Into The Depths

by Canvas

Rating: teen
Tags: Princess Celestia, Crossover, Alternate Universe, Main 6, Princess Luna, My Little Pony: Friendship is Magic, Dark, Cutie Mark Crusaders, Nightmare Moon, Adventure
Length: 3558

What happens when a dark secret is revealed, and Rapture is unleashed?

Twilight is contracted by Celestia to uncover the secrets of Rapture. This contract thrusts the mane six into a world of nightmares, and an adventure they could have never imagined. With Twilight as the key, all responsibility falls upon her; but when the mare's world and understanding fall apart, will she be able to break free?
This is a crossover of Bioshock and MLP.

Published 2013-04-01 14:10:02 UTC
Last updated 2013-04-16 14:17:37 UTC

Prologue

Darkness shrouded her vision, a sweat pouring from her burrowed brow.
"No... No... NO!" Twilight shrieked, a shroud of dark, violent blue consumed her, choking her, squeezing the breath from her compressed torso.
"Help, please..." She was fading out, the dank, damp walls around her closing in. With a final, sharp breath, the lavender mare was startled awake.
Her eyes darted around the room in blind panic. The room was still as when she fell asleep; her bed was beneath her, with Spike's beside her own, and her small, clean window allowed the moonlight to saturate everything around her.
"Twilight? Hey Twilight, are you okay?"
The breathless mare looked down as she quivered on her bed. Her panicked eyes met with the wide pupils of her assistant, Spike.
The short baby dragon poked her leg carefully, tilting his head slightly.
"You're sweating... What happened?" His mouth scrunched up in concern. Lately, Twilight had been increasingly restless, and he was beginning to worry. It was usual for the mare to panic every once and a while, but for a week straight, it was a concerning sign.

Spike hadn't seen the mare this worried since her initial arrival at Ponyville. The poor reclusive Twilight had fought the idea of having friends, arguing that she was best off with her nose in books. It took Spike some time to help her warm up to the fellow ponies.
Now, seeing Twilight in such a state saddened the baby dragon, as she had come so far. Whatever was on the mind of the studious pony must have been huge; she had tossed and turned every night, sometimes even crying or, on the worst nights, screaming.

He offered his clawed paw in a gesture of friendship; he hoped he could bring at least some comfort to his best friend.

She smiled, her heart warmed by the care Spike gave her. Ever since she had arrived in Ponyville, even through the banishment of Discord, the little purple dragon had been by her side. He was so accommodating, and she was incredibly thankful.
With a gentle nuzzle, she sighed a breath of relief.
"Thank you Spike... It was, just a nightmare. I'm fine, really," she looked up at the still-night sky. Despite her brave words, she was disturbed.
The depth and darkness of the sky brought back all the raw images of her night-terrors. It suffocated her, every night. The sheer silence alone made her fur crawl.

Spike didn't believe her one bit, but didn't want to panic the already nervous pony. With a sad sigh, he curled back onto his bed, pulling the soft blanket back over his scaley hide.
Her anxiety rubbed off on the young scaled assistant. He was in a constant state of guarding the poor Twilight, as he cared too much to let harm fall upon her.
If anyone touches a strand of fur on that mare's body, so help me... Spike thought to himself sleepily, as his mind blurred into sleep.
"Well, I'm here if you need me, Twily," he managed to mumble, before sleep finally consumed his young mind.
"Thanks, Spike," she whispered, turning to face her small window. Stars beamed down onto her soft lavender coat, causing her to glow slightly. Despite the night's obvious beauty, Twilight was still terrified. Every night for almost two weeks straight, it was the same night terror. Every night, it progressed, becoming more frightening.

Maybe it's all the books, Twilight thought to herself with a saddened heart. Granted, her reading material had been rather dark, but it didn't usually disturb her this much. Not to the point of nightmares, that's for certain. Something had to be done. She couldn't keep tossing and turning, it was interfering with her studies. The mare gasped, realising what she must do.

"Spike? Spike?!" Twilight poked the dragon with a forceful hoof, pulling the blanket off him. "Spike I need you to take a note for Celestia!"
"Hmm.. Twi, can it wait until morning?" The dragon yawned, a flicker of green flame illuminating the entire top floor of her treehouse.
"No it can't! GET UP!" Twilight flicked the dragon out of his bed with a swift movement of her muzzle, pushing him onto the cold wooden floors.
"Fine, fine," he grumpily grabbed a quill and a scroll of old paper.

