• Published 25th Apr 2012
  • 63,488 Views, 915 Comments

Better Living Through Science and Ponies - Pen Stroke

Not all is well in Equestria when a failing portal gun brings Aperture Science to the land of ponies

  • ...

Chapter 1: Wheatley, You Moron

Better Living Through Science And Ponies
By Pen Stroke
Assisted By Batty Gloom
--Author Note--
Better Living Through Science and Ponies was written before Season 2 of MLP FiM
Because of this, certain aspects of the story now conflict with the show’s active cannon


Chapter 1
Wheatley, You Moron

“Oh thank god you’re all right. You know, being Caroline taught me a valuable lesson. I thought you were my greatest enemy, when all along you were my best friend. The surge of emotion that shot through me when I saved your life taught me an even more valuable lesson. Where Caroline lives in my brain.”

Caroline Deleted

“Goodbye Caroline... You know, deleting Caroline has now taught me a valuable lesson. The best solution to a problem is usually the easiest one. And I’ll be honest... killing you is hard. You know what my days used to be like? I just tested. Nobody murdered me, or put me in a potato, or fed me to birds. I had a pretty good life... and then you showed up. You dangerous, mute, lunatic.

“So you know what? You win... just go...... It’s been fun.... Don’t come back.”

With that the escape elevator slipped out of view and the single yellow eye of GLaDOS watched as the bane of her existence disappeared. The turrets had been set up a few floors higher, if only to prove that she could have the last laugh, if she wanted it. But... no... she was done. There was testing to do, and her new cooperative robots would be far less... hazardous... to her health.

“Now... back to science.” GLaDOS said, spinning on her mount as she turned to the two robots. “Please head to the first chamber so we can begin the test.”

The two robots glanced at each other, then held out their hands expectantly.

“Oh... of course, you will need your Aperture Science Quantum Tunneling Devices. Now just let me see.” A few clinks and clanks came from the ceiling as the automated tiles shifted, eventually some opening as a pair of portal guns dropped from the ceiling. The two robots caught them gingerly, excited looks in their robotic eyes.

“Now, we have science to do.” GLaDOS said again, only for the taller robot, P-body, to raise her hand.

“What is it now?”

P-body held up her portal gun, allowing GLaDOS to lean in close as her yellow eye focused on the device. A thick bit of duct tape had been put across the surface. GLaDOS’s camera shifted anxiously, brain tripping back over the enrichment center’s control logs as she went over every little insane decision made by Wheatley while he had been in her body.

“I really wish I had been able to kill Wheatley. Because then I’d put him back together and kill him again... and again... and again... because, you know, that’s what that murdering, potato stuffing moron deserves.” GLaDOS said, picturing the moronic personality core. Floating endlessly through space was not a sufficient enough punishment.

The device sputtered, causing P-body to drop it in surprise. A second sputter shook the device, causing it to rattle on the floor before part of it began to crumble. Inside, the black hole at the core of the device was beginning to destabilize. It was a miracle the device hadn’t failed earlier, considering all Wheatley had done to try and fix it was put duct tape on one side.

Where had he even gotten duct tape?


Chell sat just outside the small, unassuming shack she had just been tossed out of. Her seat was the charred companion cube, which was surprisingly comfortable. She was in the middle of nowhere, surrounded by rolling grass as far as the eye could see. She didn’t have any food, or water... all she had was her long fall boots and the companion cube.

The mute test subjected wondered if this wasn’t one final surprise from GLaDOS. The insane AI had let her escape, to live... only to die of starvation or dehydration. She wouldn’t have put it past that test obsessed computer. Still, at the moment, Chell was just happy to see the sun. To feel its warm rays, the gentle breeze on her cheek... the ground rumbling beneath her.

Wait, the ground wasn’t supposed to be rumbling.

Chell jumped up to her feet. An earthquake... no, it couldn’t just be an earthquake, not with the miles and miles of underground laboratory just beneath her feet. Was the reactor blowing up... no, GLaDOS would have stopped that count down. That AI wouldn’t have let it just blow up, not after all that they had went through. Then what the hell?

Chell felt a shift, as if the ground beneath her had just sunk a foot. In the distance, Chell could see a ring of bright orange light surrounded the area... a familiar orange light.

Oh sweet Jesus!

