"Twilight...are you sure about this?"
Fluttershy's concern was a feeling shared by all of the Princess' other friends, and as Twilight turned to her, she smiled warmly, placing a gentle hoof upon her shoulder.
"Don't worry, Fluttershy. I know we can do this."
"Yeah, confidence is all well and good, Twilight, but if it means having to come here? Yeah, not so cool."
Rainbow's words were hardly unjustified, as their current surroundings were probably the last place any pony would want to find themselves. Dark skies, rocky terrain, barren soil that hadn't seen even a smidge of green in centuries? No, this was a place where life was not meant to be, and so naturally sent a chill down the mares' spines. Twilight, by contrast, remained firm in her convictions.
"Girls, as bearers of the Elements, we have a responsibility to fight evil wherever it may be. And this...may be the greatest evil we ever face."
Rarity, clearing her throat a little, stepped forward.
"Yes, well, I'm all for thwarting some evildoer, but do we really have to seek one out like this?"
Applejack nodded, walking alongside her unicorn friend.
"She's right, Twi! The Pony o' Shadows has been imprisoned fer, what, a thousand years? Maybe more?"
Twilight frowned.
"Yes...and legends like Starswirl and all his friends laid down their lives to see it happen."
There was a grim mood after that, and only Pinkie remained even remotely perky afterwards.
"Hey, if we work together, we can do better, right? I mean come on, there's never been a baddie we couldn't face!"
Fluttershy looked to her timidly.
"Yes...but this is the Pony of Shadows, Pinkie! The cause of all the bad in the world! That's worse than anything we've ever faced!"
Twilight frowned with determination.
"Fluttershy's right. It will be worse. But, while that ancient evil may be sealed away now, there's no guarantee that will remain the case."
She looked ahead, sighing.
"Discord broke free of his magical bonds once. Who's to say the Pony of Shadows can't do the same? And what if it happens when there's no pony to face him?"
Taking a moment to let the silence of her surroundings sink in, Twilight turned, facing the rest.
"If we face him now, while we have the power to actually stop him...we may rid Equestria of conflict and strife forever!"
The mares all looked down, to the Elements they bore, which glistened in what little light would peek through the dark clouds above. They still had their doubts, but with Twilight leading them, they at least were willing to see this through, just as they always did. With a simultaneous nod, they gave her the consent she needed, and after smiling back to them, Twilight resumed their journey. It didn't take long though, and soon, after turning one corner in particular, they came upon that which they had been seeking.
"The Temple of Darkness."
A door, as large and imposing as that of Tartarus itself, embedded into the side of a rocky cliff, lay before them. Twilight took a deep breath, and as she stepped forward, her crown, the Element of Magic, began to glow. The others followed, and before long, all six Elements began to activate in unison. Merely approaching this door had the effect Twilight was looking for, and she knew that, eventually, they would break the age-old-seal. Together, they stood, ready to face whatever came, and within moments, the Elements fired together, as they had done so many times before.
A blast of rainbow-coloured power shot forth, striking the door head on, and as that great power continued, a glow engulfed the door, which thus began to shatter. The seal was weakening, and Twilight subconsciously willed the Elements to go even further. They obeyed, and soon, the seal was at last finished, breaking apart. The power faded, and the Elements calmed, allowing just a moment of silence before anything else happened. But that silence did not last, and after a long sigh, Twilight marched onward.
"...It's time."
Her friends followed, and soon, before they even reached it, the ancient doors slowly creaked open, dust falling off them for the first time in millennia. It was dark within, more like a cave than a temple, but they continued all the same. Then, without warning, a torch on a nearby wall was lit. Then another, and another, and another, until finally, they stood in something far more worthy of the name temple. Pillars, murals, centuries-old architecture, this place was ancient by every measure of the word. And yet, one thing was strangely absent.
"Well? Where is he?" Rainbow remarked.
Twilight too was disturbed by the fact that their quarry was missing, but she said nothing, and instead continued towards the far-end of the chamber. There was a large piece of art there, that of a towering pony-like figure, bathed in darkness, facing down six others. Twilight knew those six, the heroes of legend who had fought it, and even died to contain it.
"Something's...not right."
And that was when it happened. As Twilight and her friends all gathered together, looking to the picture, Twilight's gaze fell upon their shadows. But, ever so slowly, another shadow made itself known. It rose slowly, towering above the silhouettes that the mares cast upon the wall, and even the air itself became icy. Twilight, and all the others, they could feel it now, that they were not alone. And with slow movements, they turned. When they did, they stared wide-eyed at he who stood before them.
"Welcome...to my home."
