Generator Rex: Project Equestria

by Hunter X

Rating: everyone
Tags: Main 6, My Little Pony: Friendship is Magic, Crossover, Human
Length: 4625

Black Knight finds a way into Equestria. Generator Rex crossover story.

In the midst of the hunt for the Master Control Nanites, Rex discovers that Black Knight has been working on a secret project involving alternate universes. What has Black Knight found that warrants such a change in priorities, and what impact will it have on the war? The answer will decide the future of two worlds...

This story may contain spoilers regarding Generator Rex, up to and including the season 3 finale. A basic knowledge of the show helps, but the relevant points are explained for those who haven't seen it before.

Published 2012-05-21 22:44:01 UTC
Last updated 2012-10-24 10:17:18 UTC

Prologue

"Gentlemen, I have already explained to you why we have to go forward with this project. All I need is your support."

Black Knight leaned back in her chair as the five faces on the monitor frowned at her. She'd spent the past half an hour on the line with her employers, trying to explain the mechanics of her plan and what it could mean for them, and it seemed all her arguments were falling on deaf ears yet again.

"We don't have to go ahead with anything, little lady," one of the faces spoke up. "We are the ones in control of this operation, not you."

Vostok. A former KGB agent, he was easily the most awkward of her employers to deal with and frequently took every opportunity to wave his alleged 'superiority' in her face. He had an annoying habit of referring to Black Knight as 'little lady' whenever he could, a trait that she found particularly aggravating. The two had almost come to blows on several occasions, and Black Knight had long ago vowed that he would be the first to go once she no longer had any need for her 'employers'.

"I agree with our Russian friend here," said another voice, this time Texan. "We've got no idea that this little project of yours is gonna work, and we hardly have the time to go chasing after some trivial discovery."

"I respect your concerns Mr Roswell, but I would hardly call this breakthrough minor." Black Knight responded, hiding her growing impatience behind a well-practised smile. "I've told you what this discovery could mean for us, and I highly recommend we- that is to say, you, should pursue it."

Roswell didn't look convinced. "Minor or major, it hardly matters. This thing is going to take time, and the longer we spend working on some side-project the less likely we are to find the Master Control Nanites before-"

"If this project works, we won't need the Master Control Nanites."

That shut them up. Black Knight's fake smile changed to a genuine one as she watched the expressions of her employers shift from impatience, to shock, and finally to contemplation. She could see the wheels turning in their heads as they considered the possible implications of what she had said. Her employers might not understand the science behind her proposal, but they could all spot an opportunity when presented with one.

At last, one of them spoke up. "If the project works."

"I assure you gentlemen, you have nothing to worry about. My top scientist assures me that everything will function as planned once we go ahead. By this time next month, we will be ready to end this petty war and you will finally get what you've waited five years for."

There was another pause, albeit far shorter than the last. Black Knight could tell she had won long before they responded. "Very well Black Knight. You are clear to proceed with this project." The screen clicked off, and Black Knight smiled even wider. It had taken a lot of effort, but now she could carry on with her plan unhindered. Her gaze shifted to a second monitor nearby, displaying the report Caesar had sent her only a few hours earlier. In it were plans for a new device that he had created. A device that, when applied correctly, would make even the power of the Nanites seem insignificant and obsolete.

In just a few short weeks, Black Knight would at last be able to win this game once and for all.

Chapter 1

Rex crept slowly through the corridor, suppressing the urge to cough as he did. The cloaking device built into his suit might keep him hidden from the Providence guards not ten metres away from him but it did nothing for sound, as he had unfortunately discovered on several occasions. Glancing behind him he could see nothing, though he knew Six and Doctor Holiday were close behind him, each equipped with their own cloaking devices. Rex paused briefly to allow the guards to continue on their patrol, his mind drifting back to the conversation he'd had with his brother a few hours ago.

"I wouldn't be asking you if this wasn't important Rex," Caesar had protested. "but I can't do this without you."

It was a stupid idea coming back to Providence headquarters. Ever since their little break-in attempt a few months ago Black Knight had been overhauling the security of the monolithic structure, and if they were caught it would likely mean game over for humanity; Black Knight would collect the remaining Master Control Nanites without opposition, and the Consortium would use them to gain full control over reality itself. The only reason that they were here is because Caesar claimed that this was even more important, though Rex had no idea how.

