On Sub-Atomic Nanogenes and the Realities That Bind Us

by JustAnotherFillyAuthor

Rating: everyone
Tags: My Little Pony: Friendship is Magic, Human, Doctor Whooves, Lyra, Original Character, Mystery, Science Fiction, Adventure, Derpy Hooves, Crossover, Doctor Who, Discord
Length: 4399

Subject #040496 - once a human, now a pegasus - searches for a way home. Meanwhile, the Star Bright Network has ideas of their own for her, and the Doctor finds himself caught in a battle to maintain reality.

A young pegasus wakes up alone in a field with no clue as to how she arrived in Equestria.
She was human once - she thinks - but her memory is tattered and unreliable, only coming to her in sharp, burning flashes. She can't even remember her name, and now she has to piece together the events that led her across time and space, if she ever hopes to return home.

Meanwhile, deep underground in the tunnels below Canterlot, the Star Bright Network crafts a plan to break the barrier of reality, and they think they've located the last missing piece of the puzzle.

In between it all, the Doctor and his bubbly companion investigate the strange energy that has been flowing out of Equestria's capital city. Something big is on its way, and their universe will crumble unless they can stop it in time.

Published 2022-01-31 19:20:00 UTC
Last updated 2022-03-04 23:03:51 UTC

Chapter 1

Her vision came back first, slowly but surely. Her peripherals were a blurry monochromatic mess, her head was pounding, and her vision swam with electric sparks ricocheting off the edges inside her skull like acid raindrops on limestone pavement.

She slowly raised her head, inhaled a shaky breath that pressed against her sternum in an odd fashion she couldn’t quite identify, and shook the cobwebs from her mind in a daze. As awareness reawakened her, she found herself lying on her back at the base of a vibrant green hill, staring at the breaking dawn above. A small body of water glittered a few feet away, and the trees swayed lightly in the breeze.

Wait.

She looked down at her arms. Pure white fur glistened with morning dew, and she stared at her hooves as something unfamiliar gnawed at the back of her mind.

This was wrong. Why was this wrong? She didn’t have hooves, did she? What was she? What was she before?

Suddenly, a sharp pain jolted through her skull.

“You can’t do this to me!” The young woman cried. Her screams echoed in the pale blue chamber she was housed in, an assortment of medical needles and hoses poking through her skin and holding her captive, floating in an iridescent liquid. Her breathing laboured as she took in more of the solution, each breath coating her burning lungs in chilling moisture. The veins in her pale skin throbbed angrily with each new substance injected into her, and she curled her quickly numbing fingers to bring the sensation back to them. Looking up, she glared at the sinister face staring back at her through the glass.

“Think of the sacrifices you’re making for humanity, my dear,” the man chuffed as he tugged at the lapels of his white lab coat, stained with sickeningly yellow marks around the neckline, “and just imagine how much better you will feel after this!” He straightened his coat, brushing off an old nametag from the front, bearing the name of ‘Cosmo Flaherty’ in brilliant gold lettering. Cosmo stroked the glass affectionately before making his way to a collection of vials on the table beside him. He held one up to the bright cold ceiling light, and it shone unnaturally.

She reeled back in horror, clutching at her head with her hands – no, hooves – and crying in alarm. This was not her body; she must be dreaming. She must be hallucinating. Her sluggish mind was racing to make sense of her surroundings. What was she doing here? What was she? Who was she? What was her name?

She did not remember anything.

The realization hit her like a freight-train, and she scrambled to her feet – hooves – kicking up too much dust in the process. She struggled to contain a cough as she made her way to the lake in a mad scramble and looked at her reflection.

A strange creature stared back at her; huge brown eyes wild and afraid, white pointy ears laid flat against her head, deep brown and blue mane long and untamed. The muzzle on the strange face wrinkled in confusion, and tears began to well in her eyes and dribble down her face, leaving tearstained marks. The reflection wobbled as her tears hit the pond, spilling ripples across her unfamiliar features.

This was not her – staring back at her was a pony. A white-furred, brown-and-blue-maned, chocolate-eyed mare.

She screamed, backing away madly from her distorted reflection. She turned and ran from the lake, stumbling blindly over her new hooves. Not bothering to swallow the panic in her throat. Her lungs burned and the world around her swam with unshed tears. She did not know where she was running, but she knew that she was running from something beyond her understanding. Her mind was racing faster than her hooves, and her brain felt searing hot despite the fog.

Something was very, very wrong.

