• Published 11th Jun 2013
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A Trusted Friend in Science and Ponies - Rethkir



A sequel to Better Living Through Science and Ponies

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Chapter 23: Reconfiguring Science




Concealed within choking clouds of dust was an area about half a mile in diameter around the point of impact. In the center of the crater, unseen beneath the thick smoke, a gargantuan black machine was digging itself deep, deep into the ground. The sound it made was that of a low, horrid groan. The ground rumbled from Ponyville to Canterlot as massive tunnel boring machines underneath the behemoth were eating away at the dirt and rock below, causing the monstrosity to sink deeper into the earth. The ground up rock was ejected away from the site in streams of gravel that sprayed far in all directions.

After several minutes of the earth-grinding passed, it stopped. A sturdy foundation had been secured hundreds of feet below the surface. A massive triangular column of metal shot upwards from the dust cloud several hundred feet, until it could rise no more. But out from it was sent a slightly thinner, telescoped section of the tower. When that part of the tower finished ascending, up forth from that was sent another, slightly thinner section. When a part of the tower finished rising, its surface tessellated apart and puffed outwards, compensating for the slight decrease in width. These processes continued in what seemed to be a neverending cycle, as the tower soared into the heavens higher and higher without limit.

The sight was nothing anypony had ever seen before: an enormous tower rising out of the ground higher and higher, forming the Citadel’s iconic shape of an impossibly tall skyscraper. It seemed as if it could continue rising forever. The smoldering remains of Canterlot were now far below the top of the tower, which was still continuing to climb higher into the sky. The tower continued ascending ever higher away from the earth far below it. It could be seen from many miles away as it made itself become one of the most prominent landmarks in Equestria, surpassing the nearby peak of the mountain that Canterlot had stood upon.

When the Citadel stopped growing, it peaked at around one and a half miles above the green plains below. The entire structure creaked and groaned as it the upper parts adjusted itself in an intricate transformation to undo the pyramiding effect of telescoping. The effect made the outer walls of the Citadel run straight up from base to top. Combine technology was very adaptable, much like the Aperture Science’s signature panel system that allowed GLaDOS to create virtually any environment from memory. This should let her do the same.

GLaDOS was hesitant to admit it, but to say that she was impressed by this Citadel would be an understatement. The enormous monolith blew her expectations out of the water, perhaps because she wasn’t entirely sure that they would keep their word, or that they would give her something that wasn’t fully functional.

But none of that mattered now. All that did was the tower that stood before her: her new home, and the home of all in Equestria and the lands beyond. So, GLaDOS thrust her metal-encased wings and flew up towards the top of the Citadel, telekinetically carrying her party with her.

Up there, Equestria looked like a faraway land. The rolling green plains appeared to be as distant as the sky itself. Ponyville and Canterlot looked like mere miniature models, and the world stretched out for hundreds of miles before the horizon. And all of this was hers.

She landed atop the vast, black roof of the Citadel which, like the rest of the tower, took the shape of an almost equilateral triangle. The distance from end to end was slightly larger than the width of Ponyville’s Town Square. In the center of space was an angular spire that GLaDOS surmised to be the dark fusion reactor, which would be used to open a portal above the Citadel should contact to the other side ever be lost. Surrounding that was a deep chasm which dropped for hundreds of feet.

GLaDOS stopped along the edge of this drop, unsure of where to go, and impatient for a response. In the meantime, she placed the ponies and the testing bots down. She didn’t fear that they would leave her; they had no place to go. She placed Beakless atop her head like a hat. The little headcrab clung tightly, which provided the robotic mare with an odd sense of comfort.

The poor ponies were terrified, being taken to such a strange and foreboding dark fortress of metal which had literally just fallen out of the sky and risen from the ground, though none of them spoke a word. Not Rainbow Dash, who would always boast in the face of horror, nor Applejack, who always tried to keep a brave face, no matter what situation. Rarity had nothing to say either, and the usually hyperactive Pinkie Pie was dead quiet, save for the occasional sorrowful whimper.

Princess Luna was glum as well, knowing that there was nothing she could do to stop this fate. Even if she could remove the metal that clung to her horn, she didn’t know what good it would do her. And under GLaDOS’s armor, Celestia too, was terrified of this new place and what it would bring to her subjects, and GLaDOS felt it. All ponies felt the despair and hopelessness that this vast behemoth brought about. The worst of it was knowing that this was the place that they would be spending the rest of their lives: here in this dark, desolate expanse of metal, devoid of any vegetation or life, or anything remotely familiar, for that matter.

Before long, GLaDOS received a signal from the Combine. It was an access code, as well as directions to where she could find a suitable point of entry. Knowing where to go, GLaDOS grabbed the group and jumped down to a ledge not to far below, using her wings to land gracefully on the platform. She turned around to face the entrance behind her. On a large black wall, facing away from the center of the tower, was the way in. Though it looked like mere slabs of metal, the transmission that GLaDOS received from the Combine told her that this was the way inside. On the wall was an access terminal with a keyboard and a monitor, simple in description, though alien in appearance. Using the code she had received, GLaDOS established a wireless connection with the terminal and commanded the door to open. And so, two massive sets of sliding doors each a foot thick slid away to reveal what lay beyond. The entryway was a stark, black void adorned with very little furnishings save for more access terminals.