"Dear Celestia, I fear that I am troubled. Every night for almost two weeks now I've had these troubling dreams, of dark times and an evil being," Twilight paced the length of her room, her hooves beating fretfully against the floor. The sound echoed throughout the library, reminding her of how alone she was after the nightmares.
She checked to make sure Spike was following, before continuing in a squeaky tone.
"In my dream I am struck down by a dark, shadowy creature. It has a female voice, and tells me that 'It's over'. I don't know what it means, and it's keeping me awake. If you can give me any advice, I'd be very grateful.
Your faithful student,
Twilight Sparkle."
The mare sighed with relief as Spike sent off the scroll. At least now something may be able to be done, or at least the Princess could offer some insight into what's happening.
Twilight returned to bed to try and capture a few hours of sleep, and was able to doze until morning. The pony was gently awoken by a concerned Spike, waving the Princess's reply.
"Twily, wake up! Wake up!!" He began to shake her, as she groggily opened her eyes.
"H-huh?" Twilight tried to re-focus her eyes.
The response caused her heart to skip a beat, as she read the single paragraph.
"My faithful student; the time has come. Would you kindly gather the six elements and meet me at Canterlot? We have no time to waste."

With a shiver of her purple coat, Twilight rushed to her hooves, gathering a saddlepack of vital things and books.
"Spike let's go," with not a moment to spare the mare closed the door to the library.

Author's Note

The start of my story :) Hope you all enjoy. If there are any grammar or spelling issues I'm happy to hear them out. And if you have any advice, let me know :)
Thanks for reading!

Chapter 1: The Darkness Uncovered

The early sun was rising over the sleepy town of Ponyville. In each and every house, curtains were slowly opening and doors were unlocking. Ponies were slowly waking up all throughout the small village, as warmth spread into the tiny houses and shops all around. Various of the mares and stallions opened their doors; they checked the weather to see if the early morning pegasus team had done their duty, checked that their well-tended gardens were still alive, and checked who else was awake. It was always a humble wake-up in the town, and helped everypony start off happy and connected to those around them.

In amongst the groggy ponies and lazy pets galloped a panicked Twilight, desperate to find her friends. A rushing sweat had broken out on the mare's furrowed brow, as she wheezed her way towards the sweets supply of Ponyville.
“Pinkie? Pinkie Pie!” Twilight called, thrusting the door of Sugar Cube corner open with a loud bang. The purple mare knew that Pinkie often worked in the sweets shop early in the morning, sometimes coming in before her shift to spend time making and- more often than not- eating the goods.

Sugar Cube corner had a huge increase in interest after the pink pony started working there; her endless promotion and energy for the store gave it a breath of fresh air.
Mr. And Mrs. Cake had grown tiresome not long after starting their family, and Pinkie had saved their store without a doubt. And to their additional luck, she also foal-sat.

A flurry of pink shot before Twilight’s eyes, causing her to recoil slightly. With a disembodied shriek, she felt a heavy thud against her side, sending the mare to the floor. Atop her was the ever-so-cheery Pinkie, grinning and prodding Twilight with sugar-coated hooves.
Twilight sighed and pushed her off.

“Pinkie, we don’t have time for games! Princess Celestia needs us, NOW!” Twilight’s worried eyes scanned the party-hard pony. She was chipper and bubbly, as always, and her eyes teemed with excitement and joy.
Pinkie’s jaw dropped.
“Oh my gosh, Princess Celestia needs us? Well,” she grabbed a last sugar cube off the counter before shoving Twilight out the door, “What are we waiting for!?”

Twilight was still vacant as she mentally compiled an action plan. Now we need are Fluttershy, Apple Jack, Rarity, Rainbow Dash... She panicked endlessly, her tired legs pumping hard.

Pinkie’s ecstatic plans for future parties fell on deaf ears, as Twilight galloped towards Fluttershy’s treehouse. It wasn't very far, but the studious pony was desperate to get to Celestia as soon as possible. If she were to fail a task from Celestia herself... The mare shuddered at the thought.
All Twilight heard was high-pitched chitter chatter, along with a few chip-ins from her assistant, as he lounged comfortably on her back.

Twilight’s voice was stern, as her frustration began to grow.
“Spike please pay attention, we need to get to Celestia,” she impatiently demanded, as her gallop slowed to a trot. The treehouse was only a few metres away, humble and quaint in the morning light.
“Sorry Twilight,” Spike looked down sheepishly, shooting Pinkie Pie an apologetic look.
Pinkie grinned in response, bringing a hoof to her lips and nodding understandingly.

BANG, BANG, BANG-BANG-BANG-BANG! Twilight rapped at the door eagerly, causing it to shudder in its hinges.
There were shriek of a high pitch, a bark, a roar and a harmony of various other grumbles, all from the creatures the gentle pony had taken under her care. In amongst the ruckus, the door clicked open.
Fluttershy emerged behind the large oak door with a quiet “meep”.
The fearful expression of the mare loosened when she saw it was Twilight.

