, but no matter what she came up with it always seemed to come down to a lie or felt like one to her at least. 'You know what? Buck it I will just explain to them that the Princess gave us a mission and it will take a lot of time to complete, I am certain they will understand.' As Aj completed this thought she opened the front door to her families farm house. As she does she is greeted by the sight of a empty house safe for Granny Smith asleep in her rocking chair. Surprised by this Aj figures she should get a head start on packing, she had at least figured she would bump into Big Mac 'Eh he is probably out in the orchards or on a date with Cheerilee.' the farm pony reasoned in her mind. As she reaches the top step she notices Applebloom wasn't in her room, 'eh she probably is just out playing with her friends or is in school.' with that final thought the farm pony begins packing the essentials for her trip, then heads downstairs to the living to leave a note.

Just then she hears a voice behind her "Where do you think your going?"

Aj turns around and says a bit surprised "Granny!"

Order of Affairs Part 2

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