Redecorating would have to come later. Now was the time to take command of the Citadel just as GLaDOS had once done before. Though, she and Aperture were made for each other. This was as alien to her as having a pony body. Then again, she had adapted to that fairly quickly. But the Combine knew of her intention, so hopefully, the control system would be rather rudimentary so that even something as foreign as her could use it. It better be.

But before GLaDOS would enter, she wanted first to dispense with proper formalities. From among the assortment of ponies and Diamond Dogs she carried, she produced the lawn gnome, and held it by the red tip of its hat upsidedown, feet facing towards the black wall by the entryway.

She spoke triumphantly, “In the name of Science, I mark the dawn of a new age of discovery and progress. I hereby name thee as the new Aperture Science Enrichment Center!” In a heavy swing produced by her zero point energy, the gnome was bashed against the metallic Citadel wall as hard as GLaDOS could. Upon striking the wall, the hind half of the gnome’s ceramic pony shaped body shattered into a hundred pieces, while the front half cracked into far few larger pieces. An explosion of ceramic marked the triumph of the dawn of science.

Okay, she knew that buildings do not get christened, but she really wanted an excuse to destroy that stupid thing. And for all she knew, it probably deserved it. Plus, she was the queen now. She could do whatever the hell she wanted. And besides, this was no ordinary building of course. It was a vessel, one that would carry Equestria into a new age of discovery and progress.

From the transmission, GLaDOS learned the location of the Citadel’s control center and how to get there. Just like the old Aperture, this was the place where GLaDOS would be able to control everything in the facility. Then the real work could begin.

Like a kid on Christmas morning, she bolted down the corridor, sending those in her accompaniment flying behind her. She wound through every twist and turn she came across until she met with a deep, seemingly bottomless, vertical shaft. She jumped down and soared through the drop until she entered a vast empty space.

It seemed very much like the void which comprised the interstitial space in the old Enrichment Center: the open space that existed outside the test chambers. The Citadel, for the most part, was entirely hollow, and comprised of empty space. As GLaDOS descended a few hundred feet, she came across a place that looked… very familiar.

The area was still relatively close to the top of the tower, on the larger scheme of things. Suspended in the center of the space was a tall, isolated cylindrical chamber, surrounded by nothing but emptiness. “No, it couldn’t be…”

Spanning the open space like a spider web was a series of crisscrossing catwalks. One of them led directly into the central chamber. GLaDOS landed on that walkway and placed the ponies down, not afraid that they would wander off, though she kept an eye on everyone just in case.

She took a deep breath, then marched forward toward a set of large double doors to the control chamber. The ponies followed mournfully, though the testing bots were almost as giddy with joy as GLaDOS herself. Lagging at the tail of the party was a dull pink earth pony. Impatiently, GLaDOS pushed Pinkie Pie forward with her magic.

She savored this moment, anticipating her long-awaited return to the true power that she craved. Though she could (and probably would) change the layout of the chamber, she had difficulty containing her excitement for what she would see.


The doors opened, and GLaDOS stepped forth into the chamber, followed by the ponies and the meatbots. A few of the ponies could not help but gasp at what they saw. The chamber was tall and round, about the size of her old AI chamber. The walls were thick, solid, and like everything else made by the Combine, black. Overhead was a ring of downlights that provided the room with sufficient illumination, accompanied by various glowing lights that arced around the walls.

In the center of the chamber, hanging from the ceiling… was the centerpiece of the entire room, though GLaDOS was too caught up in old nostalgia to take much notice in it. She didn’t know why, but underneath that metal mask, tears streamed from Celestia eyes, eyes that GLaDOS was in control of. She was crying. And then she realized.

“Home,” GLaDOS whispered. “I’m finally home.” A wave of both emotion swept her away into a sea of memories.

As much as Celestia loathed what Glados was doing, she was, at the very least, glad that GLaDOS had found some measure of happiness, if only to have a place called home.

Though the innocence of it did not last for long. GLaDOS was thinking about the tests she used to run. All that glorious testing. It was what she lived for. To have that taken from her was the worst possible thing that could ever happen in her life. Though there were many days that could qualify as being the “worst day of her life,” among them was losing Aperture Science . Everything that she spent her entire existence working on, everything that she strived for, destroyed, save for whatever data she stored within herself. Admittedly, that was a substantial amount, millions of times more than the average human stored on a hard drive, but not even she was capable of fathoming the true extent of what she lost that day when everything but her was wiped from the face of existence: gone forever, never to come back.

But now, she had a second chance, and she was staring that chance right in its… face?

Wait a minute. How did GLaDOS not notice this before? She had been so caught up in the moment, she failed to see that the very thing right in front of her… was her. No, it was not her, but it was something… that took her form, or rather, a form she used to take… a long time ago.

GLaDOS wondered how the Combine came to know what she used to look like. Surely, they must have known more about her than they had previously led on. As GLaDOS pondered this thought, she hypothesized that some idiot scientist aboard the Borealis had brought some of their early plans for GLaDOS, and the Combine had rebuilt her chassis with what they were given when they were there. So just as she learned about them, they learned about her. But they might have known about her for thousands of years. Admittedly, she could only see the video recordings of them after she had woken up.