Chell broke into a full sprint. This was a portal... this was a huge ass portal and it was sucking everything in. Chell didn’t know why GLaDOS had opened such a huge portal. Maybe she was trying to move the enrichment center, so that Chell couldn’t show anyone where it was. Heck, for all she knew something blew up and the massive portal was an after effect.

Despite all this, Chell was sure about one thing: she didn’t want to go wherever this portal led.

The ground began to fall more quickly, Chell starting to lose her footing. The edge of the portal was still a long ways away, but still she kept sprinting. She would not just give up, not when she had finally gotten to see the sun.

And then it all gave way. Whatever had been slowing the enrichment center gave up the ghost and everything just dropped. The ground literally fell out from beneath Chell, and soon she was caught in a terminal fall just a few feet above the rolling, golden grass.


The two cooperative robots were in a panic, flailing their arms as they floated in free fall. In a last ditch effort to save as much of the facility as she could, GLaDOS had open a hole in the floor and let the damage portal gun plummet into the depths of the facility. Past all her carefully stacked test chambers, both her favorites and the ones Wheatly had just slammed together. So much damage, but all that was repairable if she could just stay connected.

The gun hit its failure point on the border between the newest part of the Aperture Science Enrichment Center and the long forgotten incarnations of the structure, the parts built back when Caroline had been alive and the company was making their own scientists into test subjects.

With the release of the gun’s internal black hole, a huge portal had been opened up. Usually, that would not be a problem, but the catastrophic failure of the portal gun had actually forced a blue portal to open in another place. Thus the enrichment center and all the ground surrounded it began to fall through the portal.

“Newest wings of the center still intact. Enrichment Center still surrounded by solid rock of sufficient depth... well, except the bottom part. The bottom is just open to anything at this point.” GLaDOS reported, her protocols dictating she make verbal reports, even if there was no one there to listen.

“Warning: lower level sensors are detecting a paradigm shift. Laws of reality are in flux. Sensors taking account of new dimensional laws. Gravity, is still gravity. Physics, is still physics.” GLaDOS rattled down a whole list some scientist from way back made when he thought that such a cross-dimensional event could occur. Most everything was the same, but as GLaDOS reached the end of the list she began to actually find differences.

“Animal Life is identifiable. Humans do not exist. Dominate Sentient Specie is Animalia Chordata Mammalia Theria Eutheria Perissodactyla Equidae Equus Ferus Caballus. More commonly known as ponies.

“Wait, Ponies!” GLaDOS said to herself, some other thread of her intellect interrupting the reality check. “How in science are ponies the dominate sentient species? They don’t even have thumbs!”

P-body and Atlas, the two collaborative testing robots, just glanced at each other and then shrugged, their panic subsiding as the science center had been falling for a few minutes now. In that moment the event horizon of the portal reached the control room, passing by GLaDOS and her cooperative robots as surges of energy crossing over them.

“Wa..war....warning. Warning, destination universe imposing critical changes to basic structure of both organic and inorganic systems. Changes occurring primarily in hardware, minor changes detected in data... physical change is resulting in... oh you’ve GOT to be kidding me.”


“La lala La La. La lala La La.” Fluttershy sang to herself, taking bits of bread and tossing them to the fish, ducks, and other small animals around Sky Mirror Lake. The lake was the biggest in Equestria, a few hours from Ponyville but Fluttershy always like to try and get to the lake once in a while to see the animal friends there.

Several miles across, the lake was usually blissfully undisturbed, surface perfectly pristine. It was how the lake got its name, for on a normal sunny day the lake was like a great big mirror, reflecting every cloud, every bird, and matching the sky’s blue tone.

“Now, don’t eat too quickly or you’ll get a tummy ache.” Fluttershy warned with a smile. Then, a horribly loud sound cut through the air, making all the animals jump, though none higher than Fluttershy. The pegasus zipped behind a tree, looking up at the sky expecting to see a thundercloud or something. But... nothing was there, at least at first glance.

Yet as Fluttershy watched she saw, way up in the sky, a cloud that had a blue ring in it. The cloud looked so small and innocent; Fluttershy didn’t know how such a cute little thing could have caused such a loud noise. Something began to appear from the blue ring in the cloud, and after a few moments it began to fall. It looked brown and rocky. Surely a pegasus pony wouldn’t be mean enough to drop a rock from that high up; they could hurt somepony.

Fluttershy watched the rock fall, considering trying to catch it so it didn’t hurt an animal. She watched it become bigger, and bigger... and then the yellow pony began to realize that what looked like a little cloud that was fairly close was actually a very large cloud that was really far away. And what had looked like a little stone some pegasus dropped was actually a rock... no, a boulder... no, a mountain!

