The body, Equine or not, is a system like any other. It has certain orders and structures with in that are necessary for continued function.

And if it has order and structure, it can be created.

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Sparks danced across two metal spikes, cutting a slithering arc through the air. It's light cast an eerie glow on the dark basement, filled as it was with whirring and clanking from countless machines. In the corner, under the sterile white light of a single crystal lantern, sat Twilight Sparkle hunched over a microscope. Her hair was pulled back into a loose bun. Her coat was matted and had an unwashed shine to it. Beside her, a quill scratched furiously on a piece of parchment filled to the edges with mathematical formulas.

"Ok. Mitosis seems to be proceeding about as predicted." She said as she sat up from the microscope, popping her neck repeatedly. "Slightly slower, but well within sustainable ranges."

Reaching up with her hoof, she taps the lantern. It jingles quietly and it's light slowly fades out. With a kick, she rolls her chair from one table to another, her seat clacking loudly over the uneven floorboards. Reaching up into the darkness she taps another crystal, it's harsh light illuminating a blue metallic box. A multitude of cables and cords slithered from the box, winding into the darkness.

With a tap and a spark from her horn, the top of the box melted away. A frigid cloud rolled slowly over the edges and frost began to cling to the rim. A grotesque mass of pulsing flesh, winding arcane symbols and jagged crystals floated gently out.

"It means the body is ready for you," She said, kicking off and rolling towards the center of the room. When the light flicked on, it revealed a porcelain white Alicorn body, sitting with it's head bowed to the ground and the top of it's skull open and empty.

A faint wisp of blue smoke trailed out of her ears for the barest of moments causing her whole body to shake. "Yes! I mean it this time! I install the persona matrix and you will be able to jump in almost immediately!"

The wisp extended and gently caressed Twilight's chin, drawing little circles along her jawline. She shivers as she leaned into it and sighed happily. "Of course, Mistress."

She turns to the awaiting skull and the mass floats quickly inside. The wires snap towards awaiting receptors on the inside and the whole thing settles in with a sharp hiss. Twilight stepped off her stool an wormed her way under the massive neck. With a heave and a grunt, she lifted the massive head up and propped it up with a large plank of wood.

A jar filled with a clear, viscous liquid floated up and tipped it's contents out, filling the empty skull. With a jolt of energy from her horn, the flesh and bone began to knit together and close up the cavity. She walked back under the head and gently lowered down to the floor. Pulling a magnifying glass and some tweezers from the table beside her, she poked and prodded at the newly formed cranium.

"Oh...kay!" she exclaimed as she tossed the objects aside. "It's read-!"

Before she can finish her sentence she buckled over and clutched her head, screaming all the while. A deep blue miasma poured out from every orifice in her head, leaving behind a sickly black tar that dripped too the floor. The cloud crashed into the white pony and seeped in from where ever it can find purchase. The pristine white of the fur began to darken and soon only the faint outline of a pearly white moon remained amid a twisting sea of black. The eyes shot open and revealed two brilliant turquoise eyes, the slits barely visible. With sure steps, the massive creature stood up and brandished it's fangs in a menacing smile.

"Very good, Twilight Sparkle," her velvet voice slithered out. "Your work seems to be holding up quite well this time."

"T-thank you, Mistress," Twilight barely croaked out from the floor. One eye was stuck shut with the black tar, the other bloodshot from the strain. She shakily tried to stand and meet the gaze of her mistress, but collapsed with a pained grunt.

The massive alicorn kneels down and gently cradled the weakened unicorn in her magic. "Do not struggle, Twilight. You have earned your rest." Twilight gently sagged onto Nightmare's back, wincing as her head touches down.

"When you have recovered from this ordeal, we shall begin planning for the future." She said as she mounted the stairs out of the basement. Her form shrank and shifted, bones audibly cracking and shifting as she morphed into a much smaller body.

"And what a future it will be, my dear student." She said with a terrible glint in her still reptilian eyes. "What a future, indeed."

Author's Notes:

Double submission for the "Structure" prompt.