"You know Black Knight. She would only be doing this if she could gain something from it."

White Knight had heavily opposed the whole idea, calling it reckless and ill-informed. Caesar had retaliated by pointing out that anything Black Considered more important than the Master Control Nanites was worth looking into. Rex had been divided on the issue - on one hand, he wanted to trust his brother and to stop whatever Black Knight was planning, but on the other hand Caesar was in fact working for Black Knight at present.

"How do we know this isn't a trap?" Rex had asked. "Every other time we've met, you defended Black Knight's plans. Why so eager to get on her bad side?"

"That was different. The Nanite program is necessary to finish what our parents started. This could end up being far, far worse.

"Please hermano, I need you to trust me."

In the end, they had agreed to meet Caesar and see his evidence in person with White Knight and Bobo staying behind to guard the Master Control Nanites they had already collected, bringing Rex back to the present. The guards had passed by without spotting him, and Rex continued his crawl through the corridor. His brother's motives might not always make sense, but he was offering them a way to stop Black Knight from getting hold of something incredibly dangerous, whatever that turned out to be. It could be a trap of course, but Rex had managed to escape from worse predicaments in the past. Finally reaching the door to his brother's lab, he glanced down the corridor one more time before entering the code Caesar had provided him into the nearby keypad.

The door slid open with a hiss, and Rex readied himself to take out any would-be attackers behind it. Thankfully the room was empty except for surprised looking man in his early twenties. "Is that you Rex?" he called out.

Rex pressed a button on his suit and faded back into visibility, as did Six and Holiday behind him. "Alright Caesar, let's make this quick. What's so important that you're willing to betray Black Knight?" Caesar walked over to a nearby console and pressed a few keys, bringing up a series of complicated schematics and mathematical equations.

"A few weeks back I finished a design for a multidimensional relocation device. A cross-dimensional portal, if you will. At first it was just a project I was working on in my spare time, but Black Knight took an interest when I submitted a request for additional resources."

Holiday looked over the plans for the device. "This portal uses the Einstein-Rosen wormhole theory. Why would Black Knight be interested in a theory that's existed for years?"

"Up until now, nobody's managed to make it work." Caesar continued. "More importantly, I discovered that the laws of physics function differently in some dimensions. My theory is that Black Knight thinks she can harness that somehow."

Six raised an eyebrow. "You're not certain?"

"Once I finished constructing the portal Black Knight took full control. She took a team through the portal last week and orders additional troops and sealed containers to random locations every couple of days. Whatever she's found through there, she doesn't want anybody knowing about it."

"How much has she sent through that portal?" Rex asked, half-dreading the answer.

"Enough to set up a sizeable base on the other side. I don't know what was in those containers, but it could be anything from building materials, to weapons, to devices I don't even know about. Black Knight has put a lot of effort into this project, and she wouldn't have stayed there this long if there wasn't anything of interest there."

"That settles it." Rex decided. "Whatever Black Knight's up to, it's big and it's dangerous. We need to stop her."

"I was hoping you would say that brother." Caesar replied, smiling. "I've been warming up the portal for you ever since you agreed to meet me." Another tap on the keyboard opened a second door nearby, and the group walked through to see a large, circular device suspended at the end of the room. A number of wires were attached to the device and the inner edge of the ring was glowing faintly. A ramp had been positioned just in front of the device stopping just short of the inside of the circle.

"I can't send you directly to Black Knight, but I can get you close based on the average locations of the supply requests." Caesar adjusted one of the dials on a nearby control panel as he spoke, the edge of the portal glowing brighter as he did. "Once you go through, you'll have to find her base on your own."

The portal began to hum, and Rex could see the inside of the circle begin to shimmer. "Won't Black Knight know you were the one to send us?" Despite their differences, Rex had no desire to see his brother face Black Knight's anger. Caesar's only response was to smile knowingly.

"You've broken into my lab before. As far as she's concerned, I've been doing field research all day." The portal was buzzing loudly low, and the inside of the ring was rapidly being filled by a bright circle of light. "The portal should be ready in a few seconds!"

Rex looked back at Six and Holiday as the portal continued to gather strength. Holiday smiled back at him while Six simply nodded, and Rex knew they were both ready to follow him to wherever the portal might take them. A moment later the room shook, the portal now filled with a bright light. "It's ready!" Caesar shouted over the noise. "Get through before it closes!"