As she galloped further and further from where she first woke up, the world became a blur through snot and tears she could not hold back. Emerald grass collided with turquoise sky in a whirlwind of panic as the mare raced through the field, unaware of anything around her but the primal instinct at the back of her mind telling her to run, you are in danger; run as fast as you can! Searing pain shot through her skull like an angry bullet with each step and grainy despondent images of another time swam unprovoked in her mind’s eye as she stumbled with the pain.

An image of a sterile white room, a flash of blinding lights, a metallic taste in her mouth as liquid fire flowed in her veins.

She was human! At least, she thought she was human.

She stumbled as another, clearer vision exploded in her head.

“Please, stop! I live alone and I have a cat, she needs someone to take care of her!” She cried, encased in the glass tube. Cosmo inserted a bright blue liquid into the I.V. drip inserted in her left arm and she gurgled in pain as something white-hot and angry entered her bloodstream. She could feel something crawling inside her veins, taking shape, traveling through her body, clawing at her lungs and latching into her heart and brain. She screamed in terror, thrashing about in the tank as her muscles spasmed violently.

“These nanogenes,” Cosmo muttered, ignoring his subject, “are programmed to rewire your mind. Produce more neurons, act as neural gateways for your currently vacant brain. They will learn your genetic code, recalling all of what you are within their tiny little computer minds, and they will protect you from harm. Just give them time to adjust.” He knocked a pile of research papers off his desk to make room for the beaker he was holding, and he picked up a pen before scribbling something down on a rogue sheet of paper.

“Why are you doing this to me? Please, let me go!” She begged, her heart racing uncontrollably as every organ and muscle burned with the energy of Cosmo’s experiment. Her voice came out as a choke, the liquid in the tank suppressing most of her voice.

“#040496; you and I will find the meaning of life together.”

The mare growled, gnawing at her lip to keep more tears from spilling. Her entire body burned as if fire was running through her veins, and now she remembered why. Her hooves were on fire and her veins were aflame as fury and fear in equal measure collided like wild vicious animals in her brain.

At the back of her mind, she went over the event; she was human – yes – and she was called #040496. That didn’t sound right to her, though. Why couldn’t she recall her name? Why couldn’t she recall anything?

Her new hooves crumbled under her, and she stumbled into the grass, tears welling in her eyes like a dam fit to burst. Unable to hold back her cries, the silence of the morning was broken with an almighty scream, and she sobbed bitterly into her muddy forelegs. She felt the visceral wrongness of how her tear-streaked muzzle felt as she rubbed it against her unfamiliar limbs, and she cried harder, screeching in horrendous anguish. Confusion and fear coated her mind in a deep, dark fog like an afternoon thunderstorm, and hordes of irate and fearful thoughts leapt unbidden from the depths, crashing angrily against her skull and flooding her furry ears.

Waves upon waves of bitter despair crashed onto her tiny frame, chilling her bones and anchoring her to the ground as she finally collapsed under the almighty weight of emotions beating down upon her. She couldn't take it any more.

She closed her eyes, yet she still saw the clear, cold, glinting eyes of the man that did this to her. His indifferent sneer burned into her brain and mocked her slipping sanity. She cried out in fear once more, burying her head in her hooves and curling up defensively in a feeble and fruitless attempt to keep the internal attack at bay.

What was wrong with her?

All she could see in her mind’s eye was a fragile memory of an identification number. She was #040496. She was #040496.
She was #040496.
The poisonous mantra rang in her skull and crashed violently against her burning heart, and she sobbed uncontrollably into her new hooves.

There was a disturbance. He could feel it in his bones, in his ever-racing mind. The energy in the air was almost tangible, and the taste of iron and electricity prickled on his tongue, settling in his thick chocolate fur like a deadly poison.

With head turned to the late afternoon sun beating down on him like a stifling, brilliant omen, the stallion grew rigid, inhaling deeply.

His companion stopped in her tracks, seeing that he had done the same.

“What’s the matter, Doctor? Is something wrong?” The blonde pony asked in a soft tone, her head tilted slightly. Her golden eyes were crossed, one holding the stallion’s own gaze and the other looking to her left, unseeing, unmoving.

The stallion took a moment to give his companion a reassuring grin before shaking his head. He shrugged off the feeling and turned back to the skies, breaking eye contact with the mare.

“No. No, it’s fine, Ditzy. There’s something in the air, though. I can feel it.” The Doctor murmured, staring at the arching streaks of light sunbeams. Ditzy looked at the sky but could only guess as to what her friend was talking about. She had learned long ago not to question the Doctor’s logic. Instead, she fluffed out her wings and turned back to the road.