“Twilight?” The yellow pony yawned widely. Her mane was untidy, tangled and messy from a long night’s sleep.
“What brings you here so early?”
“Fluttershy we need to go, now. Celestia needs the elements of harmony for something very important! Come with me please, we haven’t a moment to spare,” Twilight shuffled back and forth, bouncing on her hooves impatiently.
“Oh my…” Fluttershy disappeared into her home, quietly closing the door behind her.

Twilight’s eyes widened; if Fluttershy didn’t come, they wouldn’t have the six elements. And if they didn’t have the six elements, that means she would fail Celestia. And if she failed Celestia, she would no longer be…
Her frantic thoughts were soon interrupted by a click of the door. The timid yellow pony reappeared, carrying a soft saddlepack on her side.
“Let’s go,” she whispered, gently flapping her wings.

It wasn’t long before the trio of ponies had reached the parlour of Rarity.
They were all exhausted, panting and wheezing after the trip to the home of Ponyville's fashionist.
“May as well get the most difficult wake-up out of the way,” Twilight murmured, knocking heavily on Rarity’s well-decorated door.
None of them expected Rarity to be awake at this hour; however the door was swiftly opened. Before them stood the meticulously clean white mare; her mane all done up and make up perfect.

“Darlings, what’s wrong? You all look exasperated!” She observed, raising a hoof to her mouth dramatically.
“Rarity there’s no time to explain, Celestia needs us all to meet her at Canterlot, it’s an emergency,” Twilight was getting tired of repeating the same story. There simply was on time.

Next was the elusive pegasus, Rainbow Dash. The early timing was a blessing to the troupe of ponies; the morning-team of pegasus had cleared the skies, leaving little room for the blue and rainbow pony to hide. She was more than easy to find.
Or, the four of them were easy to find, as Rainbow was out on an early-morning fly.
With a burst of the last cloud in the sky, she emerged, looping around before landing in front of Twilight.
“Hey guys, what’s going on? Wow Twilight you look like you need to chill a bit, your eyes are all crazy,” she laughed, nudging the frantic mare playfully.
“RAINBOW THERE’S NO TIME TO EXPLAIN!” Twilight shouted, causing Dash to jump back into the air.

The student-pony began galloping off towards Apple Jack’s barn without another word.
The blue Pegasus flew beside the trotting Rarity, a look of confusion consuming her expression.
“Jeez, what’s gotten her tail in a knot?”
“Dear Twilight has been requested to gather us and meet up with Celestia, apparently it’s a real emergency,” Rarity trotted along carefully, delicately attempting to not break a sweat. Spike had been kind enough to fill Rarity in on the past few weeks’ events nervously; blushing at the thought of Rarity’s attention.

Twilight felt a strong wind toss her mane forwards, covering her eyes. The mare was losing her temper. However, when she looked ahead, she could see a small orange speck and a swirling blue one. The two specks soon increased in size, and met her halfway to the barn.
“Thanks, Dash,” Twilight sighed gratefully.

Once the six were together, Twilight prepared herself. Her teleportation spell wasn’t perfect, and required a lot of energy. She would only be able to perform it once; if she missed or it didn’t work, they would need Celestia’s help. The mare nervously gulped, preparing her stance for initation. The unicorn's horn began to glow, slowly lifting open her saddlepack to retrieve the spell-book.
However, as she began to pull out the heavy leather-bound book, a loud overhead voice broke her concentration.

“Good work Twilight!” The royal, booming voice echoed throughout the nearby apple orchids. “You’ve done as I’ve asked. Welcome, ponies,” Celestia stepped down from her royal chariot, the escorting stallions bowing in respect. An eminant glow emited from the tall alicorn, as she loomed over the group.

All six ponies dropped to their knees, bowing their heads to the Princess.

“Now, Twilight, about the pressing issues at hoof. You all have much to learn about the past. I was hoping it would be able to wait a few more years, but it seems I cannot put it off any longer.
Would you kindly join me in the chariot, and we can discuss this in the privacy of the Canterlot library? Or better yet, my castle,” the tall princess stepped back up on the golden carriage, motioning for them to join her.
She scooted over, her flowing mane reflecting the morning sunlight in an elegant, soft rainbow.

As the six got settled in, the carriage took flight, allowing the crisp, dewy air to brush through their coats. Soon they were on their way, keeping consistant speed as the escort-stallions pulled through the fresh air.

Celestia made small talk with the six on the way to her kingdom.

“Have you all been learning lots about the elements of harmony, and the magic of friendship?” She looked across at the beaming faces, as they all nodded in response. Anypony would have been honoured to meet the saviour of Equestria.