With a thunderous splash, the mountain crashed into the lake, the water and muddy bottom cushioning the fall but not by much. All the nearby tree were almost uprooted by the force, and the rumbling felt even in Canterlot. A huge wave of water was thrown up from the lake, an inland tsunami that cascaded over the shore and swept up everything in its path.

The water crashed against the nearby trees before it began to recede, leaving a half drowned Fluttershy coughing up water as she hung from a tree branch. The pegasus brushed some pink hair out of her face, a panicked “yeep!” escaping her lips as she saw all the fishes flopping around on the lake shore.

“Oh... don’t worry little fish... I’ll get you back in the water.” Fluttershy said in a panic, rushing to start throwing fish back into the lake.


Chell groaned, trying to open her eyes only to snap them shut a moment later. God, it was bright out. Making a second, slower attempt, she managed to look up to see the picture blue sky, dotted here and there with a fluffy white cloud. Chell was lying in the golden grass that surrounded the secret exit from the Enrichment Center.

Going through the portal had felt different, a lot different. Normal portals didn’t feel like anything. It was like walking through a door; you just walked through. But this time, the portal had zapped her and it had hurt... A LOT! Enough that the mute test subject blacked out. She didn’t even remember hitting the ground. Probably the only reason she didn’t have a bloody nose or broken bone was because of the long fall boots.

For a time all Chell could do was lay there, her body numb. She began to fear that she had been paralyzed from the neck down or something, but slowly a tingling sensation started to come from her legs and hands. She could still feel them, they were still attached, so she was not paralyzed.... just numb.

As feeling returned something started to feel wrong. She could feel the grass against her skin. What happened to her clothes? Had they been zapped when she went through the portal? At the same time, it didn’t feel like she was lying bare skinned against the grass and dirt. It felt like something was between them, something short and fuzzy.

She tried to stretch and move her hands... and again something felt wrong. Chell couldn’t feel her fingers. She could feel the arm, but not the fingers. What the hell had happened?

Chell’s confusion and panic only grew as sensation returned to the rest of her body. It all felt so different and familiar at the same time, like it was her body but something had happened. Unable to stand it anymore she tried to get to her feet, but couldn’t. She teetered on her legs for a couple moments before falling forward, catching herself with her arms.

Chell took a single deep breath as she closed her eyes, mind trying to feel out why her body felt so strange. She opened her eyes again, curious as to why she couldn’t feel her fingers... and as Chell looked down her heart skipped a beat.

She didn’t have fingers.

No hands, no palms... where had once been human hands were now hooves, the rest of her arms covered in a dull orange fuzz. Panicking, Chell looked back at the rest of her body. Nothing about her was human. Her entire body covered in fuzz, her back legs much shorter than they had been and bending at strange angles... and was that a tail?!

Nerves snapping, Chell would have screamed if her voice had allowed. Instead, all that escaped her throat was panicked breathing. She needed a mirror... something reflective. She had to see what had happened.

Unfortunately, walking was a challenge. After failing to get back onto her legs again, Chell stayed on all fours, walking with slow deliberate steps towards the metal shack. Most of the metal was rusted, weather worn, none of it really reflective, but Chell finally found something: an old chrome hub cap with a flat surface in the middle.

Chell stretched out a hoof, the appendage trembling as she cleaned some of the gunk from the chrome’s surface. A few scrubs, and Chell’s reflection stared back... a reflection that Chell didn’t recognize.

If not for her muteness, the ear splitting scream that would have escaped Chell’s mouth could have cut the air like a hot knife through butter.


Fluttershy smiled as she tossed one final fish back into the lake, smiling as she saw it swim away. It had taken a lot of frantic work, but she had got them all back in the water. It was a small miracle, one Fluttershy was thankful for. But with the fish safe Fluttershy’s attention turned to the mountain that had dropped out of the sky. When you witness something like that and survive, even a normally very cautious pony like Fluttershy is going to be curious.

Standing a few miles high, the mountain was imposing. Fluttershy began to slowly ascend, moving along the rock surface. The cliff sides were perfectly vertical, the whole mountain looking like someone had taken an oval shaped plug out of the earth and just dropped it in the lake. Like cutting out a cookie using a cookie cutter. The shape was just too perfect; the mountain couldn’t have naturally been like this.