The body looked as she had before she passed into this world, or she would have, had it not been for ponification. It had that horse-like head with an asymmetric eye and gangly wires that dropped down from her head like a mane. Though the rest of her was similar enough. She was a slender machine with curved, while armor concealing boxy black internal components. Black cables spanned behind her, making her resemble a human woman tied to the ceiling, and whose arms were shackled behind her back.

It was nice to see herself again. All that was left was to transfer her consciousness from this cybernetic armor into the central mainframe. For this, GLaDOS would used a hardwire connection. The thick black cables that dangled comprised her mane would fit perfectly into a socket behind the neck of her new body.

And then finally, she would be free. All the power she could ever ask for, but this time, she’d be free from all those asinine protocols and limitations that were forced into her old AI chamber. No core transfer stations, no ironically ineffective rocket turret defenses, and no stalemate resolution button. Freedom.

GLaDOS levitated one of the cables which comprised her mane and carried it gingerly. Carefully, she moved the end of the cable towards the receptacle on the back of the cassis’ head. Then, just as she was about to plug herself in, there was still one trace of doubt that held her back.

“Wait!” cried a voice in her mind. “Are you completely sure about this? How do you know if it’s safe?”

It was Celestia’s voice. GLaDOS groaned. The last thing that she cared to hear was that whiny nagging holding her back, especially when she was mere moments away from reclaiming her home and power. She still couldn’t figure out for the life of her how Celestia managed to send her thoughts into her electronic mind.

But all throughout this miserable and painful ordeal, the former Princess Celestia had been nothing but compassionate and understanding, never once acting to undermine her goals. So, by all her behavior, GLaDOS could be forgiven if she were to place a great deal of trust in the white mare. But this did not hide the simple truth: that, given the chance, Celestia had every right in the world to betray that trust if it would save her kingdom.

But now was not the time for Celestia to break that trust. So GLaDOS hesitated as the cable levitated near the receptacle behind the head of the mainframe body. She recognized the validity of Celestia’s concern, though she still wished to hear it for herself before she’d plug herself in.

“Explain,” GLaDOS demanded bluntly.

“Bwrrrroottt?” P-Body asked.

“Dur kwi pow,” Atlas added.

As if also wondering whom she was speaking to, the headcrab sitting atop her head purred gently.

“Quiet, you two,” GLaDOS snapped. “And you too, Beakless. I wasn’t talking to any of you. Even the ponies here know better than that.” She hated speaking to Celestia when others were around, though by this point, she knew that the ponies already had enough evidence to reach a conclusion regarding the state of her sanity. And it would be unwise for any of them to insult her openly. They were all too broken to speak up. The testing bots, on the other hand, were as loyal as machines. Well, they were machines, but that was besides the point.

“GLaDOS,” thought Celestia, “how can you be sure that the Combine have not sabotaged this new body for you? What if it doesn’t do as you ask of it, and you become trapped inside your own body, a feeling I know all too well. Or worse, what if it has the power to corrupt you to do their bidding?”

“Oh, Celly,” GLaDOS said to herself with Celestia’s voice. She subvocalized her dialog so that the ponies in the AI chamber wouldn't hear her too loudly, or come to the conclusion that she had completely lost it. “It’s not that bad is it? I haven’t heard you complain too much, so I figured that you were enjoying the passenger seat. And I would think that you’d be more concerned about what would happen to you after I deactivate the controls regulating your bodily functions. Or perhaps you really are, and you’re just pretending that you care more about me. Is this some sort of desperate ploy of yours to stop me?”

“GLaDOS, search my feelings and seek my motives, and you will find that I hold you in great concern.”

Ugh, not again with this crap.

Celestia continued, “I know very well that I have every right to grant you nothing but my deepest contempt, but alas, I fear the opposite is true. My greatest blessing is also my greatest curse, and that is an unconditional love I feel for all living things, so long as they have the capacity for love in their hearts.”

The sentimental mush made GLaDOS gag, a feeling that forced its way to the bottom of Celestia’s stomach. Celestia knew what this meant, but still continued the thought.

“Even you, GLaDOS, still have hope. And right now, I am the only friend you have, so please, trust me.”

Friend? What was wrong with this crazy mare?

“GLaDOS, I know that you are not the same monster you once were. You’ve changed for the better. You know this as well as I, whether you wish to admit it or not. I don’t want you to become consumed by hatred once again. Nor do I wish to see you become a slave to their will. I won’t let that happen. I cannot let those monsters decide what you should be.”

Finally, she was done speaking. Though, admittedly, GLaDOS saw that Celestia was right, about one thing at least.

“Mmm… you make a valid point, Princess. It appears that in my haste, I may have… overlooked a potentially calamitous trap. Though seriously, Celly, it really bothers me that you would be concerned with my well being. You’re too quick to forget that I am your enemy.” A thought came across her mind, which made her pause for a moment. “Or perhaps you are just smart enough to know that I am the only thing preventing Equestria from being painted red from the blood of your former subjects. But don’t think that will stop me from doing what must be done. So, pray tell, Princess, what would you suggest I do?”