“Well then,” She began, taking a few cautious steps forward, “Let’s get going!”

The Doctor responded with a noncommittal hum, his mind somewhere else entirely. Uncertainty prickled at him as a familiar anxiety settled into his skin. He had seen too much and had been alive for too long to brush off the sense of carnal uncertainty that had taken hold of him; the universe had shifted skeins, and something was different in this universe now.

Whatever it was; if it was to be a problem, he would have to solve it.

Author's Note

This story is fully written. I will be proofreading each chapter and uploading them one by one over the course of the next several weeks once I am happy with the results.

This fic is well over 100k words and I have enjoyed writing every single bit of it, so I really hope you enjoy my work. :-)

Chapter 2

The woman - no, the pony - hadn’t a clue how long she had been lying on the ground for, but when she finally ceased her crying, her fur was considerably warmer than it felt earlier that morning. She cast a glance to the skies, a deep blazing shade of sapphire blue, and the sun was much higher than she remembered.

The vibrancy of her surroundings brought an ache behind her eyes, and she raised her hooves to her head. She had no fight left within her, energy sapped from her emotional outburst. She felt numb; staring down at her hooves, she felt nothing but a hint of resentment.

‘You are #040496’, the last angry dredges of her consciousness hissed at her. She was far too tired to argue this time - instead, she chose to rise from her position and shake off the warmth in her fur and the cold in her mind. #040496 looked around and decided on a direction of travel; putting one hoof in front of the other felt like a monumental task, but ever so slowly, she began to descend from the base of the hill.

Her hooves were like tar, gripping her soul to the cold ground, and she dragged her unwilling body through the grass and in the direction of the fields below her. A vast expanse of rolling green stretched as far as she could see. In the far distance, a mountain range glittered with snow as they reached up to touch the skyline, shimmering in the light like iridescent soap bubbles, suspended out of time. The trees that dotted the fields below stretched out to the heavens like their lives depended on it, swaying in the midday breeze.

As soon as she laid her eyes on the ground beneath her hooves, however, the scenery began to shift.

With an almighty jolt of electricity in the air, a burst of energy rippled the ground like a rock skipping on a pond, and the grass changed from green to a deep chartreuse from under her. She almost choked as she reared her hind legs, a new sense of dread flooding her mind as the skies themselves opened into a sickly coral haze. The air grew swiftly thick with the scent of sulphur and she gagged uncontrollably as more strange energy ricocheted through the atmosphere, bringing the changing colours and sickly stench with it like lightning as it forked overhead. Pinpricks of dread brushed her fur like an omen and #040496 shrieked as the ground beneath her changed once more into a fine wet soapy texture, and she lost her balance on her new hooves.

She careened down the hillside into the fields below, and she choked as her screams died in her throat.

She finally slid to a stop in front of a large wooden cardboard tree. She quivered violently and her mind raced, pulling menacing shadows out of the corner of her eyes and calling her attention from all sides, demanding she pay attention lest she fall victim to the chaos around her. Waves of fear rushed her mind and roared in her ears, her muscles twitching and burning. Tears sprang to her eyes once more and she curled up behind the cardboard tree, rubbing her temples before realising she had hooves instead of hands.

‘It’s only a nightmare, it’s only a nightmare, it’s only a nightmare,’ she whispered, her voice hoarse and dripping with uncertainty, ‘calm down, calm down, calm down!’

Suddenly, the world was plunged into darkness as the sun vanished from the sickly green sky. #040496 jumped to her hooves clumsily and ran, primal fear flooding her senses and commanding her body in absence of her mind. She tripped over cardboard foliage in the blackness, blinding pain shooting up her foreleg as she did so. Grinding her teeth, she paid it no mind as her thoughts came rapid-fire at a blinding rate to her hooves; how did she get here? What was happening to her? What was going on? Where was she? Who was she?

‘I am #040496’, her mind echoed instinctively, attempting to quell her racing thoughts and slow her pace. She skidded to a halt suddenly as the daylight returned and assaulted her senses. She stumbled backwards and her eyes burned with the sudden light. Sunbeams slammed on her eyelids and demanded access, and she shielded the sun with her hooves in a futile attempt to get a better view of her surroundings. Sunspots coated her vision, dancing erratically with her eyes. She whimpered and splayed her body against the violet checkerboard ground, eyes blind and hooves useless.

040496 prayed that death would take pity on her shaking, unfamiliar form and take her quickly.

