Shadow Wars: The Empire Strikes Back

by Void Streak

Rating: teen
Tags: Death, Alternate Universe, Other, Thriller, Original Character, Cutie Mark Crusaders, Scootaloo, Adventure, Violence, Crossover, Main 6, Gore, My Little Pony: Friendship is Magic, Dark
Length: 3762

After being pushed out of Equestria, Emperor Nightwing, devises a plan to strike back at his former master.

After being pushed out of Equestria, Emperor Nightwing devises a plan to strike back at his former master. With himself currently in exile, Emperor Nightwing is forced to send his new apprentice to infiltrate Equestria and spy on a potential threat to his power. Meanwhile Nightwing, orders the construction of a new secret weapon.

***

Third story in the Shadow Wars series.

Published 2024-09-23 22:30:00 UTC
Last updated 2024-09-23 22:30:00 UTC

Chapter 1

She was in complete darkness and silence, what she had considered to be a simple training exercise had turned into something that was extremely difficult. Emperor Nightwing watched as a small, orange pegasus filly, who was wearing a blindfold and noise-cancelling headphones, got pelted by paintballs.

Nightwing sighed in frustration as he switched the training droid off and pulled the headphones off her head, however, he still kept the blindfold on. "Shadow Wing, you must concentrate and use the aura, and stop trying to dodge them, you should be using your magiscaber to deflect them."

Shadow Wing's ears flattened against her head, "I'm sorry, master. I'm trying, I promise that I am."

Nightwing leaned down so that his muzzle was only meters away from hers before snapping, "Do or do not, there is no try."

Beneath the blindfold, her eyes furrowed in confusion, but before she could question her master, Nightwing instead instructed, "Get back into position and use the aura, envision the droid in your head and use your senses to sense which direction the paintballs are coming from and then let your reflexes do the rest."

Shadow Wing groaned as Nightwing placed the headphones back over her head, plunging her into absolute silence. Shadow Wing held the red magiscaber so that the blade was in front of her face, clearing her mind she tried to sense where the paintballs would come from, but as she was about to duck, she felt something hard hit her on her cheek and the feeling of paint began to seep down her face.

With a deep breath, she centered herself, recalling the lessons he had drilled into her about harnessing the aura. She gripped her red magiscaber tightly, its warmth grounding her in the darkness. Shadows flickered around her, dancing just out of sight. Each noise echoed, amplifying her senses, and for a moment, she imagined herself not just dodging paintballs, but commanding the very energy around her.

Suddenly, she sensed the first paintball whizzing through the air. It was coming from her left. Without hesitating, she raised her magiscaber and swung, deflecting the projectile back toward the training droid. The satisfying thud and splatter of paint confirmed her success, igniting a flicker of confidence within her.

The paintballs came much faster and a flurry of paintballs came at her from multiple directions. Instinctively, she ducked and weaved, using her blade to block as many as she could. The adrenaline coursed through her veins, each impact a reminder of her shortcomings, yet also a testament to her resilience.

As the training session came to a close, Nightwing switched off the training droid and allowed the silence to settle in. Shadow Wing, panting heavily, pulled the headphones off her ears, rubbing her sore cheek where the paint had hit her. The stinging sensation was a reminder of her struggle, but she didn’t dare voice her frustration.

“Enough of this!” Nightwing barked, cutting through her thoughts. “We need to move on to the next phase of your training. Come.”

Shadow Wing quickly got to her hooves, her heart racing as she followed Nightwing through the dimly lit corridors of the Sky Destroyer. The metallic walls loomed over her, casting eerie shadows as they walked. She tried to keep pace with him, but her mind still lingered on the training—she felt she had disappointed him.

They reached a heavy door marked with the emblem of the Imperial Empire, and Nightwing pushed it open. Inside, the classroom was stark and utilitarian, filled with rows of desks facing a large projection screen. The atmosphere was thick with the scent of polished metal and the faint hum of machinery.

“Sit,” Nightwing commanded, gesturing to one of the desks.

Shadow Wing obeyed, taking a seat at the front. She could see the flickering lights of the projector as Nightwing walked to the front of the room, his magiscaber hilt hanging ominously at his side.

“Today,” he began, his voice deep and resonant, “we will discuss the reality of our world and the importance of loyalty to the Empire. Knowledge is power, Shadow Wing, and it is time for you to understand the path that lies ahead of you.”

With a flick of his hoof, the screen lit up, revealing images of Equestria in ruins, followed by clips of the Imperial forces restoring order. The visuals were stark and brutal, designed to evoke a response. Shadow Wing’s eyes widened as she absorbed the propaganda.

“This is what happens when weakness prevails,” Nightwing said, his gaze piercing through her. “Those who do not follow the strong are left behind. They are trampled upon by those who seek power. The Imperial Empire exists to bring strength and stability to a world filled with chaos.”

He clicked through images of heroes from Equestria, those who once stood against him. Each image was met with a commentary laced with disdain and contempt. “They were misguided, Shadow Wing. They preached love and friendship while the darkness grew. They failed to see the truth. Only through strength can we create a lasting order.”