The Pony of Shadows, standing taller even than what the mural had depicted. A being of pure darkness, menacing and dangerous. Yet his voice had been calm and measured, more like a Grandfather than a nemesis. But Twilight, who had faced many enemies before, did not hesitate any further, and so readied herself.
"NOW!!!"
Her friends roused from their shock, and together, they again awakened the power of the Elements. Once more, that rainbow power shot forth, engulfing the newly-emerged Pony of Shadows, blasting him with the same force that had vanquished Nightmare Moon and Discord. Twilight could feel a sense of triumph, as she had in her past victories, but when the light of their artefacts began to fade, she was instead greeted with, of all things, that same calm voice.
"Well now...not quite the homecoming I'd have wanted."
Twilight, to her utter horror, saw that the Pony of Shadows was still there, unfazed and unscathed from their attack. A power that had served them so well in the past, now seemed to have had no effect whatsoever on this greatest of adversaries.
"T...Twilight?" Fluttershy muttered, clearly wanting answers.
The Princess, though taken aback by this unexpected failure by the Elements, soon recomposed herself, and frowned deeply at her enemy.
"Pony of Shadows! I, Twilight Sparkle, Princess of Friendship, vow to defeat you, and forever rid Equestria of the darkness you brought forth!"
She stepped forward.
"Together, my friends and I will undo all the evil you have done, and bring true goodness back to Ponykind!"
But while her friends too seemed to get caught up in that sentiment, the enormous stallion was, thus far, unimpressed, and let out a sigh of his own.
"I see."
He turned, looking upon the mural that depicted his ancient battle against Equestria's heroes.
"Some things never change, it would seem."
Rainbow scoffed.
"What are you talking about?!"
The stallion raised an eyebrow.
"Your predecessors made the same assumptions, the same mistakes, and look at what happened. They gave their lives to seal me away. All that effort...for nothing!"
Twilight fumed.
"It wasn't for nothing! They gave Equestria a time of peace! A time when you were not there to corrupt the hearts of ponies!"
The Pony of Shadows chuckled, causing no small measure of annoyance for the Princess.
"What's so funny?"
Her enemy slowly shook his head.
"Princess Twilight...the story you believe in so strongly, the story that led you and your friends here to, as you say, 'vanquish' me? None of it was true!"
Applejack walked beside her alicorn companion.
"That's a lie, Twi! He's tryin' ta get under yer skin!"
"Oh, I assure you, this is no lie, young one. This is the greatest truth you will ever hear! And Stygian is a stallion of his word."
Twilight gained a look of confusion.
"Stygian?"
The stallion appeared deflated at that remark.
"So...even my true name has been lost."
Growing impatient now, Twilight resumed her frown.
"Alright then, Stygian. If you have something to say, say it now."
Stygian smirked.
"You know, considering that I'm being more than hospitable to those who came to my home to try and kill me, I'd suggest you take a more diplomatic tone than that, Princess."
Twilight's expression did not change.
"No matter what you say, nothing is going to convince us that you aren't a danger to our people."
Stygian did not smirk, or sneer or look in any way happy, yet he simply nodded respectfully, and so began to slowly stand tall and walk around the collected mares.
"Do you know how I first came to be? How I became what I am today? I was, in days long past, a minor spirit. Little more that a wisp of smoke, drifting from here to there. And as I happened upon communities of ponies...I would feed."
He gained a nostalgic look.
"Wherever ponies disagreed, disputed or even outright fought one another, I would grow stronger."
Rarity looked to him, intrigued.
"Like a Windigo?"
Stygian chortled.
"Yes, quite. We were much alike, them and I. Though in the start, I was far less than they."
Seriousness came to him.
"But, with you ponies being what you are, there would always be a time when the conflicts ended and you would go back to the peace you always loved so much. Many of my kind were driven off, or outright starved when such calms came."
He paused, looking again to the paintings on the walls.
"And that...was when I noticed."
Slowly, he drew nearer to the image of himself.
"When all others of my kind had given up on ponies, or left them behind, I realised something. I, alone and unique of all my kind...did not lose the strength I gathered from the conflict between your people."
He looked back to the mares.
"I kept that strength, and over time, no matter how small the strife between you...I would keep getting stronger."
He faced them fully, starting to walk closer.
"Over the years, I became more than what I was, and after a time, I took the form you now see. A thinking, speaking being, far above the base and primal spirit I began as."
A dark grin came to him.
"It was good, those far-off times. I moved from place to place, feeding off all the petty squabbles you ponies had, all the while becoming...more."
Here, Twilight had heard enough.