In a deep, blinding flash, the skeins had shifted, and the world surrounding the Doctor and Ditzy shimmered in a deep, booming staccato as colours danced and flickered in the waxing light. The well-ridden dirt pathway that arched towards Ponyville turned into a consistency akin to soap bubbles and the Doctor careened into his companion at full speed, knocking the wind out of himself as they tumbled down a hill and landed with an unceremonious thud into a paddock. A sharp pain ripped through the Doctor’s foreleg, and he groaned as he sat up, looking frantically for Ditzy.

With a sigh of relief, and then confusion, he locked eyes with the mare who had broken her fall on a winged pig and was soothing it with gentle chin strokes.

“I’m sorry, little one!” She cooed. The Doctor might have chuckled if not for the absurdity of the situation. He rose to all four hooves and extended one to Ditzy, and she took it gratefully.

“What’s going on, Doctor?” She whispered. The skies above them flashed a deep indigo before settling into night-time at a rapid pace, only to be replaced by the sun mere seconds later.

“I’m not sure, but I think it’s time we find out,” he murmured in a tone too jubilant for the occasion, and with a short, disapproving glare from Ditzy, the two set off into the small town, following the trail of chaos.

As the two wanderers cautiously made their way to the centre of the town Ditzy once called home, the scenery around them changed. Objects winked in and out of sight in the Doctor’s peripheral vision as bright cardboard replaced houses and trees, and a possessed pony with swirling red eyes pushed him aside with a great shove in a daze of confusion. To his left, he saw Ditzy reel in horror as they passed a tiny shack and saw a mare with a deep, despondent grey mane and coat attacking a carrot patch, ripping up her life’s work with fervour.

“Golden Harvest?” Ditzy whimpered, staring with one good eye at the mare tearing up the garden.

The Doctor rushed to the possessed mare’s side and was promptly bucked away. Unswayed, he scrambled to his hooves and approached from the front, dodging a swift kick. In that moment, he saw Ditzy take to the sky with a flutter of her wings and he bemoaned his own lack of wings.

He was at least thankful that the pony in front of him also lacked such appendages; he wasn’t sure if he could deal with a flighty pegasus.

“Golden Harvest? Can you hear me?” He crouched down and grabbed her by the muzzle, locking her jaw and, for a brief moment, forcing her to look him in the eye. Dull green marbles stared back at him, and a deep sense of unease gripped his stomach. There was something so achingly wrong behind them. Golden Harvest struggled against his grip and hissed.

Suddenly, a deep red scaly tail wrapped itself around the Doctor, and he dropped the possessed pony in surprise. He cried out angrily as the form of a giant beast materialised around him, a mishmash of a variety of creatures all combined haphazardly onto the one body as if constructed by a toddler. The beast smiled at the pony in its grasp with his elongated horse-like muzzle, revealing a row of sharp yellow teeth.

“Hello there.”

The creature’s raspy tone grated on his ears, and he found it hard to stare at the beast’s glowing red eyes, the yellow sclera underlining something far more sinister than the Doctor was prepared to admit. He struggled and strained as the beast’s tail wrapped even tighter around him, and for a cold instant, he wondered if the beast was squeezing the life out of him.

The creature did not seem to need to obey the laws of gravity as his two tiny, mismatched wings were barely flapping, and yet he was flying a few feet off the ground as he brought the Doctor closer still to his face. A look of recognition breezed past the beast’s face, so quickly that the struggling stallion almost didn’t notice.

“What have you done to these ponies?” Cried the Doctor through gritted teeth, the beast’s cold scales and even colder talons from one of his hind legs caressing his fur, burning like ice into his skin. “Who are you to treat these creatures like this?”

With the Doctor flailing in his grasp, the beast paused and wrinkled his muzzle in confusion. “You really don’t know who I am, do you?”

The beast immediately wound himself tighter around the Doctor’s torso, squeezing with sudden delight as a low chuckle emanated from his dark chest.

In the commotion, the Doctor did not see his companion approaching the beast from below.

“Get off him!” Ditzy screamed in a high-pitched tone, sounding more like a whine than a battle-cry, but just as welcoming to the Doctor’s ears as it was frightening. Before he could cry out a warning, Ditzy slammed her body against the creature, but he only stared at her in mild amusement.

“Aww, aren’t you adorable!?” He cooed, his attention now to the panicking mare throwing herself into his tail. He stroked his tiny white beard in thought. He turned back to the Doctor.

