Chapter 1: Awakening.
Twilight floated in darkness. Nothing but endless darkness in all directions. She couldn't think, move, feel, see, or smell anything. At first she thought she couldn't hear either, but then noises floated up at her from the darkness. Distant and echoing, they made no sense at first. It took all of Twilights will to slowly realize they were words. Somepony, or several someponies, were speaking. What they were saying took even longer to comprehend.
“...not sure they're going to like this. This was never supposed to happen.”
“It's all right... We can fix this, but she has to come out of it first.”
By now the darkness had begun to glow, replaced by blurry colors, and Twilights sense of touch was coming back as she realized she was stretched out on something soft.
“But explaining things? Won't that just cause more problems?”
“It can be fixed, but she'd a living, thinking being, she needs to make that decision for herself.”
By now the colors were becoming intense and twilight had to squint to see anything. There were bright lights hanging overhead, and two colored blobs nearby that seemed to be talking.
“You're going to get us in a lot of trouble,” the voice Twilight was now able to identify as a mares continued, “We're going to loose our funding and they'll shut us down for sure then.”
“I'll take full responsibility then,” the other voice, a stallions, replied, “If worse comes to worse I'll get the boot and you all can continue on with the experiment.”
“You know we can't continue this project without you, Brian. We'll be up a creek either way.”
Twilight's inquisitive nature was getting to her, she had to get up, she had to know what was going on. Where was she? Who were these ponies? What was the Experiment? How was she involved? Unfortunately trying to get up was about a million times harder than trying to see at the moment, and she only managed a soft grunt of exertion.
“She's coming around,” the stallion muttered, “Just let me do the talking. It'll be fine.”
“We're doomed,” the mare sighed, resolved to her fate.
Twilight heard the sound of hooves on a metal floor as the unseen pony approached. Her eyes still adjusting she was able to make out an orange figure with brown hair as he appeared over her.
“Good morning Twilight Sparkle,” he stated warmly, as a doctor speaking to a child patient, “How are you feeling?”
“W...w-wh-ere...?” Twilight wheezed, her throat feeling unusually tight.
“That's a long story,” The figure above, which she could now tell was wearing a white lab coat, replied, “For now let's focus on the basics. Can you feel this?”
Twilight felt him touch her stomach gently and she managed a very slight nod.
“Good, how about this?”
This time the sensation came from her leg, and again Twilight nodded, but something didn't feel right either.
“Wonderful. And how about this?”
Again the doctor touched her at the end of her front legs. Only not. Twilight felt him moving extremities that shouldn't have been there. She counted them.
Five digits where her hooves should have been.
Twilight's breath came faster, her fears pumping adrenaline through her body as she struggled to fight back the sleepy feeling she'd had before.
“Whoa, take it easy!” the doctor yelped, “Don't struggle, you're just going to hurt yourself.”
Twilight didn't care. She had to know. It took a supreme effort, but she lifted her front limb to her face.
No hoof. Instead an appendage with five smaller digits extending from it.
Hands. Fingers.
Twilight had studied some animals in school. It was much like a monkeys extremities. Already her mind was leaping to conclusions as her heart began to race. Maybe she'd been caught by some mad scientist who'd chopped her hooves off and stitched on some animal limbs? What if he'd done more horrendous things to the rest of her? What if she was some sort of sick monstrosity her friends would scream and run from? What if the Princesses sent out the royal guard to hunt her down like some monster? What if...?
A pain in her shoulder and a moment later her heart rate began to slow.
“Take it easy,” the stallion assured her, “You've been through a lot. Just relax, I promise everything will be explained in time.” He gripped Twilights hand (not hoof, some part of her mind screamed) and as her eyes began to close she saw for the first time that he had hands just like hers.
Twilight awoke again some time later. This time coming up felt like she was waking from a normal dream. Silently she prayed that was all it had been, that she could wake up in her own bed and find Spike snoozing in his basket close by. Another normal day in Ponyville and another normal part of her life.
Sadly it was not to be.
Opening her eyes yielded the same gray tiled ceiling as last time with the strange light fixtures dangling overhead. The bed was hard an sterile too, like something from a hospital.
“Welcome back,” the soothing voice of the stallion from before washed over her, “Sorry about the seditive, but you would have done more damage to yourself if we'd let you struggle.”