This is THE Celestia! Twilight thought to herself nervously, blushing at the royal presence. Her mind soon turned back to the question at hand, as she furiously nodded. The mare had studied hard, learning as much as she could over the past few months.
"Definitely, Celestia... We've all learnt so much already about the elements."
“Good… You’re going to need those lessons, and all the new knowledge I will give you all. This task is unlike any I've ever given you, any of you. Especially you, Twilight,” Celestia turned and looked gravely at the sweating purple mare.

What if I haven’t done enough? What if I can’t do it? What if I fail? Twilight’s mind went on a frantic spree, as she clacked her hooves together in anxiety.
“Twilight, it’ll be fine,” Spike reassured her, gently touching her shoulder. “You’ve studied hard, I’m sure you’ll be ready.” Her anxiety always frustrated him, but it was one of the many unique things about her that made Twilight so special. And of course, one of the main reasons she was the most faithful student.

Beneath them, the green grasses of Ponyville soon turned into various landscapes, all passing under them like a scenic conveyer belt. Apple Jack peered down to see a sandy plane, sporting a tiny village. The huts were the size of marbles to them; the carriage flying on cloud-height to avoid being seen.

“What in the hay?” Apple Jack spotted a small canyon, one she had never seen before, etched within the sandstone landscape. Scattered throughout it were tiny black structures.
“Now who would live down there? They must be unlike anypony I’ve ever seen, to survive livin’ in the middle of nowhere!” The country-style pony scrunched her face in confusion, shooting a look to Twilight and the princess for some form of answer.

Celestia turned and viewed down the gorge. “I will send my guards out to make sure they’re okay,” a concerned look choked the smile off Celestia’s face. The majestic princess sighed in defeat, rubbing a adorned hoof on her forehead.
“We try to make sure everypony is well looked after,” she looked back up at the six before her, hanging on her every word. “But when ponies insist on living alone, out in places as baron as this, it can be hard to care for them. It’s a tough job, and it puts my men under stress. But alas, it must be done, for the good of everypony.” Her tone was deep and sinister, one of grave concern and frustration. The edge in her voice made Twilight shiver.

Clean, shiny buildings soon came into view, as the chariot lowered down from the cloud cover. A reflection of gold, silver and bronze absorbed the carriage, reflecting beautifully off the guards' armour.

The beaming city of Canterlot soon consumed their vision. It was by far one of the grandest cities in all of Equestria; housing the princess meant that a huge amount of wealth was by default put into the design and building of the citadel. It had been a work in progress since the downfall of the destroyer of Equestria, the one who undid it all.

“Welcome, my students, to my domain,” Celestia gracefully jumped out of the chariot, gliding on her soft white wings to the main entrance of the castle.
The mane six waited for the chariot to come to a halt, before feebly stepping onto the polished marble.
Twilight wobbled slightly, uneasy from a long flight. She had never been one for long-distance travel, and even under the care of Celestia, it still made her uneasy. After taking a deep breath and regaining her balance, the mare looked up and gasped at the site before her.

Twilight was soon joined by a chorus of gasps, all at the site of the main city; the huge ten-foot golden doors stood before them in glowing, holy aura. The city had come underway after the banishment of the destroyer, and Celestia had taken it upon herself to design its new appearance.

“Come in,” she said as she gently nudged open the grand doors. Not even a peep was heard from the mountainous entryway.

The entirety of the marble floor glistened in the newly introduced light, each inch carefully polished by the worker-ponies.
Golden statues of each of the pony-greats lined the side walls, all placed on stone pedestals. They each held their own past, their own provinence for the future, and their own moral. The beautiful busts held part of Equestria's make-up, what brought all the ponies to where they were today, under the care of the Princess.

Twilight, despite studying under the princess for such a long time, would never get used to the site of the palace. It was the most majestic site in all of Equestria, and each time she had the honour of travelling there, she was breath taken.
“Now ponies I need you to listen very carefully,” Celestia sat upon her throne. A sturdy tone and stern look crossed her face, as she began to focus and draw the attention of the six elements standing before her.

The princess’s horn began to glow blue, before illuminating the entire room with the consuming aura. The marble floors glowed with the incandescent light, causing Twilight to squint.

A figure soon emerged from the bright blue light; a mare, the height of Celestia herself, cackling and throwing her head back in laughter. All six jumped back at the booming, menacing laughter, shivers rattling their spines.

“This, is Nightmare Moon," Celestia's voice echoed throughout the hollow, ominous room that had become the castle innards.
With dark look in her eye, Celestia stared down at the six ponies, taking in a shallow breath.
"This is Nightmare Moon. And this, is her story."

Author's Note

Sorry for the huge amount of time it's taken to get this out! Lots of Uni work, but now I'm on break, so back to writing it is!
Enjoy :) And as always, constructive feedback and crit are welcome.
Thanks for reading, everypony!