Let's look back at the days before Equestria...

Long ago, in the world before it was given its name, Equus, there lived all kinds of creatures. Ponies, sure, but there were also Horses, Zebras, Deer, Moose, Cows, and many more things yet to be discovered.

They paled in comparison, however, to the creatures once known as "Mankind". Even though they lacked the physical capability to use Magic, they still had ways to manipulate the world, and bend it towards their own will... all by just using their minds to develop technology through Science and Manufacturing.

Their Scientific Methods helped make things easier in life... even going as far as Gene Manipulation, which would eventually be used to create the first intelligent Pony, and bring Griffins and Changelings into existence!

In short, they were the Founders of Equus... but at the same time, they were the ones who destroyed Earth. Using their Sciences as a weapon of genocide, they ended up freezing the sun in place, as well as the moon, which held far too many repercussions to count... in fact, it's because of those very things that the Princesses, to this day, have to move the Sun and Moon manually!

Those of us who were preserved in the Underground Stables, which were built as a safety precaution, should the opposing forces react as they did, were spared the atrocities of the End War... but after the First Alicorn, Father Time, broke free from his Stable, he used his knowledge to, eventually, evolve himself, and create Magic.

Using this Magic, he re-shaped the world, and moved the Sun and Moon in order to balance out the world's atmosphere once again. Eventually, though, he would ascend, giving his power to the world... and granting his Magic over the Sun and Moon to his two dearest daughters, Celestia and Luna.

And yet, while so much was lost during those dark times... in the end, those who survived managed to thrive into the communities that would eventually become the cities that we see today.

Despite their existence fading from the History Books, we still find a few archived notes about these Humans... for they may have been the ones who made us, but they were also the ones who nearly killed us all!

But, to be fair, they had some technology that we use, under heavy control... things like Helicopters, Computers, Games... those things!

I smile sheepishly while standing at the front entrance, while Bon-Bon continues telling me the story of Equestria... and more specifically, about Humanity's half of it.

I gulp, nodding my head in response to her questionable gaze she throws my way. "Uh-huh... a-and... as usual, you tell these stories to bring up a point, which I'm sure is going to be a very, very good one!"

"Point? No-no-no, why would I try bringing up a point about this?!" she says, before doing the whole eye-twitchy thing... yep, she's definitely bringing up a point.

I raise my hoof up and open my mouth to speak, but she cuts me off. "I mean, why would I bring Humans up in the first place? It's not like you've told me thousands of stories about them in the past, right?! Right?!"

"Umm... Bonnie, you're starting to scare me..." I whimper, but she only walks up to me, smiling even wider, while her pupils shrink.

"What?! Why would I be scaring you, Lyra?! I'm your friend! I've been listening to your stories and theories of Humanity, even when others claimed it to be nothing but old mares' tales!" She wraps a hoof around my neck and begins to walk me towards the Basement Door.

"I'm pretty sure you're angry with me about something, Bonnie..." I say, only for her to turn towards me again... in a scary way.

"Angry? Pfft, nah! I'm not angry with you, Lyra... though I'm glad you're at least here to clarify something!"

"... And that is?" I hesitantly ask.

And then, she glares at me. Yep, she's angry.

She practically punches the Basement Door open, revealing the stairway. At the bottom of the stairs, however, there's a tall biped sitting on the wooden floor, covering his exposed nudity with a nervous expression adorning his features.

I'm partially happy that he's still doing well, and not doing anything that could potentially pose a risk for our safety, but due to my friend's Death Glare, I'm mostly still nervous because she might be the one risking my safety at this point.

I giggle nervously, and rub the back of my neck sheepishly. "Ohhhhh... that... r-right, well... you see, what had happened was-"

"Lyra..." Bonnie says, pinching the bridge between her eyes. "I've put up with your shenanigans for over ten years, now... so I need the absolute, honest truth. And so, I'm gonna ask you in as blunt of a way as I can ask you."

Oh, dear... not the blunt way! "B-Bonnie, I-"

"WHY IN THE FRUITY-PEBBLED FK IS THERE A HUMAN IN THE BASEMENT, LYRA?!" she roars, causing the house to shake. The human winces and closes his ears with his hands, while I, in turn, close my ears with my hooves.

"O-okay, Bonnie! Just calm down, and-"

"Don't you 'Okay Bonnie' me! I want the actual truth! No. Excuses!" Bonnie demands, pushing her snout up to mine and glaring deeply into my eyes.

I gulp and smile sheepishly, before nodding my head. "Alright! I'll talk! I'll talk!"