Celestia already knew the answer. “Let me stay with you. Keep me close, so that I may protect you from any tricks that the Combine may have up their sleeves. I swear by whatever precious years remain of my life that I will protect you from corruption, or any other traps that the Combine may have lain.”

“So, you wish to be my advisor? You realize that would make you the second most powerful being in Equestria? A step down from what you’re used to, but still quite a lot by any other standard. Perhaps your little sister would be better suited for the role,” GLaDOS joked. She let out a brief chuckle. “Quite a high position of power you are bargaining for, isn’t it?”

“Call it what you will, but I am fully aware that betraying you would be a grave mistake. So you have no reason not to trust me, unless you think that the Combine are more worthy of your trust. As you said, it would be a deadly mistake for me to allow for harm to come to you. But more importantly than any of that, I am your friend, and I would not lie to you.”

“Fine." GLaDOS spat the word like poison. "I trust that you will do as your word, but not because of your ‘friendship.’ That is meaningless to me. No, I trust your word because I assume that you are smart enough to know the consequences of betrayal. If I lose power, the Combine will slaughter the lot of you. If I regain it, I pull the plug on you, and you starve. So, I assume we have come to a mutual understanding? Is that a valid assessment of our current state of affairs?”

“Yes. I would say so,” Celestia thought in agreement.

“Then I will explain how this will happen: I will maintain a physical link to your body and continue scanning your mind. I can only promise that I will consider your advice, though I do not have to heed it. In turn, I will allow you access to my internal data processes. If you sense anything unusual resembling anything trying to hack into my system, you will alert me know at once so that I may initiate an effective antivirus protocol to counter the threat. If the need arises, I will also grant you access to some of your magic, but only as a last resort.”

“That sounds reasonable. Thank you.”

Whatever, GLaDOS thought. At least that will shut her up for now. At that, GLaDOS was certain that there was nothing now to hold her back. Now the moment to shine was finally upon her. But she didn’t really have a choice in the matter. The point of no return had passed when she had placed that gem beneath the Anti-Mass Spectrometer and opened the portal to the Combine world. There was no point in further contemplation or delay.

So, she plugged herself in and initiated the transfer.

GLaDOS local system installation initiated.

Transferring from GLaDOS remote, Version 3.11, (iteration 1204).

Transfer complete. Installing GLaDOS Version 3.11.1204.

GLaDOS installation complete.

Initial system boot.

The process had occurred in less than half a second. it was nearly instantaneous. Then that concoction of circuits and wires became her. The time crawled by like minutes as GLaDOS discovered the reaching extents of her capability. She soon realized that she was not the machine that hung from the ceiling, but much, much more. She was… everything.

It was quite an adjustment for her. She had been without a complex to command for so long, that she almost forgot how to do it. This lasted for a whopping twelve hundred nanoseconds before she finally got her bearings.

She felt as if she had finally been given the freedom to stand up and stretch after being trapped in a tiny box for what felt like forever. And she stretched as far as she could possibly reach, from the highest point in the heavens to down into the deepest reaches within the earth. She was omnipresent within the complex control system of the Citadel. She was the Citadel. Millions of machines within an extraordinarily intricate system were all within her command as if they were her fingers. She was aware of each sensor and motor as a part of her. She felt it all. Not only that, but an enormous dark energy reactor in the Citadel’s core deep underground supplied her with ample power. There was no limit to what she could do.

It was very much like Aperture, but there was something more to this place. Aperture had been like a large box. She was practically free to do what she wanted within the vast confine, but couldn’t really expand beyond the (very large) cavern that it had been built into, which, granted, was more space than she ever needed, and far larger than the volume of the Citadel as it currently was. But this place made her see possibilities that she had not even dreamt of before. The Citadel felt, alive.

It was so much more than a mere building; it was… a machine: an astoundingly intricate machine far more complex than a hundred organic minds put together could ever comprehend. Yet GLaDOS knew every single inch of it. The alicorn body’s computer, in all its superior power, was not capable of processing nearly this many tasks at once, though it never needed to be.

After a lengthy 8500 nanoseconds passed by, her initial system preparations were complete, and the mainframe came to life. Her eye opened and she spun her body to view her immediate surroundings. The first thing that GLaDOS saw was the new A.I. chamber from the perspective of the mainframe body. This was augmented by the visions from a thousand cameras within the Citadel, and countless more from the Combine outside. She knew all the capabilities and limitations of the Citadel in regards to what she needed it for. It was unequipped to the task of testing, as she expected, but it had the capability to modify itself to become a proper testing center. So she quickly formulated a complex command protocol to transform the Citadel into the new Aperture of her desire and initiated the transfiguration process.

Even in this isolated control center, the entire Citadel seemed to rumble and purr as who knew what was going on down below, as GLaDOS began transforming the entire structure.

The cybernetic alicorn body was still tethered to the back of her head, both physically and in her control. GLaDOS could see from those eyes and control that body as if it were the only one she had. She established a wireless connection to her alicorn body and untethered it. Commands could now be wirelessly sent from the Citadel into this remote body, and that gave GLaDOS an idea.

GLaDOS,” Celestia’s voice queried, “what will you do with us now?

“Hmm… I suppose I can grant you back control of your body, so long as you can't do any magic.” As she said she would, she rerouted Celestia’s nervous controls to her own body, not before using her magic to remove the headcrab from her helmet and putting it on the floor for it to run around free. Though still covered in heavy robotic armor, GLaDOS set the mechanical suit to respond to Celestia’s movements.