"That's right! You poisoned Ponykind against each other! Every bad thing our people have every done is your fault!"
Stygian again frowned to her.
"My dear child...you believe I am the cause of your people's shortcomings? Have you not been paying attention?"
He turned, looking her right in the eye.
"You make the same error Starswirl once did. I did not cause ponies to be as they are. Ponies...caused me."
Twilight was incensed.
"That's a lie!"
Stygian shook his head, albeit very slightly.
"No...it is not. When that battle began, I had no intention of making Starswirl and his colleagues into my enemies. But they saw the connection I had with the darker side of pony behaviour, and they came to the same swift conclusion..."
He grimaced.
"...that I must be the cause of it."
The bitterness in his voice was palpable, and yet, as he dwelt on that, he actually started to look, of all things, amused by something.
"It's funny, when you get to it. They, who so revered the Tree of Harmony, never considered it when they faced me."
Curiosity got the better of Twilight, and she took a cautious step forward.
"What do you know of the Tree?"
Stygian looked back down to her.
"I know its power when I feel it, and I feel it on you this day, Twilight Sparkle."
His eyes focused on their Elements.
"The Tree of Harmony, you know it yourself. You see it as the source of all that is good and decent and harmonious in your land."
Again, he looked amused.
"But consider this...were ponies incapable of becoming friends before the time of the Tree?"
Twilight looked like she was about to answer, only to suddenly find herself at a loss for words. Realisation came to her, and though she said not a single word on it, Stygian could recognise it on her.
"That's right...the Tree came after. It did not introduce friendship and harmony to your people. But it grew strong and healthy over the course of history because of those things."
Raising an ethereal hoof, Stygian placed it onto his own chest.
"It and I are the same in that. Two sides of the same coin. You ponies believe we brought harmony and conflict into the world...but those forces created us."
His tone had become calmer, almost at peace, even when continuing to speak to those who had come here specifically to ride the world of him.
"I do not cause your people to hate one another. How could I? And nor do I seek them to be harmed, as you so assumed. The Tree and I, we represent light and dark, but we do not control it."
A hearty laugh.
"Did you not wonder why your Elements did not hurt me? It is simple? I am not evil, and nor do I cause evil. Thus, the power of the Tree cannot do me harm."
A long sigh was heard from him.
"You ponies look to one such as I, you see the darkness from which I am born, you recognise my connection to the evil in your hearts...and you all invented a story. A parable to tell for generation after generation. To the world, I am the source of all that is wrong...because nobody ever tried to ask if it was true."
Walking forward herself, Rainbow continued to look sceptical.
"Why would ponies make something up like that?"
Stygian's eyes narrowed.
"Isn't it obvious?"
He walked forward, much to the mares' concern, and he leaned closer, bringing his face right up to Twilight.
"It...was...convenient."
A small smile crept onto his lips.
"After all, why admit to being responsible for one's own failings, when it's so much easier to blame some evil spirit?"
He stood tall once more.
"Oh, we ponies aren't responsible for all the bad things we do! It's the fault of the Pony of Shadows! He puts evil thoughts in our heads! He whispers in our ears! He turns us into enemies!"
A slow shake of his head.
"Honestly, the things some people do to avoid accepting their own flaws."
Twilight had been silent for some time, taking in every single word that had been said to her. When Stygian had began, she had been sceptical, as all of them had been. But now, having heard this story, one that had caused her to ask many unexpected questions, her resolve wavered. Every once in a while, her eyes would flicker, showing just the tiniest bit of uncertainty. Yet she stood firm all the same.
"And what do you expect us to do? Just...let you go? To continue growing strong off all the bad things we ponies do?"
Stygian regarded her carefully.
"And what else can you do, exactly? You cannot end the terrible deeds of the world by bringing me down, because I never caused them to begin with. You cannot fix your people because they were never flawless. And above all else...I never once sought to attack your kind, in spite of all the stories you've made of me that say otherwise."
In stark contrast to what a mythic being such as him would have been expected to do, he shrugged.
"Conflict cannot be ended...just as friendship cannot be ended. To believe otherwise...is foolishness."
Silence fell between all of them, and the mares all looked to Twilight, hoping she would have some plan or guidance for them, as she always did. But she remained quiet, thinking over all she had learned. Stygian, for his part, simply stood there, in that nonchalant way of his, looking to the young Princess with only the mildest of curiosities.
"Well, Princess Twilight? What is it to be?"
Slowly, Twilight looked over her shoulder, to all of her friends. She could see how lost they were, just as she was, and though they didn't say anything, she knew they were all thinking the exact same words. Words which, in this ancient place, she now spoke.
"I...don't know."
