The Lords of Harmony: Shadow of Malice

by Whinifree

Rating: teen
Tags: Adventure, Princess Celestia, Main 6, My Little Pony: Friendship is Magic, Dark, Other, Nightmare Moon, Princess Luna, Mystery
Length: 4267

Equestria is under siege by shadowy creatures led by Nightmare Moon. While Celestia rallies the ponies to push back, Twilight and her friends must journey beyond Equestria to uncover the secrets of a dark, crystalline substance called midnium.

The wicked Mare of Darkness, Nightmare Moon, has returned to the world and in a body all her own. Wielding the power of the enigmatic Alicorn Amulet, and with an army of shadowy creatures called The Animus at her disposal, she has turned Princess Luna into her thrall and warped the Crystal Empire into a nightmarish wasteland. From this new seat of power, she sets her sight on the very heart of Equestria.

While Princess Celestia rallies the ponies to fight back against the dark horde and does her best to maintain the Equestrian way of life, it falls to Twilight Sparkle and her friends to find a way to break the power of the Alicorn Amulet and free Princess Luna from Nightmare Moon's dominion. With only Luna's thousand-year old journal to guide them, they set out on a journey that will take them beyond Equestria as they seek to learn more about a dark, crystalline substance called midnium; a journey that will shed new light upon the literal darkest day in Equestrian history.

-part 2 in The Lords of Harmony series. takes place mid-season 3, before Keep Calm and Flutter On.
-this story assumes there is a one-year time frame for each season of the tv show, give or take a couple months
-edited by BronyDad. Many thanks to him! Give his stuff a look, as well!

Published 2018-02-06 22:50:06 UTC
Last updated 2018-02-06 22:50:06 UTC

Chapter 1 - Visions of a Princess: Heart's Fire

A memory stolen by the beating of time.

The timely beating of a scattered heart.

One wish...

An altered world...

How long has it been?

I wish... I wish I could remember...

Slowly, the passage appeared on the blank page and etched into the deepest corners of Princess Celestia's mind. Lying still on the thick carpet of grass with her mane and tail flowing gracefully in their regal manner, she kept her gaze turned down at the book that sat open at her hooves.

The minutes ticked by. Only the soft zephyr that blew gave some manner of life to the open field. High in the sky, the full moon showered its brilliance down upon the land, and the light seemed to reflect off the very tip of each blade of grass, creating a gentle, silver aura that bathed the area in a restful illumination. Complementing the divine body at the center of the canvas, the night sky was filled end to end with flickering stars and swirling galaxies from the deepest reaches of eternity.

Celestia read the passage aloud, and her voice echoed all around her. Each word flashed gold when it was spoken. Though the pages of the book flapped in the breeze, they did not turn from the page that the princess was focused on. A moment later, an orb of golden light, slightly larger than a snowflake, drifted down into Celestia's view and vanished upon touching the ground next to her left foreleg. She turned her gaze up and spotted several more of the little orbs directly above her. Rising to her hooves, she backed up several inches and watched as they floated down. As one of them came into her reach, she held out her hoof.

The orb landed softly on Celestia's hoof.

The princess eased herself closer until the orb was almost touching the tip of her nose. A gentle warmth emanated from the little sphere, and she smiled as she peered into it for long enough that the sight of it blocked everything else from her view. She held this position for several moments then allowed the globe to slide off her hoof and fall to the ground where it immediately vanished.

Celestia let out a sigh and looked up once more.

Suddenly, the stars and the swirling galaxies in the sky faded from sight except for the moon which remained at its zenith. The little glowing orbs began to drift down from the sky in greater numbers; their paths seemingly unaffected by the wind. The light they gave off shifted from gold to silver in an endless cycle. Within minutes, they had spread across the entire field as far as could be seen through their luminous glow, and they descended at a rate that resembled a calm snowfall. These ones did not make contact with Celestia, instead they passed right through her like they were ethereal, and each one vanished upon touching the ground just like their predecessors.

Celestia stared blankly as the orbs passed through her body, but the eeriness it caused within her did not last long. Her smile returned, and it grew wider as she sat down on her hindquarters. She remained there, losing track of the time as she watched the spectacle with a serenity in her being that increased with each passing second. After a while, she returned her attention to the book. Rising to her hooves, she approached it and glanced down.