Rex passed through the portal, and everything went white.

The first thing that Rex noticed about the place was how... normal it looked. The portal had led to a forest, with a thick canopy of branches and leaves blocking out most of the sky. "Really?" Rex asked. "We could've landed anywhere, and we end up somewhere exactly like Earth? Talk about an anticlimax."

Six adjusted his tie as he looked around the area. "Don't let your guard down. Black Knight wouldn't be here if it wasn't special in some way."

Holiday pulled out a small device, pressed a few keys, and frowned at the result. "Odd," she said. "None of my scans are responding correctly. Guess we'll have to find our way around the old fashioned way." Picking a direction at random, the three of them set off.

"I wonder where Black Knight is." Rex thought out loud. They had been walking for half an hour but had seen no sign of Providence's mysterious leader, nor any of her pawns. A standard Providence installation would have spotted them long before they reached any structures, but there had been a distinct lack of bullets directed at them on their journey through the forest.

"If there's any civilisation in this universe she'll probably have set up nearby." Holiday answered as they continued walking. "Our best bet is to find that first, which should lead us to Black Knight."

They walked on in silence for the next few minutes, passing a river as they did. Thankfully the water level was low at their location in the river, allowing the three of them to cross with relative ease. As they crossed the river, Rex could have sworn he heard some kind of roar in the distance, though he had yet to see anything more than a couple of birds in the forest - a troubling fact in itself considering a forest of this size should be teeming with life. Tightening his fists, Rex pressed onwards, though not without glancing around to make sure whatever had made the noise wasn't heading towards them.

"Something about this forest is giving me the creeps." Rex muttered as they walked.

"I'm more concerned about why none of my scans are working," Holiday responded. "This device is designed to take accurate readings under intense weather conditions and radiation levels, yet it's acting as if there's nothing for it to see."

Six pointed ahead of them. "Looks like you won't have to worry about that much longer Rex." A little way ahead of them was a gap in the trees through which daylight could be seen. Sighing in relief, Rex picked up the pace, eager to get out of this forest as soon as possible.

Just before they reached it however, something passed through the gap heading towards them. It was about half Rex's height and coloured deep purple, with some kind of horn protruding from its head. The thing's face displayed an expression resembling shock, then fear, then a fierce determination. It was clear it did not want to let them leave the forest.

"So that's Black Knight's plan!" Rex exclaimed. "She's creating an army of EVOs in this universe, so she can take them back to ours! Well, she's not gonna get away with it." Bright blue lines traced intricate patterns down Rex's arms as the nanites deep within his body activated, which then expanded and re-solidified into giant robotic hands. Rex began to sprint towards the EVO, but only managed to take four steps before being blown backwards by a blast from the creature's horn. The force of the attack shattered Rex's hands, leaving just his normal arms behind, but he spun in mid air and landed safely upon a pair of newly-formed robotic legs and charged again. This time, when the creature tried to shoot him down he was ready for it, and swiftly jumped over the blast.

The EVO's expression changed back from determination to fear, as a glowing purple sphere materialised around it. Rex landed right on top of the bubble, causing it to ripple slightly but hold. Jumping off the shield and allowing his legs to return to their normal form, Rex rebuilt his robo-hands and began pounding away at the purple orb in an attempt to break through. Holiday shouted something, but Rex paid no attention as the shield began to crack. A final punch shattered the barrier into a thousand pieces, the creature collapsing from the strain of holding the shield together.

Rex approached the creature. "Alright little EVO, time to cure you." Holiday called to him again, sounding very concerned.

"Rex, I don't think that's-"

"Just a second doc, I gotta cure this thing before it wakes up." The creature stirred slightly, but appeared either unable or unwilling to stand back up just yet. Rex knelt down and placed a hand on the creature's body. The same blue patterns as before expanded across the creature, spreading out a few inches around his hand. As they did, Rex's expression rapidly shifted to shock and disbelief. He lifted his hand and the lines vanished, taking a step back from the creature.

"It... it's not an EVO!"

Chapter 2

Twilight's head felt like it was spinning. The lavender unicorn struggled to remember where she was and what had happened to put her in such a state.

"...I don't think..."

Unknown voices echoed through her skull. She recalled heading into the Everfree Forest to borrow some supplies from Zecora, but something had gone wrong...

"...Just a second doc..."