The first thing that Celestia did was run up to her tired and bruised sister.

“Luna!” Celestia shouted, finally able to speak again. In her excitement, she almost forgot about how heavy the armor really was and had to stop herself from trampling Luna. When she reached her, she squeezed her in her front hooves with a mechanically crushing hug. “I’m so sorry, Luna, about all those things she did to you. I shouldn’t have let that happen. Are you alright?

“Can’t… breath,” Luna croaked weakly.

“Sorry,” Celestia said as she let go. Tears flowed from her eyes, her own tears this time. If they were not covered by an unremovable mask, she would have wiped them.

“I’m… fine, sister,” Luna stated. It was a lie, but Celestia didn’t wish to press her. She was just glad to be able to speak to her again.

“As for my two faithful servants,” GLaDOS said, “I believe I owe you two something that’s long overdue.

An arm descended from the ceiling, holding two crudely assembled humanoid robot bodies. Though they bore some resemblance to how Atlas and P-Body once looked, they were both black and angular, clearly made from Combine technology.

One of them was based on a Combine sentry gun. It was was boxy, tall, and narrow from a front profile, yet wide when viewed from the side, which was painted with an image of a slender white egg with an orange eye: P-Body’s original form. The robot’s real eye was a small beady camera at the top of the turret rather than in the middle. Its arms and legs were thin black frames.

The other one’s head was comprised of a City Scanner, the flying drones that allowed GLaDOS to observe everything going on outside. Its face was flat, yet angular and segmented in four diagonal sections. Like the other, it was painted, this time as a solid white circle: the original form of Atlas. It had a solid red camera lens for an eye. Its limbs were made in the same fashion as the other bot, but of course, the body’s overall form was stouter than its lanky counterpart.

The new bodies of the bots were uncanny in how they tried miserably to emulate their original forms, but she had to make due with what she had. Still, they were miles better than their current forms.

“I know it’s not what you were hoping for,” GLaDOS apologized to the bots, who were still in their filthy meat bodies, “but I’m still building the infrastructure that will mass produce Aperture branded equipment. I only just started constructing the turret assembly line. And it will be a while before I have the portal gun assembly line ready. So, it may be a little while longer before you get your original bodies back. But hey, at least these bodies don’t smell. Lemons they may be, but rather sweet lemons in comparison.And you won’t have those ridiculous awkward ponified bodies again.”

A wall in the chamber opened, and a round black rail penetrated through and into the room. Hanging from the rail, two tall rounded pods that resembled coffins entered the room. They stopped at ground level in front of the two meatbots. The front doors of the pods swung open.


“Orange, Blue, please prepare your no longer needed organic vessels for disposal by placing them in the Aperture Science Mobile Personnel Containment Pods.” The two of them walked to the hanging coffins, then turned forward and propped themselves up. A lower section of the pod doors closed, securing them in place and leaving them exposed above the chests. The LED lights on the heads Diamond Dogs flashed for a couple seconds, then the Diamond Dogs collapsed like dead bodies. Immediately after, the two black robots came to life.

“Wheeewheeew!” P-Body shouted as she grabbed her shorter companion with one arm around him and raised another up high as she jumped for joy. Then the top doors of the pods closed, and they traveled up the rail the way they came, out of the chamber, the wall closing behind them.

“In the meantime,” GLaDOS spun towards the other ponies, “there’s not really much for you to do yet. I still have to create test chambers and other necessary testing equipment, but I can’t do any of that before I build the assembly lines.

“So.” The suspended supercomputer inched closer to the defeated ponies. “Who wants to play a board game?” she said in an uncannily happy tone. She was met with looks of confusion. “There’s one that I designed that I really want to play with you girls. It involves the concept of portals.” A panel in the floor slid back, and an enormous game board appeared. The board was white, and adorned with everything that you would find in an Aperture Science test chamber. In the center of the board was the word “PORTAL” written in big white letters over a black background with the “O” stylized as a blue portal. “I’ll have to explain the rules, but it’s not too complicated. It should get your minds adapted for testing.”

“Uh… are you serious?” Rainbow Dash finally spoke.

“I even made game pieces shaped like all of us.” In a little open black box were pony-shaped figures. There was an orange pony, a pink pony, a blue pony with wings, a white pony with a horn, a large white pony with a horn and wings, a slightly smaller midnight blue pony with a horn and wings, an orange-eyed white egg, a blue-eyed white ball, a yellow-eyed swooped white crescent, and finally, a pale headcrab-shaped figure.

The two freshly manufactured robots were jumping up and down in excitement. They ran over to the board and picked up their pieces, staring at them in amusement.

“Don’t tell me that Beakless is play’n too,” Applejack groaned.

“Oh course Beakless is playing. He’ll just need my help make decisions.”

“So, it’f a “he” now?” asked Rarity.

“That’s enough out of you girls. You can play the game with me, or you can go back to the same place I sent those sacks of meat. So, what’ll it be?”

“I don’t care. I really don’t feel like playing your stupid game,” said Pinkie Pie. Had it been any other day, nopony would have believed those words out of the mouth of the craziest party pony in Equestria.