Author's Note
A while back, I was talking about MLP with an old friend of mine, and during the discussion, I was inspired to write this story. Jeremy, better known to all of you here on FimFiction as Jay David, was talking about how much he disliked the season seven finale, Shadow Play. And while I didn't share his problems with the episodes, I was interested in hearing how he would have done things differently.
So, he basically gave out a few ideas, largely concerning the episode's villain, the Pony of Shadows, and one of the ideas he said really stuck with me. The idea of him being a character that people only thought was evil. Someone who had been miscast as a villain by generations of false stories, and who, in reality, was symptomatic of the problems of the world, rather than the cause of them.
This idea fascinated me, and since Jeremy is at this point no longer interested in writing new stories, I asked if maybe I could take a stab at it. He said it was fine, and so here we are 
"So...this is how we say goodbye."
Twilight's sadness was there on her face for all to see, and she walked slowly to the devastating sight before her. The Tree of Harmony, once so great and magnificent, now nothing but a shattered ruin before her. The Elements, gone, their power vanished from this world forever. And while victory against the darkness of king Sombra had indeed been accomplished, there was no escaping the bitter feeling that she'd still failed. As she approached, she took a single crystalline fragment of the Tree that was, holding it in her hoof as she sighed.
"I'm sorry. I wish I could have done more to save you."
She knew the Tree couldn't hear her, but she needed to say it all the same. The piece fell from her hoof, and her head hung with shame over her belief that she had failed. But in this time, alone in this place, a new feeling came to her. It was a coldness in the air, and a chill down her spine. She didn't think much of it at first, yet as the moments passed, she began to feel as though this sensation were familiar to her somehow. Soon, her eyes widened, doubly so as a voice spoke softly behind her.
"So, it is as I sensed. The Tree is gone."
Twilight spun in place, looking on as she saw the one whom she'd suspected was there. Stygian, better known as the Pony of Shadows, towering above her and looking down with that face that was so hard to read. Twilight's wings flared up, and she readied herself for a fight, but the ancient being of Equestrian legend made no move against her.
"Peace, Princess. I do not come here for battle."
Twilight didn't know how to feel. This was a figure who had plagued the stories of pony children for generations, yet her last encounter informed her well that this was not the slathering monster of the fables, but something entirely different. But she did not cease her wariness, and narrowed her eyes towards this new arrival.
"Stygian. Why are you here?"
The enormous and dark figure walked past her, with Twilight keeping her eyes on him at all times, and she watched as he too approached the broken remains of the tree. A silence fell between them and Stygian merely looked down to it for a time. Finally though, he spoke.
"I came to pay my respects. This power has, since ages past, been my equal. My opposite. It has always been the two of us through these long millennia. Yet now...
He sighed.
"...now it is only I."
Twilight felt herself calm down, but only by a little, and she furled her wings again before walking alongside him. Sadness returned to her, and she drooped her ears.
"It was my fault. I was so confident the Elements had beaten him. Too confident. And then...and then..."
She didn't finish, instead looking away from the Tree's remains in shame. Stygian did not look to her, yet spoke all the same.
"Darkness has always been sly and cunning, Princess. Take it from one who knows it best."
Another silence, but it did not last long, for Twilight soon heard a sound she was not expecting to hear. It was laughter, and one that caused her to look to her unexpected companion.
"You think this is funny?!"
Stygian, whose laugh was fairly dry to hear, slowly shook his head.
"Not exactly. I simply recall an odd thought of mine from long ago. Which of the two of us would fade from this world first? I'll be honest...I never expected it to be the Tree."
His brow furrowed.
"Seems everything is changing these days."
Twilight had no idea what to think right now. This was, after all, the avatar, the embodiment of all darkness and evil in their world. Yet here he was, almost mourning the thing that embodied all of the opposite. Light, goodness, friendship, that was the Tree, yet Stygian seemed to miss it as much as she did. Regardless, her attention was drawn again to the fact that he was moving, giving her a quick nod before staring to walk towards the cave entrance. And here, for whatever reason, she felt compelled to speak out.
"Wait!"
Stygian halted, turning back to look at her. He said nothing, instead waiting for her to speak first, and while she hesitated to do so, words did eventually come from her.
"The tree is gone...and so are the Elements. Our chief weapon in the fight against evil is taken from us, and I don't know if there will ever be something we can find that can replace it."
She took a single step forward.
"You're powerful, Stygian. Powerful enough to be the Tree's rival. I was wondering..."
The Princess faltered, but only for a moment.
"...could you be an aid to us? Like the Tree was?"