The message written upon the page was aglow with the same shifting gold and silver as the spheres that drifted from the sky.

A loud rustling from behind Celestia broke the peace of her surroundings. Her left ear swiveled in the direction of the sound and she looked back.

In the midst of the gentle snowfall of glowing orbs, dozens of them were hovering a meter off the ground. The amount that halted their descent quickly became too numerous to count. The ghostly visages of ponies of all kinds started to appear, positioned so that the spheres of light sat where the ponies' hearts would be inside their bodies.

Celestia's eyes widened and her mouth hung slightly open as she became completely surrounded. She turned in slow, full circles, taking in the scene with a growing warmth in her heart that touched her to her core. Longingly, she gazed upon the ghostly images. They gazed back.

The phantasmal ponies did not move or speak. All of them wore a smile on their countenance, beaming at the princess with a brightness that was matched only by the shifting gold and silver orbs that continued to fall from the sky all around them. The spheres within the ponies' see-through chests started to pulse in a manner that resembled a heartbeat. One by one, they bowed to Celestia, and the orbs moved with them, remaining fixed within the ponies' spectral forms where their hearts would be. Once they returned to their standing positions, they turned their attention toward the heavens and gazed upon the full moon.

Celestia recalled the aftermath of Nightmare Night. Ponies all across Equestria had assembled together and held candlelight vigils to mourn over Luna's abduction.

The princess also recalled the words she had uttered that evening.

Their sorrow burns like the sun. Their love, a million points of light.

Celestia's eyes began to water, but from sorrow or joy, she could not tell. After a moment of reflection, she resolved to believe it was both.

The glowing spheres ceased to fall. Celestia wiped the wetness from her eyes, and looking up, she let out a gasp.

The sky was no longer dark. It was ghostly white and luminescent but the light it gave off did not reach the world below, leaving the land engulfed in shadow. The moon had also changed. It wasn't bright silver, now it was dark.

Sweat ran down Celestia's brow, and her breath quickened as she stared at the moon's abyssal surface. It seemed to stare back.

Despite the changes to the scenery above, the heavenly orbs within the spectral ponies' forms continued to shine and pulse like a heartbeat. One of the unicorns in the crowd walked up along Celestia's right side and held her foreleg over the princess's shoulder. An earth pony took to Celestia's left and mimicked the unicorn's gesture. Two pegasi rose into the air, hovering just above and on either side of the princess.

Celestia looked to each of the ponies flanking her. She peered into their eyes, and the love she beheld filled her such that she stopped sweating and her breathing returned to a gentle rate. She beamed at them. They smiled back.

The spectral ponies parted before the princess like they were creating a path for her to walk. A great gust kicked up which tore the page with the message from the book. The page rose into the air until it was level with Celestia's sight, swaying and turning in the breeze as the princess watched it with curiosity. Suddenly, the page flew away, and disappeared into a forest that stood just beyond the path that the spectral ponies had created.

Celestia stared ahead and her breaths quickened again, but feeling the warmth of the ghostly ponies that surrounded her, the tension did not last long. She closed her eyes, and recalled somethings that Princess Luna once said.

The ones we love are never truly apart from us, so long as we keep them in our hearts...

We can't let fear stop us...

With a new fire in her heart, Celestia proceeded down the path. Her gaze did not sway even an inch as she walked along, and everything went dark as she crossed the threshold into the shadows of the Everfree Forest alone.

After a cautious trek through the abyssal woodland, Celestia emerged into a large clearing. There was no light save for the magic light coming from her horn, and it still only stretched several meters as if it were being devoured by the darkness past a certain range. The wind had ceased. There was no sound except for the princess's hoofsteps on the tall grass. A deep gorge ran through the center of the clearing. The ghostly white sky was visible above, as was the large dark moon.

Celestia walked up to the bridge that spanned the gorge and stopped. Her gaze landed upon a stone structure on the other side.

The midsection of the building was obscured by the darkness of the area, but it's tall spires rose up high enough that they were clearly outlined by the moon. Stone chunks of various sizes littered the ground before the structure, and an archway was built into its base atop a small flight of stairs.