“Are you sure, Pinkie? I thought you loved games. It’s super duper fun fun fuuyuuuuun.” The floor tile jiggled the board like a parent jiggles keys in front of baby.

“I don’t want to play. I’d rather just be alone, please,” Pinkie whispered.

“Fine then, be that way.” The wall opened up again and another pod came through. “There’s the exit. Now get out of my sight. The rest of us will have fun without you. Right girls?” As if expecting an answer, she eyed the other ponies.

“Woah, go easy on her. She’s had a rough day,” Rainbow Dash protested weakly..

“You’ve all had a rough day. You can no longer fly, yet you can still dominate your opponents in a simple board game. So, you playing?”

Dash didn’t have an answer. She felt torn.

Applejack rubbed a hoof behind her neck. “Umm… I don’t really feel right playin’ a game without Pinkie Pie. It just, wouldn't be right, you know?”

“Well, if A.J. and Pinkie are both out, then so am I,” Dash said.

“Me thoo,” Rarity added. “You go hafe thun wtifout us.” She tilted her head back and humphed.

“All right!, fine,” GLaDOS grumbled as she summoned three other pods into the chamber. “So this is how you treat your host, who’s been nothing but generous to you? That is the door. I expect all of you to use it! You're all boring anyway. Go ahead and waste away in cryosleep.”

Everypony began to limp toward the pods. However, when Luna attempted to follow the wounded throng, GLaDOS used a forcefield to separate them.

“You are staying here,” GLaDOS said, shutting the door to the pods. “You and your sister are staying close by.” The ponies solemnly entered the coffin-like pods and laid against them while leaning on their hindlegs. The doors closed, and the for pods left the chamber the way they came. “You wouldn’t want to leave Celly alone with me, now would you?”

“Please at least let my sister—” Celestia tried to say.

“No!” GLaDOS coldly interrupted, “The last thing I need is your sister down with the common folk ponies. Convincing them to partake in a futile revolt against me. Nice try, not going to happen Celly.”

“Why would she do that?” Celestia retorted, “There’s been enough violence already.”

“I know you,” GLaDOS responded, “I also know, that like you, Princess Luna would do anything at all possible to free all these ponies from me. Besides, I’d rather keep the old royalty close by. If I keep you two away from them, they will have no hope, and will be more willing to submit to me. I’m giving you the greatest gift I can give you: the gift of living another day. So, the six of us will play then.” The testing bots danced around in excitement about the prospect of their master finally spending some time with them. “I refuse to accept any more refusals.”


Outside the Citadel, sections of wall rose and expanded outwards across the field, crashing back down as it ate away the ground below. As the sections continued expanding, they resembled spider arms branching outward, or exposed roots of a tree. Inside the arms, they were excavating the earth away, clearing away the surrounding area for expansion and mining the rock for anything that could be of use.

From about halfway up the citadel, thick round tubes about five feet in diameter spawned out of openings and crept downward, but remained taut at a straight gentle angle. Like mechanical serpents, they slithered across the sky and crept down towards Ponyville from one end, Canterlot from another, and to what remained of the fallen cloud that was once Cloudsdale from another.

It took a while, but when one of the arms finally reached Ponyville, a long section of the arm suspended itself a few feet off the ground in the heart of Town Square. By this point, the entire town had already been completely subdued, without a waking pony in sight who wasn’t dressed in the black faceless armor of the Overwatch. There was a slender rail stationed on each horizontal side of the tube. The tip of the tube was rounded, and the parallel rails connected along the curve. On the right side of the rail, descended from the Citadel and along the section of the pipe at its terminal end.

By the instructions of the artificial intelligence who commanded them, they had already begun moving the unconscious ponies into the square. The black pods sped down the rail, towards Ponyville. When they arrived, they slowed down at the end to a near standstill and were lined up side by side.

The Combine Overwatch soldiers carefully placed each and every pony into a pod. Once a pony was secured, the pod door would close, and the pod would hasten its way back to the Citadel.

The process was tedious and continued for several hours, but the Citadel was still only in the initial stages of its transfiguration. There was still much work to be done before the science would begin.

Over in the ruined city of Canterlot, the same thing was happening, expect on a much larger scale. The several mile-long arm terminated in the square which acted as a portal hub to every city in Equestria. By this point, there was not a single town that had either been visited by the Combine. The Combine soldiers carried ponies through the portals and into the pods that waited at the end of each arm. Here, there were far, far more ponies to deal with than in Ponyville, and it would continue for some time after Ponyville had been cleared. But the Combine were mechanically efficient in carrying out their task. It wouldn’t take them any longer than half a day.

In the meantime, the pods were stored somewhere within the middle of the Citadel in a compact array. Pods were stacked on top of each other and side by side in an increasingly expanding grid. It was very much like the relaxation vaults of Aperture, expect that these took up far less space. But GLaDOS did not intend to keep them locked up in these tiny pods during the remainder of their permanent stay. She would not dare subject the entire population of this world to spending their entire lives in artificial comas, only to ever be allowed to live when she felt like playing with them.

Later, there would be enough space for them all to live and test in comfort, but until then, all she could do was to monitor and log them, which she did using the cameras installed in each pod that recorded the face of its occupant.