Memories stirred at the sound of the voices. She had just entered the forest when she had found herself face to face with a trio of monsters, one of which had attacked her on sight and presumably knocked her unconscious for a short while. The thing had been using some kind of magic to alter its body, but the only spells Twilight knew of to perform such a feat were lengthy and exhausting - this creature had been changing its appearance every few moments as it attacked.

"It...it's not an EVO!"

The startled cry brought Twilight well and truly back to reality. The monster was standing right next to her! It took every ounce of her self-control to avoid screaming and running, as she was certain it would be able to easily catch her in her weakened state. No, if she wanted to escape she would need to wait until it was distracted or better, left entirely.

Twilight heard the creature take a few steps backward, and risked opining her eyes a crack. The three creatures were tall and bipedal, but lacked any fur except on the top of their heads. All in all, Twilight would have described them as some twisted parody of a monkey or ape - not unlikely, considering the other inhabitants of the Everfree Forest and the strange effects imposed on them by the region. The one nearest to her, the one that had been standing over her just a moment ago, was wearing a red jacket and navy blue leggings, while the one on the right wore a dark green suit and black glasses, with a slight frown on its face. The third creature, which Twilight guessed was a female of the species, sported a lab coat and was fussing over a small electronic device.

This was odd. While a number creatures in the Everfree Forest were intelligent and capable of speech (dragons and sea serpents among them), none had mastered the use of technology. What kind of creatures were these things?

The female creature spoke up. "That explains why none of my scans are working - this device is designed to measure nanite energy readings and extrapolate data on the target based on anomalies in the measurements, but here there are no nanites for it to analyse."

Twilight had no idea what a 'nanite' was, but evidently it was keeping the creatures distracted from her. Realising that it was only a matter of time before they turned their attention back on her, Twilight decided to make her move. Scrambling to her feet, she made it only a few metres before collapsing again - the strain of holding a force field against such powerful and repeated impacts had been too much even for her, and it would take time for her strength to build up again.

In the end, all she had accomplished was to draw the focus of the creatures back onto her. Twilight slipped into full panic as they slowly walked towards her. This was it; she had attacked them and now they were going to take their revenge and there was nothing she could do to stop it and-

"Take it easy, we're not going to hurt you."

The voice snapped Twilight out of her panic, and she realised she had curled up on the ground out of fear. Looking up, she saw the female creature offer a reassuring smile. "My name is Doctor Rebecca Holiday, what's yours?"

"T-Twilight Sparkle." the lavender pony responded, still somewhat shaken.

"Twilight Sparke?" The creature in the red jacket snorted. "What kind of name is Twilight Sparkle?"

The creature called Doctor Holiday shot him a brief glare. "It's very nice to meet you Twilight." She gestured towards back towards the first creature, then to the one in the green suit. "This is Rex, and that is Six." Despite his earlier demeanour, Rex smiled and waved at Twilight, while Six simply adjusted his glasses.

"Why are you called Six?"

The green-suited figure barely reacted to the question. "It's because I'm the sixth most dangerous person in the world." Twilight recoiled slightly at the implications, but otherwise maintained her composure; she was still alive, which had to count for something. Although the way he said this so matter-of-factly was interesting - Twilight had read a number of books on dangerous creatures, but none of them had been numbered by their dangerousness, and Six had featured in none of them. She could think of a reason why this could be the case, but it was extraordinarily unlikely.

"And where...is your world?" Twilight asked, deciding to test her theory.

This time Holiday was the one who responded. "We come from a dimension that runs parallel to this one. We got here by passing through a rift between the two worlds." She was right! These creatures were from another universe! Before Twilight could stop herself, she launched into a cascade of questions. What differences are there between the dimensions? Did the two worlds share the same landscape or history, or were they completely independent from one another? Do the wildlife and plant-life share any similarities? Did they use the wormhole theory or entanglement theory to create the rift? How much power did it take? How did they generate that power?

"Slow down a second," Rex interrupted, holding his hands up. "Perhaps I should explain a few things for you."

Twilight sat down a bit more comfortably as Rex began to tell his story. Apparently the three of them were a species known as humans and came from a world without magic, but a team of scientists had been attempting to create something similar via microscopic devices known as nanites. The nanites were able to alter matter at a molecular level, and would have been used to cure diseases, grow food to end hunger and generally improve the quality of life for all humans.

But before the project could be completed, there was an accident.