Celestia stared at the ruins of the ancient castle where she and Luna had once resided. She took a moment to catch her breath and stepped onto the bridge. When she reached the other side, the cadence of chattering ponies reached her ears and she paused, looking all around her with her ears perked.

The voices were soft, but they slowly became louder. What they were saying was incomprehensible, but gave the impression that they were having a conversation with each other.

Realizing that the voices seemed to be coming down the path that led toward the ruins, Celestia turned her attention back to that direction. Soon, the voices had come close enough that the princess could make out the voices of five ponies and one other individual, all of whom sounded very familiar.

“You think it's safe for her to stay behind, all alone, in a place like this?” inquired one of the voices.

“Of course it is, Apple—” another began to reply before stopping and clearing its throat. “I mean, Mistress Marevolous. There's nothing in this forest that she can't handle. And even if there were things she can't, she's a quick getaway with that teleportation magic.”

Celestia's eyes widened.

It's Twilight's friends!

“If'n you say so, Zapp. I still got this feelin' though...”

“Well why didn't you offer to stay with her then?”

“I would have but she said it was just to clear her head and I figured that couldn't take that long. I didn't want to seem pushy neither.”

The conversation became incomprehensible again as the voices passed by the princess. They quieted as they seemed to start crossing the bridge, and soon faded completely.

Silence returned to the area. Celestia watched the bridge for a minute then turned back to face the old ruins.

I wonder...

Without further hesitation, Celestia walked up the path. She weaved through several pony-sized chunks of fallen stone and ascended the steps. She kept her pace as she passed through the archway and entered the ruined citadel, using the magic light of her horn to guide her through the pitch-black outer foyer and then the corridor beyond that.

Eventually, she came to a spacious chamber large enough to hold a crowd. Banners bearing the crest of Equestria hung from the walls. At the far end of the grand hall, two marble thrones sat upon a raised platform. The sun was engraved on one throne, and the moon on the other. Unlike the rest of Celestia's journey, there was light in this room, but only enough that the center of the chamber was fully visible as were the old thrones. The rest of it was partially obscured by shadows.

In the center of the room, Twilight Sparkle was seated on her hindquarters facing away from Celestia and staring up at the ceiling.

Celestia smiled and took a step closer, then sat down on her hindquarters just in front of and to the side of the archway she'd entered from. Her horn stopped glowing and her magic light faded. She watched Twilight momentarily before turning her gaze to the dark corner behind the throne with the engraving of the moon.

She watched, and she waited.

“Someday, we're going to rebuild this place,” said Twilight.

Celestia glanced at Twilight but remained still.

“We'll make it even better than it was before, and ponies will live here again.” Twilight rubbed her chin, and letting out a sigh, she turned and started to make her way toward the exit near the princess.

Celestia gasped under her breath when she saw Twilight's face.

Two sets of three parallel, pitch-black lines were apparent on the unicorn's face. The lines for each set started at opposite sides of her head just below her ears then running down and crossing over both of her eyes, meeting slightly apart above the ridge of her snout.

The scars? She didn't get those until weeks after Nightmare Night. Why am I seeing them here?

A rustling suddenly came from the opposite end of the grand hall.

Celestia immediately turned her gaze in the direction of the sound. She lurched her head forward and strained her eyes. She saw only darkness where the disturbance had come from.

Pausing within Celestia's reach, just before she was about to step through the archway, Twilight paused and looked back. After a moment, she let out a soft hum and again started toward the exit. Her walk was instantly halted though when the rustling came again.

Celestia blinked a few times as the outline of something sitting in the corner behind the old thrones came into view.

The figure appeared pony-like in shape, but it was obscured by the dark clouds that seemed to swirl about its form. It wore a large cloak as dark as midnight, and a hood was pulled up over its head, shielding its face from view.

Celestia glared at the shadowy figure.

Twilight whirled around and scanned all along the back wall, seemingly not spotting what Celestia had. “Hello? Is somepony there?”

The unicorn waited for a response, but none came. She lit her horn and the space around her became illuminated in magic light. When she at last noticed the new arrival lurking in the back corner, she took a few steps closer to the raised platform where the old thrones sat.

“Uh, hello,” said Twilight. Her tone was gentle, but carried a level of reservation. “My name is Twilight Sparkle. Who are you? Were you back there this whole time?”

The shadowy figure gave no reply.