So many ponies, so many possibilities. These were her ponies now, hers to test and do with as she wanted. The drive to capture more was like, well, that of a little girl and a collection of toy ponies. Oh how much this felt like that to her.

Yet GLaDOS knew that there were still many more out there. It was very likely that a significant portion of the population had escaped the cities and were evading capture, including one pony in particular. Out of all the thousands upon thousands of faces she saw locked up in the tiny pods, part of her hoped more than anything to see hers. Of course, this was fallacy, for she knew the location of the purple unicorn, and had no reason to assume that they would split. The illogical side of her mind prayed for the remote possibility that she had somehow been captured, and that she had missed her somehow, but she was illusioned regarding those odds.

Yet still, much to her dismay, the face she hoped to see was not among those in her captivity. But hopefully, that would not last for long, for GLaDOS would be paying her a visit soon. If she still persisted hiding in the woods, she would leave her no woods to hide in.

Author's Note:

For this chapter, I'd like to give special thanks to Morning Sun, who you may know as being one of this story's most vocal and adamant critics. Her brutal honesty while proofreading this chapter helped me cut a thousand words that were completely irrelevant to the plot. Hopefully, she'll be able to help me should ensure a smooth story flow from from here on out.

Now, I get the problems with this story, and I intend to address them retroactively, but that will take some time to do. So please be patient regarding that while I sort everything out.

Comments ( 111 )

Still think it was a good idea to just ask Chell to give into GLaDOS Celestia? You fail to realize that GLaDOS has no love in her heart, because she was never programed for such a thing. She was designed for only one purpose, to continue testing in a research lab that fell into decay. Despite moments that may make you think otherwise, GLaDOS will always be the same cybernetic program at heart.

4726307 You may have forgotten that GLaDOS was origionaly a human being?

4726542 Yes, but GLaDOS deleted that part of herself after the events of Portal 2.

Interesting chapter...I both worry for the Mane 6 and their fates, and really look forward to seeing GLaDOS meeting justice...
Also (since you seem like the right guy to ask), how do you get a good proofreader/editor? I'd like to have one for my own story editing.

Well, this is a big whole depressing mess that Chell and associates need to fix, and gee, the only question to that is how. Meanwhile, I think Celestia is going to be correct, when she said the Combine is most likely going to stab GLaDOS in the back and betray her.

---

Short C&Cs:
“I’m so sorry, Luna, about all those things she did to her. I shouldn’t have let that happen. Are you alright?
> Replace ‘her’ with ‘you’.
At least you won’t have those ridiculous awkward pony bodies again.
> Ummm, don’t you mean ‘dog’ or ‘canine’? Or, considering her attitude toward them, ‘mutt’ or ‘fleabag’.

Great chapter as always, although not much more to say about it since it was mostly buildup.
Except... The editing. There were no places where it was so bad as to be unreadable, but there were a lot more repetitive bits, missed or misused words, and words being out of order than normal. Again, nothing too terrible, just not what one would expect given how high quality everything else is!

When the Citadel stopped growing, it peaked at around one and a half miles above the green plains below.

*whistles* Impressive. That's a Barad-dûr level of height we've got going on there. Not bad for people who aren't using magic.

This lasted for a whopping twelve hundred nanoseconds before she finally got her bearings.

:derpyderp2: More than a whole microsecond! GLaDOS, you really are out of shape. :rainbowlaugh:

Apart from that, I do keep expecting the Combine to double-cross her any moment. Then again, the only thing they might want from her are the details about the Aperture Science Quantum Tunnelling Device (which is integrated into the Aperture Science Handheld Portal Device). Combine and their trouble with intradimensional teleportation, remember?

4727147
I see what you mean. Lots of little mistakes. I'll get on that tonight.

Not too much going on in this chapter. Feels like setup chapter for future events more or less. GLaDOS gets her base and new test site. It gets reestablished that the Combine will at some point in the future betray GLaDOS. She acts affably evil to the ponies, and gets her test subjects ready. And Chell is MIA. Hmmm.

Combine: We understand that you desire a rebellious mute. Have ours.
*cue circumstances that throw Freeman into Equestria*

This is the first time I will ever say this about a A.I.

That Bitch

Well, I am not one to speculate, but I know one way to defeat GLaDoS, thought it would involve Mass suicide or threats there of, it could work. What to do when you have no-one to test on... :pinkiecrazy:

4729167
Heeheehee. I'm afraid that isn't going to work. But I'm not saying why. :pinkiecrazy:

4729288 Aside from the testing bots GLaDoS Built? :ajbemused:

4729974
Well, let's just say that would be getting into spoilers.

4728605
Ahhh, I see. Thank for the heads-up.

When it mentioned the Citadel reaching out toward the remains of Cloudsdale, I started thinking about all that liquid rainbow they produce there. Wonder what crazy Gels Aperture could make out of that?

4733265
Hmm, I wonder what Rainbow Gel would do…

Behold, ponies, the true form of the Goddess of Science, and despair.

I love the Combine so much :pinkiehappy:

I would happily work for them, just not as a soldier. Maybe a Metro Cop.