A huge explosion ripped through the underground laboratory that housed the Nanite Program, destroying the town above it and spreading the millions of uncompleted nanites across the globe. Without any instructions to guide them, groups of nanites would spontaneously activate, rapidly mutating their host into a monstrous creature known as an Exponentially Variegated Organism, or EVO for short. Humanity descended into panic and chaos; for many it seemed like the end of the world had arrived.

But all hope had not been completely lost. Funded by the original investors for the Nanite Program rose Providence, an international organization dedicated to countering the EVO threat. Their directive was to contain or kill all rampant EVOs, while simultaneously working with the world's best scientists to try and rediscover the science of the nanites, long since lost in the original explosion, in order to try and find a way of undoing the madness plaguing the world. They had been able to slow the descent of humanity and even restore a sense of order to the world, but ultimately there were far too many EVOs for Providence to handle. They needed a cure, or mankind was going to die out.

Five years after the Nanite Event, they finally got that cure.

On a mission to hunt down an especially powerful EVO, Agent Six had encountered a young boy who possessed the ability to manipulate the nanites in and around his body, yet displayed none of the mindless violence typical of an EVO. Taking him back to Providence, it was discovered that the boy had the ability to deactivate nanites within an EVO, returning the host to their original form. What's more, he remembered nothing but his name - Rex. Seeing an opportunity to turn the tide of the war, Providence's leader White Knight decided to keep the boy within the organization as a 'secret weapon' against the EVOs.

Over the next couple of years, Rex began to rediscover snippets of his past, as well as the true purpose of the Nanite Program. Rex's parents, Rafael and Violeta Salazar, as well as his brother Ceasar, had been researchers within the project, and were forced to inject Rex with nanites to save his life after a crippling accident. Unlike the nanites which would soon cover the globe, these nanites were fully programmed, and granted Rex the ability to communicate and control other nanites, which he would later learn to utilise in order to modify his body into various mechanical weapons and to cure rampant EVOs.

Near the end of the Program, Rex's family made a shocking discovery. The founders of the Program - a group known as the Consortium - had realised that, properly programmed, the nanites would be able to rearrange the very fabric of reality itself - gravity, energy, matter, all of the laws of physics could be rewritten with the correct commands. A set of five Master Control Nanites were created, which would be able to direct the other nanites to accomplish this task. When Rex's parents discovered the Consortium intended to use the Master Control Nanites to essentially ascend to godhood, they were left with only one option - overloading the main nanite reactor would disperse the five Master Control Nanites randomly across the globe where they could never be used. Caesar and a few other scientists made it out, but Rafael and Violeta were caught in the explosion.

Over time, the Consortium's plans gradually became more apparent. When he began to resist, White Knight was forced out of Providence and replaced with the sinister Black Knight. Providence moved away from the old methods of Cure, Contain or Kill and began to research ways to control EVOs, while simultaneously seeking out the Master Control Nanites so that the Consortium could finally achieve their goal.

This didn't sit well with Rex, and along with Agent Six, Doctor Holiday, White Knight and a few other allies he has been fighting against Providence ever since, trying to collect the Master Control Nanites before Black Knight can get her hands on them.

"That still doesn't explain why you would be here." Twilight spoke up at last. "An explosion would hardly be sufficient to transport these Master Control Nanites between dimensions."

"Yeah, we're still not sure about that ourselves." Rex responded. "Black Knight came here a couple of weeks ago, but we have no idea why."

Odd. If other humans had appeared in Equestria, Twilight was sure she would have heard about it. "If she's here, then she hasn't been seen since she arrived." Rex's story had taken some time to tell, and glancing upwards it was clear even through the dense canopy of the Everfree Forest that it was getting late. Twilight had no intention of staying out here at night, when the more vicious monsters of the forest began to wake up. "We should probably get you somewhere safe, but if you walk into Ponyville it'll cause a panic." Safety was not Twilight's only motive - Princess Celestia would want to hear about this, especially if this Black Knight was as dangerous as Rex implied.

"We can take care of that." A tap of a button on Rex's wrist, and the human immediately vanished into thin air. "Just lead the way and we'll follow." Rex called out, assuring Twilight that he was still there. Following his lead, Six and Holiday also activated their cloaking devices.

Having regained enough strength to do so, Twilight stood up and began the trek back towards her library. One way or another, she had a feeling it was going to be a long night.