To say that Stygian was taken aback was an understatement, as he looked utterly astonished at such words, to the point of being speechless. But after almost an entire minute of saying nothing, the ancient darkness finally responded.
"Princess...you ask me to be your ally in the Tree's place?"
Slowly, Twilight nodded, and Stygian was left with this uncertainty that, perhaps, he'd never felt before in his life. Twilight nervously awaited his answer, but instead, what she got was another dry chortle.
"Oh my...I honestly never thought I'd get to know what that felt like," Stygian remarked.
Twilight frowned slightly.
"What what felt like?"
The spirit glanced back to her, his expression softening.
"...Being wanted."
Twilight's ears drooped again, and for just a moment, she remembered the isolation that this being had endured its whole existence. Shunned, feared, locked away because of how ponies perceived him. And now, in this place, having somepony come up to him and let him know that he was actually needed. It must have been the most foreign experience in the world for him. She wondered if that alone would compel him to accept her offer. Yet, as she heard him sigh, she knew in her heart that this would not be.
"I thank you for that feeling, Princess...but I cannot stand by your side."
The young alicorn hung her head slightly.
"I see. So...darkness has outweighed light after all."
But here, Stygian shook his head.
"No...it will not."
Twilight looked back to him, confused, and listening well as he explained.
"The Tree and I...I said before we are two sides of the same coin. But we are also of an age. An ancient age. An age that, while certainly casting a large shadow on the time you live in, may well have outlived its place in this world."
He again turned from her, taking a step towards the entrance.
"If this world no longer has the Tree...then perhaps my time has come as well."
Naturally, Twilight was shocked to hear that.
"What?! Wha...what are you talking about?!"
Another long sigh from Stygian.
"Twilight...darkness I may be, but I have never sought to disrupt the balance of this world. If Harmony has faded...so too must I."
Unbeknownst to her, the ancient force smirked slightly.
"Though know that neither of us may be as gone as we appear to be. There may be some things yet that surprise you."
But Twilight was still not handling this well.
"All these things...learning I'll be ruling Equestria...losing the Tree...I just don't know what I'm going to do."
Stygian did not look to her, at least at first. But after a time, he gradually cast a glance to her.
"Oh, Twilight...the past generations really did spoil things for you youths, didn't it?"
Twilight looked up to him as he explained.
"Discord, Tirek, myself, all problems those of the past failed to deal with. Ancient shadows that plagued your generation. Inheriting the past's problems should not have been what you and your friends were made to do in your lives."
Twilight understood his words, and perhaps on some level she agreed with them. Yet as she looked back to that life, she couldn't help but smile.
"Maybe...but I wouldn't have traded my time for anything."
A small smile crept onto Stygian's shadowy lips.
"Then perhaps you are indeed the wisest alicorn of all."
He again looked away, walking towards the cave entrance, but as he did so, Twilight trotted a few steps closer to him.
"There'll be something else, won't there? Some other evil we'll have to fight?"
Stygian, having finally reached the entrance, chuckled.
"Oh, my dear child, there will always be evil to fight. Darkness did not end when your mentor and her sister vanquished Sombra and Discord in their day. It did not pass when you and your friends defeated Tirek and the Storm king. And it will not pass when the next generation has their turn to fight it."
He looked back to her.
"Darkness and light. Peace and conflict. Harmony and strife. A cycle of one leading into the other. Such it has always been, and such it will always be."
Twilight was understandably upset by that notion. That no matter how hard she and her friends fought, some evil would always be out there, ready to hurt and dominate after the passing of years. Stygian recognised this in her, and so, in a moment few would expect from the avatar of darkness, decided to show some kindness in his final moment in this world.
"But perhaps...that is simply the cynicism of an old stallion."
Twilight looked up to him, just in time to see a smile on his face.
"Take heart, Princess Twilight Sparkle...for you and yours may well strike evil from this world forever. And if so...I wish you luck in the world you usher in with its fall."
Twilight was stunned, but she nevertheless smiled back, giving a small bow of her head. Stygian bowed back, then looked up, to the shining sun in the sky, and took a final deep breath. Twilight watched, astounded, as he began to fade away, like a mist being blown by an especially strong wind. Where once there was an imposing stallion of shadow, now he was diminishing, growing smaller and smaller until he was naught by a wisp of smoke, and that too passed on in the moment that followed. So, he was gone, perhaps forever from this world, and had left her all alone in this place. She didn't know what she and her friends would do, but having seen and heard what she had, she knew at least what she needed to say.
"Farewell, Stygian, Lord of Shadows...and thank you."
Author's Note
Given recent events in the show, I decided it might be worth having a follow-up chapter.