Twilight raised her brow. “Can you hear me?”

“I was drawn here by the magic of this world...” The deep but ghostly voice echoed across the grand hall.

Twilight winced and rubbed her horn. “I'm sorry?”

“There is a hole in this world...”

“What do you mean?” inquired Twilight.

“Deep as the endless void. It binds them together as one...”

Celestia's glare intensified as she listened to the exchange. If only this wasn't a vision I'd stop you right here and now, Nightmare Moon... Alicorn Amulet or not.

Twilight took several steps back. “Well, whoever you are, you better stay back... Who are you and where exactly did you come from?”

The figure was silent for a few moments. “You do not yet know what hides within the veil...”

Twilight trembled and rubbed her foreleg. “Nothing you’re saying is making any kind of sense. What hides within what?”

“Born on the wings of nightmares...”

“Nightmares?”

"I walk this path now. Down the dark corridor, to the place where things go to disappear...”

Several beads of sweat ran down Twilight's brow and she glanced behind herself at the door.

Celestia blinked a few times as the cloaked figure suddenly vanished from sight, and for a moment, she saw a trail of dark smoke rushing up into the air and out the large hole in the back wall. It was all departed before Twilight even returned her attention forward.

“I'm very sorry,” said Twilight, “but I don't know what you—”

Silence returned to the room. Frantically, Twilight turned about and cast her magic light over every inch of the grand hall. After that, and keeping her horn aglow, she sprinted through the archway that led out of the castle.

Celestia rose to her hooves and moved to the exit, peering into it just in time to see Twilight's image disappear into the darkness. Once the sound of Twilight's hoofsteps faded, she turned toward the old thrones and stared at the spot where the cloaked figured had stood. She made her way up to the dais, stopped a couple meters from the broken balcony between the thrones, and gazed up at the large hole in the back wall.

So, that must be how she infiltrated the Canterlot vaults and got her hooves on the Alicorn Amulet. Mist form... I should have suspected such, but I didn't know she could move so fast like that. It had to have been at night. She probably moved so fast the vault guards didn't even see it, just like how Twilight didn't see her enter or exit the ruins on Nightmare Night.

As Celestia stepped closer to the balcony, her horn started to tingle slightly. She winced a little and rubbed it.

Negative energy... There aren't any midnium crystals around, but there is definitely something here. Could it be some lingering field from when Luna summoned the eclipse? Magic that powerful does tend to leave part of itself behind, but even something as empowered as that should have dissipated after a while. Could there really still be some of it in the old castle? Seems like it's coming from the balcony...

Celestia took another step toward the balcony. Without warning, a blinding flash engulfed the grand hall and the princess's vision turned solid white. She could no longer feel the ground beneath her hooves. The strange sensations that began to course through her made her feel lighter than air, but it lasted only for a moment and it suddenly felt like she was falling. She tried to flap her wings, but it seemed like all control of her limbs had left her body. She started to feel dizzy, and everything went dark as her eyes forced themselves shut.

The princess let out a weak groan as she slowly came to. Dizziness wracked her head. She could not feel any part of her body, and she lacked in strength so much that she could not open her eyes. She could hear nothing save for her own slow breaths, and she rested there for a length of time which she could not count. Eventually, the feeling in her body began to return.

She felt something soft beneath her; soft, but grainy. The ringing in her ears lessened, and the sound of sloshing of water reached her. It grew in volume until it was almost overpowering, then lessened until it was barely audible before rising again, and it repeated this motion endlessly.

The sonance filled Celestia with a serenity that helped to calm her racing mind. Finally, enough of her strength had returned that she peeked her eyes open. She blinked until her vision cleared, then stared in confusion as the ground she was fallen upon came into clarity.

Sand?

Lying on her right side, Celestia eased herself up onto her stomach and folded her legs in a little. She rubbed her throbbing head then stood up. Her legs trembled with fatigue, but she was able to keep herself steady. Shaking the remaining sand from her fur, the princess's eyes widened as she beheld her new location.

She saw that she was under the same ghostly white sky and large, dark moon from before, but during her unconsciousness, she had relocated to a sandy beach. To her left was the unmistakable growth of the Everfree Forest which stretched as far as the beach did. To her right was a vast sea, but the surface of the water did not mirror the whiteness of the sky. It was as dark as the moon, and its waters glided up and down the shoreline. The area seemed to be illuminated like it was under a full moon, complemented by endless soft flashes of silver light from the water's rippling surface.