"Well start talking, then!" she orders once more, before backing from me, and sitting down, crossing her forelegs across her chest.

"W-well... it all started three days ago, when-"

"IT'S BEEN IN THERE FOR THREE DAYS, NOW?!"

"... Y-yeah... but I've fed him, and watered him, and-"

"IT'S NOT A FKING PET, LYRA!" she shouts in my ears, forcing me to wince and cover my ears again. When I recover, though, I glare back at her and gently press my hoof in her mouth, then push her back a couple paces.

"I know that, Bonnie! And it's a HE, FOR FK'S SAKE! Now will you let me tell you what happened, or not?!"

She takes a deep breath and sighs, before nodding her head and motioning for me to begin.

It takes me a little bit of time to calm myself. Taking a few meditative breaths, I clear my throat, and then begin my tale.

It started shortly before I packed my things in Canterlot. I had just received that letter from you, inviting me into your home here in Ponyville, when I saw my friend, Twilight Sparkle, rushing through the road in a hurry. I tried waving her attention my way, so that I could let her know, but it seemed her mind was preoccupied, so I decided to shrug it off and continue on my way back home. I asked Lemon Drops to tell her, though, since I was also in a hurry.

Anyways, once I made it home, I started to pack my things, when I noticed an odd-looking Arcane Book lying around on the floor. I knew I didn't borrow it from the library, because it didn't have a Book Card behind its cover.

So, after skimming through it, I saw that it had the potential to open up a portal within Space and Time, itself... however, the stars would have to align a certain way, which only happens once every thousand years! I knew, right then, that I had only one shot at this!

And so, I packed up only the essentials, hurried my way to Ponyville, and after we got my stuff settled in, I got to work immediately!

After going over the chants in my head, double-double-checking the runes on the ground, triple-triple-checking the placements of the candles and stuff, I opened up the book, and began to speak the words at the right time.

Thankfully, my works paid off, because as soon as I finished the words, the symbols glowed white, and as soon as the stars aligned, the portal to our world was opened!

... For only a split-second, at least. Once it picked up a reading, he popped up!

I had so many questions to ask him, but sadly, it seems he doesn't understand what we say. And when he started speaking to me, I couldn't understand him!

And so, we stuck with drawing pictures to communicate. He said that he was hungry, so I fixed him some Oat Meal, gave him some water, and let him use the restroom when needed!

Of course, I warned him about the Outside World being way too dangerous for him, using a few pictures of Ponies in Lab Coats experimenting on him... he seemed to get the picture.

And so, for the past three days, I've been hiding him inside the Basement, which is now his new home!

"And the rest, as they say, is history!" I conclude with a smile and a nod.

Bon-Bon just stares at me with an annoyed, deadpanning look. "So, wait... let me get this straight... you opened a portal to EQUESTRIA?!"

I look up and rub my snout in thought, before nodding again. "Yep... pretty much!"

I groan and plant a hoof into my face. Of all the stupid friends I've made, why did it have to be LYRA of all ponies that nearly destroys the whole world by summoning an Ancient Evil... perhaps TWO Ancient Evils?! IN MY OWN HOUSE, NO LESS!

"And... you didn't think that some other creatures would've noticed that portal, and jump at it as well?!" I ask.

She shakes her stupid little head, still smiling at me, completely oblivious of her actions! "Nope! Besides, the only inhabitable planet between here and the stars would've been the one that the human came from!"

I feel a strand of my mane unfurl. An eye twitches, while I try to visualize the apology letter I would probably be writing to Princess Celestia for killing one of her subjects...

I'm about to say something, when she shrugs it off and stands back up. "Besides! It's not like I summoned Nightmare Moon, or anything like that! That would be silly!"

... Scratch that, the letter won't be necessary. They won't even be able to find the body.

I begin to reach towards Lyra's neck with my hooves, when suddenly...

Lyra and I freeze in place, as our ears pick up the sound of something crunching.

And there it goes again! We both turn our heads towards the kitchen, and my blood runs cold, as the Human from downstairs just casually sits there, on the floor, with a bag of Potato Chips in his hands!

His eyes are staring at the bag, while he pulls another chip out, opens his mouth, and draws the chip closer.

He then reaches into the bag again, and scoops another chip. When he lifts it up into his mouth, however, his eyes trail up to Lyra and I, and he pauses.

The three of us just stare silently at each other, as if observing the threat level of our company.

I see that his muscles are far from unfit... if anything, he looks like he could best a Minotaur in an arm wrestle! And that's saying a lot!