“What's happened to me?” Twilights voice was dry and raspy, but at least she could form sentences again, “Where am I? What's going on?”
“Take it easy Miss. Sparkle, there's a lot to explain and trying to give it to you all at once is just going to cause more stress,” The Stallion moved in close as she was able to see his brown hair and tender green eyes, the horn on his head profe he was a unicorn like her, “I promise I'll explain everything, but you have to take it slow or you'll just hurt yourself.”
“Alright,” Twilight sighed slowly, trying to calm down a little, “Alright. I'll try... Where am I? Who are you?”
“A tough question to answer and an easy one,” the doctor nodded with a smile, “I can see why you're so intelligent. Where you are I can't explain in full yet, but to suffice it to say you are not in Ponyville anymore, and yet it is closer than you think. As for my name, I'm Dr. Brian Sturgeon. Yes I know, I've heard all the jokes before.”
Twilight couldn't help but smile a little at his casual nature.
“And these?” she asked, holding up her hands and wiggling her fingers.
Oddly it took the doctor a moment to get what she meant. “Ah, you mean your hands. I'd forgotten. Well... this might be hard to believe, but this is how you've always been Miss Sparkle.”
“What?” Twilight looked confused, “No, I had hooves just yesterday, I've always had hooves...”
“Calm down,” the stallion tried to sooth her, “I promised I would answer all your questions. But you won't understand some until you have the whole picture. I promise you this, those hands you have, as well as the state your body is in, are all natural. Nothing has been altered about your appearance. This is who you really are.”
Twilight said nothing for a moment, letting that information roll around in her mind. Finally she looked up at the doctor. “Can I see?”
“Of course,” the stallion nodded, “Just take it slow, remember you're still recovering, so you need to be careful.”
Twilight nodded as he gently helped her sit upright. Already she could tell something was different. Her body was not shaped like it should have been. Her rear legs were longer than her front legs... or arms, if that's what they were. The joints bent differently, and yet they moved naturally at the same time.
The stallion helped guide her legs out of bed, some part of her was glad to see she still had hooves at the end of her legs, though they seemed a bit wider than she recalled. Carefully Twilight was shifted to a sitting position before the doctor put an arm around her and gradually helped her to stand.
Almost at once Twilight felt like she'd fall over. Walking on two legs was a far cry from what she remembered, but somehow she was able to maintain her balance for the most part.
A few shaky steps followed, her hooves clopping loudly on the cold floor as the doctor gently held her and guided her to a nearby mirror hanging on the wall. Twilight almost didn't want to look, fearful of what changes she would discover, but her scientific curiosity got the best of her and soon she stood in front of the mirror, scanning her body with a analytical eye.
She was pleased to see much of her looked the same. Purple fur was still visible under the hospital style dressing gown, and a quick check revealed her cutie mark was still in place. Her mane and tail were the same color, if a little unkempt., her muzzle, ears, eyes, horn, all of it seemed to be as she recalled.
The biggest change was the different shape her body had, now upright with arms instead of front legs and hands instead of hooves. There was something else too, a pair of small soft mounds on her chest that she knew she hadn't had before. She reached up to feel when the doctor gently grabbed her wrist. “That's for another time,” he stated with a faint blush in his cheeks.
Twilight looked at him quizzically, but decided not to push it.
It was then she noticed his form.
Similar to hers, though mostly hidden under a white lab coat, and blue pants, he was similarly upright as she was, even a bit taller.
Twilight looked him in the eyes, her mind growing sharper by the minute. “Where am I?” There was no anger in her voice, but it was clear she wanted answers.
The stallion sighed, “If you must know. You're in research lab nine, in the city of New Haven.”
“There's no city by that name in Equestia,” Twilight was confused, again feeling her fears nibbling at the edge of her mind, “You said I was near Ponyville.”
“You are,” the doctor sighed, “For you see, Ponyville, Canterlot, and all of the Equestria you know, is contained within this building.”
“That's impossible...” Twilight was feeling decidedly nervous now, “You're lying.”
“No, I'm not,” the stallions eyes seemed to show both concern and immense sadness at the same time, “Twilight... You've been living in a dream for the last six months.”