Definitely still dreaming...

Celestia's mouth hung slightly open as she took in the sight. She looked at the edge of the forest for a moment, but then she stared along the beach and darkened sea, both of which stretched out further than she could see. Though the environment sent shivers down her spine, the uneasiness that poked at her being was somewhat lessened by the sound of the waves.

Standing tall, she gazed out across the dark waters while her mane and tail flowed behind her. Occasionally, the waves reached up the shore far enough that her front hooves became submerged, but she did not recoil.

Celestia remained in this position for a while. Finally, she sighed under her breath and began to turn toward the forest, but she stopped partway and furrowed her brow. Lurching her head forward and straining her eyes, she spotted something on the beach not too far away.

Her breathing hardened and her legs seemed to lock in place as she stared at the unknown object. She swallowed hard, but then the tension that had suddenly gripped her legs vanished and she stepped closer and closer until she was able to make the object out. Quietly, she gasped.

A pony-shaped creature stood there, wearing a large dark cloak that completely concealed its features, and was staring out at the sea.

Every memory of everything that had transpired on that fateful day over a thousand years prior invaded the princess's mind. It was immediately joined by every memory of everything that had transpired since the most recent Nightmare Night. Celestia's stare turned into a fierce glare and every ounce of her being urged her forward, but she had not advanced another meter when a loud crack like the snapping of a twig stopped her in her tracks. She looked in the direction of the disturbance.

Shortly following the snap, the sound of rustling grass and bushes reached Celestia's ears which quickly grew louder.

Something's coming, but who or what else is here?

Celestia's eyes widened as another figure emerged from the darkness of the forest.

Similar to the first figure, the new arrival had a pony-like shape to its body and their movements matched that of a pony. It also wore a large cloak that hid its features from view. However, there were two discernible differences about them: they were a head taller than the first figure, and what appeared to be a large horn could be seen coming up out of their head. The new arrival moved up and stopped alongside the first figure, which blocked the first from the princess's view.

Stepping to her left a few paces so both of them were once again in her sight, Celestia's gaze rapidly switched from one to the other. The longer she stood there while neither of them spoke anything, the more sweat ran down her brow and the harder her heart pounded in her chest.

“So, you actually came...” said the first figure before glancing at the new arrival. The voice was that of a male. It was a little deep, but also had a mildly soothing quality to it. Despite sounding a little hoarse, the figure's words had come out perfectly clear.

The horned one gave no reply and simply stared forward.

“Does this mean there's still a chance?”

"Their little festival will begin soon," said the second figure. The voice was that of a female. She sounded scornful, but there was also a strong hint of anxiety in her tone. "We are ready and waiting..."

“Then why are you even here?” asked the first.

Again, the second was silent.

Celestia furrowed her brow and sat down on her hindquarters, swapping her attention between them as each one spoke.

The first stared at the second for a moment longer before looking back out to sea. “I've been to see it. Even being near it, I felt such, such peace. Such harmony...”

“How many years has it been since I felt such things?” asked the second. “I wish I could remember.”

“I have seen the unicorn and her friends.”

The second let out a snort. “Those wretches destroyed our hopes once before, but this time will be different. I have a new weapon at my disposal.” She raised her foreleg and rubbed her neck. “And soon, I will have another...”

“The ponies talk about you from time to time. Are you truly so desperate?”

The second lowered her foreleg and looked down. “The light in their hearts is rapidly fading. If I don't do this, we will be lost, and their suffering will be my failure." She sighed heavily. "This... this is the only way..."

“I will ask again. Why did you come here to me?”

Remaining where she sat a number of yards away, Celestia watched as the second figure turned and strode back into the shadows of the forest. The princess kept her gaze on the spot where the second had disappeared from sight. After the rustling of dense foliage ceased, Celestia returned her attention to the first.

The minutes ticked by, and the sound of the ocean tide upon the shore was once again the only audible thing in the area.

The first continued to stare out to sea. Eventually, he raised his foreleg and rubbed his neck.

Celestia furrowed her brow again, and everything turned dark.

Author's Note

Thanks for reading!