The top only increased Fluttershy’s belief that something very weird was going on. Not only were the sides of the mountain perfectly vertical, but the top was flat, covered in rolling fields of golden grass.

Taking a little more altitude, Fluttershy searched for any animals that were hurt. Still, she couldn’t see any, the only noticeable feature of the mountain a single, tiny house in the very center. Flying over, Fluttershy landed gracefully and swung her head to get a bit of pink hair out of the way. The tiny house... actually, it was probably fair to call it a shack… was made of old worn metal in strange shapes.

The only other thing Fluttershy could see at the moment was a charred gray and white cube with pink hearts on each side. She moved up to the cube, poking at it with a hoof and wondering why the cube was so appealing. She couldn’t get over the sense that it was just sitting there wanting to be her friend. Yet, as Fluttershy examined the cube, she noticed strange tracks in the dirt, tracks she didn’t recognize.

“Uh... hello?” Fluttershy offered. “If there are any little animals here, you don’t have to be scared. I’m not going to hurt you.”


Chell jumped at the sound of another voice, having become completely lost in looking at her reflection. It was a moment when her muteness was an asset, because most people would have probably made some scream or yelp after being startled like that.

Taking a moment to calm her heart beat, Chell stepped over to the corner of the shack. She peeked around the edge, ready to retract her head if she saw anything that looked like a turret or another Aperture Science device. Still, what met Chell’s eyes was something that looked completely harmless. A little yellow pony with long pink hair and... did she have wings?

The mute test subject backed up, the sight of the yellow pony making her glance back at her own reflection. Chell didn’t know how, why, or when it had happened... but she had become a pony. She could have just as easily said horse, but at the same time that word just didn’t feel right. Like some part of her subconscious knew exactly what she was and that she was, in fact, a pony.

Horse or pony, it didn’t really change the reflection staring back at her from the old chrome hub cap. She was an old orange color, much like the jump suit had been wearing as an Aperture Science test subject. An orange tone that looked a little sun bleached, a little dirty... just not a fresh, rich, new orange. A dull orange. Her hair... or rather mane and tail were still brown, cut short and roughly. Her eyes... they looked familiar but at the same time seemed large for her head.

The most dramatic change was simply the fact she was now shaped like a pony. Hands and feet replaced with hooves, and on those hooves a set of four matching long fall boots.
The final detail, and maybe the strangest of them all, was that Chell had a pair of portals on her body.

Where the yellow pegasus had pink butterflies, Chell had a portal on each flank. And no, it wasn’t just a drawing of the swirling, oval shaped quantum tunnels. No, they were fully functional. A blue portal on one side, the orange on the other. With a little bit of experimentation Chell had proven that those two portals were linked and working, having tossed a rock through one which popped out the other side.

“Oh, hello.”

Chell jumped at least a foot in the air, spinning around and landing, looking around in a startled panic. The yellow pegasus had come around the corner of the barn, catching Chell as she examined her reflection for what had to be the twentieth time.

“Oh... I’m sorry... I, um... I didn’t mean to startle you.”

Chell’s heart started to calm down, no longer trying to burst out of her chest. That voice... it was so gentle and soothing... and in a way fragile. Like it was a glass vase that could break with a single misplaced touch. Chell began to relax a bit, breathing calming. While she didn’t know this pony, she doubted that a yellow pegasus with pink hair was going to be very dangerous.

“Um... I... I didn’t think I’d find another pony up here.” The pegasus admitted, using her long hair to hide her face from Chell. “Um... I’m Fluttershy... what’s your name?”

Chell blinked a couple times. Okay, this was a new problem. The last time someone had actually needed her to say something was when Wheatley asked her to say Apple... and at the time she had tried to communicate to him through jumping because she was mute. Considering how well that went over, Chell began looking around for another way to communicate.

Going with the first thing that came to her mind, Chell reached out a boot clad hoof and scratched at the ground. It was a little awkward writing upside down, since the letters needed to be legible from where Fluttershy was standing. Still, with a few strokes Chell had written out her name in the dirt, pointing at it with a hoof.

“Chell..” The pegasus read, pausing a moment before her brain connected the dots. “Oh, is that your name?”

Chell did what she could, nodding a reply.

“That’s a lovely name, but... um... why did you write it in the dirt?”

Again, Chell looked down, this time scrawling out a few more letters before stepping back.