My eyes trail down to his broad chest, his toned abs...

And his legs are crossed in front of his pelvis, where I can see brown hair gathered around his-

My cheeks immediately flush red, while Lyra whistles, impressed. I give her a glare, which she doesn't even respond to, before turning to face the Human again.

He looks between us, chip still in opened mouth, before his eyes lock onto me.

...

He then folds the top of the bag shut, rolls it in circles, and places it on the counter, before cupping his hands over his groin, and standing up.

I shield my eyes (though I doubt if Lyra does the same), and turn my head away, while I hear him side-step back into the Basement, closing the door slowly and gently.

When I hear the door close, I open my eyes and glare at Lyra.

"Maker-Dammit, Lyra! Do you even realize what you've done?!" I growl at her, making her smile sheepishly back at me.

She gently pushes me away, and shrugs her shoulders. "Relax, Bonnie! I'm sure we can get him assimilated into Ponyville no problem!"

"No, no, NO! We can't just let him wander into Ponyville! Do you even realize what happened today?!"

She rubs her snout in thought, before gasping. "Oh my gosh! The Summer Sun Celebration was today, wasn't it?!"

And again, I deadpan at her. "Wait... you mean you weren't there?!"

She shakes her head. "Nope!"

"But... but I saw you there! AND I saw you in Twilight's Library!"

"Wait, TWILIGHT MOVED HERE, TOO?!" Lyra cheerfully shouts.

"W-well, yes, but-"

"Then THERE'S our answer! If anypony knows how to figure things out, it's her! C'mon, let's-" As she starts to trot off, I quickly bite her tail and pull her back, making her fall on her belly.

"Oww... hey, what gives?!" she asks.

I roll my eyes and shake my head. "No, Lyra! We will not get anypony else involved with this! If word goes out, then there could be panic on the streets! We could potentially be charged for nearly getting the world destroyed, or worse! We could get on Princess Celestia's BAD Side, and be banished from-"

"Alright, alright, sheesh! A simple 'no' could've worked..." Lyra deadpans, before standing back up and brushing her tail off.

My eye twitches again, as she casually trots into the kitchen. I turn my head, and see her pulling the bag of chips from the counter and opening the bag. She then casually trots into the living room, bag floating beside her, and sits on the sofa... in a way that looks very, very uncomfortable.

"Umm... Lyra, why are you-"

"It's how he sits! If I'm gonna make him feel more welcome here, I'll start by adopting his mannerisms, so that he doesn't feel all alone!" she replies, before levitating a chip from the bag, and levitating it up to her snout. She opens her mouth and eases the chip into her awaiting mouth.

My eye twitches again, before I trot into the kitchen. With a frustrated groan, I take a seat over in the Dining Area, and firmly slam my head into the table.

"... I need new friends..." I mumble. The sound of the chair next to me scooting back doesn't even make me budge.

However, I decide to eventually look towards the source, only to find the Human looking back at me, with his hands clasped together. I look down at the sheet of paper that he, somehow, slipped towards me.

It's a picture of a smiling face.

I look up at him, and he simply smiles and waves.

"... You don't count." I reply to him, before returning my face onto the table.

He stays there for a moment longer, before eventually deciding to leave the Kitchen.

When I lift my head from the table, I notice that he left the sheet of paper, but added another doodle below it... it's a doodle of himself standing between two ponies - a Unicorn and an Earth Pony. Likely Lyra and myself.

I stare at it for a moment, before sighing and standing from the seat.

"I can't believe I'm even considering this..." I mumble.

As I enjoy another chip, I notice the Human looking towards me with a pretty sad-looking frown. I smile warmly at him before levitating the chips his way.

He stares at the chips in awe, and he begins to smile once again. He then accepts the chips with a grateful nod, before reaching his hand back into it.

When he swallows the chip, he clears his throat and starts to say something... however, I'm unable to really understand what he's saying.

Looking at the way how his hands move, however, he appears to be gesturing towards my flank... or maybe he's just talking about the way how I'm sitting?

Whatever the case, I shrug my shoulders and reply, "Hey, don't worry, buddy! It's actually quite comfortable, once you get the hang of it!"

He tilts his head confusedly, while I giggle and lean back, relaxing my forelegs on the back of the couch.

That is, until Bonnie trots inside. She appears to have a strange red mark on her forehead, but I don't question it... after all, I can kinda-sorta guess she wouldn't want me to talk right now.

She takes a deep breath, before sighing and sitting next to me.