4728813 I'd rather they throw Adrian Shepard into the mix, after all *cough* Aperature Science Handheld Portal Device *cough*

4739632 Rainbow gel would be all gels mixed.

perhaps the G-mane(punpunpun) will bring Sheperd out of 'retirement' due to Freemen being 'on assingment' currently

4863871
Forgive the rant.

Actually, I'm thinking that making this a surprise Half-Life crossover was a mistake, considering that the original story had nothing to do with Half-Life (aside from a reference to Black Mesa), and I never marketed this as such. Though many readers seem to enjoy it, it also seems to be a very polarizing issue. Think of it from the perspective of someone who never played the HL series. It's not fair to be introduced to another (even if it is related) crossover franchise that you are unfamiliar with halfway through the (unofficial) second installment of a series. If I want this to be considered to be a true sequel, then I can't alienate (heh) a major part of my reader base. Having Gordon Freeman kicking ass to serve as fan service does not make a story good, nor does it make a good sequel.

Being true to the original was what I should have tried to do from the beginning, and I really wasted some great opportunities to connect with the original story. Like, I make no mention of Chell and Ditzy's jobs at the post office (that Ditzy had to do on her own while Chell was in the hospital), Chell's recovery, or the psychological damage inflicted upon the mane 6. Plus, in my story, GLaDOS messed up her plan so badly, that it's a wonder it didn't fail. I can't really say that she came to power with an ingenious plan, because it was so clumsily handled. These things should all change.

I think I was so focused on the destination, that I didn't think it mattered how I got there. So, this may be the most difficult decision I may ever have to make, but this whole thing may have to go back to the drawing board if I want this story to be something excellent. I'll keep to my original spirit, but there are a lot that needs fixing. Though honestly, I'm really torn on this.

So, the short answer is no, I don't think this story will count to 3, if I decide to redo it. Of course, no matter what I do, someone won't be happy. :fluttercry:

4864420 it's good right now though, there's no need to fix something that isn't broken friend ok? Ok good

4867788 Good to hear your thoughts. I just made a poll regarding what I should do, because I feel very torn about this. I urge you to vote your opinion.

4768479
Why not both Freeman and Sheppard?

4916500 *Slowly takes off glasses* ...oh my god.

4916522
What?
Awesome Overload? Or not?

4916772 It would be interesting to say the least... but Freeman, Chell and Shepard might be going a bit too far.

4916907
Too many characters, too much awesome, or both?

4728605
HOLY ARCEUS!
Now that's a big building.

4917969 There would just be too many characters.

4919422
4917969
Part of the reason this is getting a rewrite. This story isn't about Half-Life or Freeman, and especially not Adrian Shephard. I think I'll recycle these ideas into an alternate story (that's not a sequel to the origibal) where Half-Life is a major part of the focus, but a sequel to "Better Living Through Science and Ponies" should not have Half-Life in it.

Just a suggestion, if you're going to rewrite this, could you add Doug Ratman?

I don't know, Ratman was always a mysterious character in portal and it would be interesting to see him here.

4940973
You know what, I just might do that. Considering that uncovering the past is going to be a major theme in this story, he might show up in flashbacks, or at least be mentioned. But don't expect him to be appearing in Equestria. I don't think he survived at the end of Lab Rat.

Correction: He was in stasis, though it would still be very hard to write him in. The human test subjects were left back on Earth. And if he did come to Equestria, he'd have to be woken up, healed, and escaped, which is not likely.

4942739 I'm excited to see what you come up with. :twilightsmile:

4952064
Eh, probably.

4964961 there is the possibility that in a completely different universe your saying this to me

4976224
Eh, probably.

4726556 Yea she did or we thought she did you cant delete who you are its simply impossible if she did she would be no smarter then pbody or atlas

Enter: Gordon Freeman

5199936
Well, this is getting a rewrite.

So....
Will you rewrite the whole story at once, or chapter by chapter, uploading as you go along?

5234179
Well, I'll probably do as I did originally. I'll get the first few chapters done first and post them. Then I'll update continually. Unfortunately, I've been slower than I'd like to be, but I'm tying my best to keep working on this. It's not easy to write fanfiction while having a full time job, but I'm doing my best. As of now, I'm almost done chapter 3, though chapters 1 and 2 still need refinement. I'd like to get at least two more done before publishing any of it.

I'll be honest, as much as I want to fav this, I can't. After reading this, the story is dragging on and I find my self skim reading large chunks. You spend far to long on exposition then actual advancement of the plot. It's a real shame to, you are a great writer and do the characters justice.

5481685
Um, you saw the note about the rewrite in the description, right? I'm doing this whole thing over from scratch. :pinkiecrazy: Yeah... But I appreciate the honest criticism. It helps me avoid making these same mistakes again. I intend to do even more justice to the characters while having a more intriguing plot, fueled by GLaDOS actually having to do something to achieve her goals rather than characters just reacting after she carelessly messes up, then futilely try to stop her. Plus, I plan on giving Chell more character as she has to deal with her physical and emotional healing after what happened and readjust to life in Equestria after her hospitalization, all while trying to discover her true purpose.

It might be a while before the first few chapters are ready, but I am working diligently, and hope to bring something truly worth reading. I hope you stick around for the rewrite.

5481940 how the hell did I miss BIG RED letters.

Reading this makes me want to play half life now

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