“Can’t... talk.” Fluttershy read. ”Oh, you can’t talk? I’ve never met a pony that couldn’t talk before. I... um... don’t talk that much myself... but... I don’t know what I do if I couldn’t. So... uh... oh... how about... no... oh, I know. I’ll just ask you yes and no questions. Is... Is that okay?”

Chell replied with a nod. Yes and no was something she could handle.

“Oh good... but, how about we get off this mountain first? Are you hungry?”

The ex-test subject couldn’t nod her head fast enough, the very energetic reaction making Fluttershy giggle a bit.

“I guess that’s a yes. How about we go back to Ponyville then? We can talk on the way, and then we can stop by Sugarcube Corner. It’s a wonderful bakery.”

For a third time, Chell nodded her head. All she had to eat in the enrichment centers were tiny black squares of tasteless, artificial tofu. It kept the test subjects healthy and provided all the nutrients that the body needed. It was, however, not real food... and Chell couldn’t hide the fact she would do anything for some real food.


“OhohoHOhoH... my hard drives. I think I slipped a hard drive.” GLaDOS murmured, the AI lifting her body off the floor after what was a decidedly rough landing. “No, death is too good for Wheatley... even endlessly repeated death. No, I’d take that little personality core apart piece by piece and then put him back together the wrong way. That way, he’d have to listen to his own thoughts for the rest of eternity. Then a year in the incinerator, two years in the cryogenic freezer... then twenty years in room of screaming robots... Oh yes... then I’d kill him again... and again... and again.

“Beginning facility stability check. Reactor Core, stable. Testing Chambers, minor damage... Test Subject Cryogenic-Chamber, missing... must have been left back on Earth. Shame... that was all my spare test subjects.

“Neurotoxin Generator... oh wait, that’s right. That was destroyed... pity, I’d really like to warm up the neurotoxin right now. Maybe vent it outside... see how many little animals I can kill before I run out of deadly neurotoxin. That sounds like a wonderful test.

“Cooperative Testing Robots...” GLaDOS muttered, returning to her checklist. She then turned to look at P-body and Atlas... only to pause. Her once humanoid robots were now stumbling around on four feet instead of two, with decidedly equine features. Their very skeletal like bodies supported their heads, P-body’s turret based head actually seemed to fit well with the pony like body, while Atlas’s round head looked almost out of place.

“Operational...” Was all GLaDOS replied, the moving panels around the room receding as several large display monitors shifted into view. The monitors clicked to life, showing video footage from a number of cameras that were positioned outside the facility. They were, of course, Aperture Science’s own sniper scope cameras. The magnification of a telescope with the fine control of a hawk’s eyes and only half the deadly mercury as previous models.

The camera’s began to show off different parts of the outside world, GLaDOS seeing villages, towns, even proper cities of ponies. They came in a rainbow of colors, each marked with some design on their haunches. The sight of those marks made GLaDOS glance back at her two little robot testers, noticing that their back hind legs were marked with the Aperture Science logo.

“Hmmm... interesting.” GLaDOS murmured to herself, continuing to take in the video from the outside world. She watched as pegasi moved the clouds, created rainstorms, and then brushed them away. She saw unicorns with glowing horns making objects move and shift around them, as if by telekinesis... and even some unicorns seemed capable of sub-atomic matter reorganization.

“Fascinating... intriguing... unresearched...... I see... possibilities.”

GLaDOS shifted, reaching out her control. Lights flicked on across the facility, the Aperture Science panels beginning to shift on their robotic arms. Assembly lines began to whirl to life, and old robots that hadn’t been online since she had flooded the enrichment center with neurotoxin were clicked on to continue their labors.

“I must continue testing, but now the parameters have changes. All my old data on humans is useless when surrounded by ponies. The old tests must be redesigned... new tests made... new research begun. After all... we have no data on these sentient equines. What of those that can fly? What of those that manipulate matter mentally? How would they pass through the tests... what kind of tests would they require?”

GLaDOS laughed a little to herself, starting to feel a rush of simulated liveliness she believed was beyond her. The facility reflected the excitement that was building in its mistress, test chambers already starting to adjust themselves to new height parameters.

There was so much to do, so many calculations to run... so many things to build and reorganize for the new tests. Oh, and most importantly, she’d need test subjects... lots and lots of new test subjects.

Questions, Comments, Concerns?

My Little Pony, Friendship is Magic © Hasbro
Portal & Portal 2 © Valve

I do not own the intellectual properties this fan-fiction is based on.