"So... if we're going to be keeping a human in my house, we'll have to go over some ground rules." she finally says, after a few quiet minutes of her thinking.

I look at her with a wide smile, and gasp. "Bonnie! You mean you'll let him stay?!"

She deadpans at me in response. "Not by choice... but as it stands, he'd be safest with us."

"Yay!" I cheer, only for her to place a hoof on my mouth, silencing me. "Mm-hmm!" I mumble with a nod, before motioning for her to continue.

"Rule 1. Do NOT let anypony else know about him!" she begins. I nod my head in response.

"Rule 2. Do NOT let him out of the house!"

"Ooh, you addressed him as a HE!" I interject, only for her to glare at me. Shutting up, now...

"Rule 3. If you start teaching him how to talk, do NOT misguide him. I'll buck you in the flank for every curse word he says!"

Well, there goes that prank...

"Rule 4! Do NOT make him feel uncomfortable! If you try to push any of your weird fantasies his way, and make him uncomfortable, I'll lock you in a cage, and stuff an Inhibitor on your horn!"

Gulp...

"Rule 5! If HE makes you feel uncomfortable, then let ME know, and I'll deal with it! If he persists, then I'll be sure to make him know!"

I raise a hoof, but she shushes me, making me lower it back down. I was gonna say that he might not be fully aware of the Cultural Norms, such as petting behind the ear, or touching a Unicorn's horn... n-not that I minded, but I have a feeling he figured that one out the moment I made those noises...

"Rule 6! He is not allowed in my room. Period!"

Oh, good! Then at least I can still-

"Rule 7! He is not allowed in your room, especially!"

"Oh, COME ON!" I complain, throwing my forehooves in the air. "You gotta lock him up in-"

"If he sees those drawings under your bed, how do you think he'd react?" Bonnie asks.

... Okay, that might be a good point...

"Rule 8! He's going to be wearing clothes from now on! It's clear he's a biped, but his lack of fur, and lack of a sheathe to hide his... genital area... means that he'll need something to keep himself looking decent... which speaking of...

"Rule 9! After he's been given clothing, he is not to sit naked on the sofa!"

"Umm... aren't we sitting naked on the couch, though?" I ask.

She deadpans at me. "Yes, but we still have fur, thank-you-very-much!"

I giggle at her, before nodding my head.

She then goes over a bunch more rules. I'll have to eventually go over them with Mr. Human, once we've got him properly educated!

I can't help but wonder, though... just what, exactly, is going on in his mind right now?

I really, really wish I knew what the hell's going on right now... first these colorful little pony-things drag me into their world, and next thing I know, I've gotta hide in here for a while?

At least the unicorn seems to be trying to adapt to my way of sitting... odd, and likely uncomfortable-looking, I point at her and say, "Umm... you sure you wanna sit like that?"

She shrugs her shoulders and replies with more of their odd words.

Hmm... the cream-colored one seems pretty pissed at the unicorn for some odd reason... not gonna lie, it almost feels like they're used to this kind of thing, though... might have to keep an eye on them.

They look at me and begin speaking to each other... but unfortunately, as stated before, I can't even slightly understand the words they're saying! It's all weird syllables and clicks, followed by the occasional whinny and snort... kinda a mix between words and your average horse noises.

But then, the unicorn starts drawing more things on a scroll of paper. When I get a good look at it, I see a bunch of pictures, with symbols below them.

One, in particular, is an apple. From the looks of it, there's five letters in it, just like English.

Going through the sheet of paper, I realize what this is... it's an Alphabet Chart.

With that, I smile. Communication by words?! Finally! If I study these things, then I can probably get some answers!

For all I know, they probably summoned me here because I've been chosen for some sort of quest! Yeah! And they're probably just trying to teach me their language first, so that I don't get myself in trouble!

Perhaps once I've completed this quest, they'll finally send me back home, right?

... Right?

Author's Notes:

Imagine the SPOKEN curse words as a Squee, if you'd like!

Anyways, I may have found the idea that'll keep my attention for a long time, now! And it, of course, is this one right here!

I'll still keep working on the other stories, but as far as writing goes... I had fun writing this chapter, which isn't something I could say about the rest of my stories!

And so I'll likely make this story my Main Focus!

As one might expect, it's based way back in Season 1, and takes the whole story of MLP, then bases it on what happened between these three in the background!

Also, here's a single answer to a potential critic that might poke at this one detail:
There's no Plot Holes in the whole "Lyra being in multiple places" thing. It was deliberately avoided by her, but will be brought back up in due time.