“I’ve met you once before, don’t you remember me? It isn’t often I meet another creature who has lived as long as I have.” He muttered at the struggling stallion. The Doctor paused at this, and he raised his eyebrow but remained silent as Ditzy flew in a tight circle around them, attempting to draw the beast’s attention away from the stallion in his grasp. The beast considered the mare no more than a pesky fly and he waved her away as such, his left claw striking her side as he did so. Ditzy yelped and, with a flutter of her wings, flew a few feet backwards. Small, soft tears leapt unbidden to the rims of her eyes and she blinked them away rapidly, and with each blink, her right eye changed directions as her left continued to be locked onto the beast and the Doctor. The beast found this to be quite amusing as he crossed his eyes to imitate that of the pony flying around him, giggling like a child mocking another on the schoolyard playground.

“Hey!” The Doctor growled. “Don’t you dare hurt my friend!”

“Are you really in the position to be making demands?” The beast snarked, his forked tongue running threateningly over his bright fangs. The Doctor, however, remained stone-faced, glaring at the beast and occasionally struggling against the grip of his tail. He writhed angrily, the sharp scales now digging painfully into his skin. The beast seemed to enjoy this, his grin growing wider with each passing second.

The Doctor sighed. It was time to change tactics.

“You’re right. Who are you?” The Doctor asked, his tone soft but steady and his gaze unwavering into the mismatched eyes of the beast before him. He felt the creature bristle slightly, and the Doctor took a mental note of his reaction. He had been in countless situations like this before – such was the life of a wanderer like himself – but he would never admit that he looked forward to the dangers of it.

The creature seemed momentarily stunned by the question but covered it with a small chuckle and a shake of his head. He ran a clawed finger through his beard, perhaps in thought, or perhaps buying time, the Doctor could not be sure.

“I see that we’re doing introductions again. I am Discord, spirit of chaos, and you, my friend,” The creature poked the stallion’s muzzle with his right paw, “Are the Doctor!”

Discord chuckled, and the Doctor cocked his head. “I don’t recall ever meeting you, Discord.”

“I’m not surprised.” Discord said nonchalantly, shrugging. “It has been over a thousand years.”

The Doctor only nodded, biting his lip. A million responses crashed like a tsunami in his ever-turning mind as, in a split-second, he weighed each one and determined the best to say. Looking into the eyes of the beast, it would not be worth admitting to him that, perhaps they had met once before.

They might have met in Discord’s past, but in the Doctor’s future.

Time travel was rather fickle that way.

A flash of amusement soon danced in Discord’s eyes as he unceremoniously dumped the stallion onto the lilac grass, fluttering his wings violently as he did so. Ditzy yelped as she rushed to her friends’ side, and they watched as he twisted in the air like fractals of light trapped in a cracked gemstone.

“Excuse me, friends!” He said, his raspy voice filled with delight as he waved his paw. “I need to meet a unicorn who needs my assistance!”

In an instant, the beast snapped his claws, and he dissipated in a sudden burst.

With fury in his voice and a pit of uncertainty in his stomach, the Doctor yelled out a command to return, bellowing as loudly as he could, but the beast did not hear him. Or, if he did, he did not respond. The Doctor could have kicked himself; how could he have allowed the beast to escape? He had to track him down. His hearts thumped excitedly in his chest and his rapid breaths were loud and raspy in the air, and a sharp unwelcome chill descended upon him with its chaotic fervour. Determination gripped him and pulled him up as he rose to his hooves and grasped his companion’s front foreleg, pulling her up with him.

As the pair scrambled, a terrific bang erupted from behind them, and a blast of wind knocked them back as a barrage of brilliant rainbow light poured over the magenta sky, emanating from a whirlpool of colours behind a stack of cardboard buildings. A dreadful screech erupted in the distance alongside the electric magical blast of rainbow colours, then faded into silence as the world slowly melted. The Doctor and Ditzy shared a look of desperate confusion before running in the direction of the blast.

Less than thirty seconds had passed, but when they turned the corner around a small brick cottage, the rainbow dust had settled on the ground and the taste of metal was heavy in the air as Discord lay still in front of them, encased in stone, with his claws curled in panic and a stunned expression on his face. Surrounding him, six ponies of various colours and creeds lay on their haunches, panting heavily from exertion. Each bore a coloured necklace of jewels glowing with no aid from the sunlight, save for one lavender unicorn, on her head a crown of starlight, similarly shining with her companion’s accessories.

Just as quickly as he had appeared, the spirit of chaos had fallen.