Shadow Wing watched the images with deep interest, she had hardly ever seen the outside with her always being on the Sky Destroyer.

“Do you see?” Nightwing continued, his tone growing more intense. “These so-called heroes turned their backs on the true way. They want to keep Equestria weak. But you—” he pointed at her, making her jump slightly “—you can change that. You can be part of something greater.”

“Do you want to be a hero?” he pressed, leaning closer, his crimson gaze burning into her. “Or do you want to be strong?”

“I want to be strong,” Shadow Wing replied instinctively, her heart racing at the weight of his words.

“Good,” he said, straightening up and stepping back. “Then you will embrace the dark side of the aura. It will grant you the power to protect those you care about. Together, we will reshape Equestria into a place of strength and unity, where weakness will no longer be tolerated.”

He clicked the projector off, and the classroom was plunged into silence. Nightwing’s presence filled the room, a looming shadow that felt both comforting and terrifying.

“Now, let’s begin your education,” he said, a sinister smile creeping across his face. “Today, you will learn the ways of the dark side.”

Chapter 2

The dim glow of the training chamber on the Sky Destroyer flickered as Shadow Wing stood in front of Emperor Nightwing, her body tense and her mind still racing from the indoctrination session. The weight of his words still hung heavy in her thoughts. Strength, power, control. It echoed in her head like a mantra she needed to embrace.

Nightwing, tall and imposing, circled her like a predator studying its prey. His deep crimson eyes burned with cold intensity. "Now that you understand the importance of power, it’s time for you to learn how to wield it. Only then can you begin to reshape the world in our image."

Shadow Wing swallowed, her wings twitching slightly as her nerves danced under her skin. She had deflected paintballs with a magiscaber before, but now she would be taught real combat, real power, the kind that could destroy.

Nightwing ignited his own blood-red magiscaber, its hum filling the air with a low, threatening buzz. "The aura will grant you abilities beyond your wildest dreams. But it will also devour you if you do not control it."

Shadow Wing nodded, determination overtaking the fear in her heart. "I’m ready, Master."

With a sly smirk, Nightwing lowered his blade. “We shall see.”

Nightwing led Shadow Wing deeper into the training hall, where conduits of energy ran through the walls, pulsing faintly with power. He turned to face her, his voice resonant and commanding.

“The first power you will learn is Aura Lightning. It is the manifestation of your anger, hatred, and will. When harnessed correctly, it can incapacitate, or even kill.”

He raised a hoof, and from his foreleg erupted a sudden burst of blue lightning, crackling with raw energy. The bolts danced around his hoof before arcing out toward a practice dummy. The moment the lightning struck, the dummy convulsed violently, falling to the ground, charred and smoking.

Shadow Wing’s eyes widened in awe, though fear bubbled beneath her surface thoughts. Could she truly do that?

Nightwing stepped closer, his gaze piercing into her. “Channel your emotions, Shadow Wing. Feel your frustration, your anger, your pain. Let it flow through you.”

She hesitated for a moment but then closed her eyes. Her mind swirled with memories, the isolation aboard the Sky Destroyer, her failed attempts to deflect the paintballs, and the pressure to impress her master. The anger slowly grew within her, like a fire, and she pushed it outward.

Her foreleg tingled, and for the briefest moment, a flicker of electricity danced across her hoof before dissipating into nothing. She gritted her teeth, frustrated by her failure.

Nightwing's voice cut through the silence. “Again.”

Shadow Wing focused harder, letting the frustration at her own weakness turn into deep-seated anger. The tingling returned, this time stronger. Lightning sparked and crackled around her hoof, and with a roar, she flung it forward. A weak bolt of electricity sputtered out, striking the dummy with only a faint hiss.

Nightwing raised an eyebrow, though his lips curled into an approving smile. “Good. You are beginning to understand. In time, the lightning will come naturally. Continue to feed the anger inside you.”

The next stage of training moved to the sparring arena. Shadow Wing held her red magiscaber with both hooves, its weight familiar now, but still intimidating. Nightwing stood across from her, his own blade ignited.

“Combat is not simply about swinging your weapon. It’s about precision, tactics, and exploiting the weaknesses of your opponent,” Nightwing explained, his voice sharp. “Now, let’s see what you’ve learned.”

He struck first, his blade coming down in a fast, precise arc. Shadow Wing reacted instinctively, blocking the strike with a swift upward motion. The impact sent a shockwave through her hooves, but she held her ground.

“Good,” Nightwing growled. “Again!”

Their blades clashed, the red glow of the magiscabers lighting the arena with eerie flashes. Shadow Wing’s movements were frantic at first, but as the sparring continued, she found her rhythm, deflecting Nightwing’s attacks more fluidly.

“You must anticipate your opponent’s moves,” Nightwing lectured, parrying one of her strikes with ease. “Do not just defend—attack!”

Emboldened by her progress, Shadow Wing swung her magiscaber in a wide arc, aiming for Nightwing’s side. He dodged with ease and retaliated with a swift strike aimed at her legs. She barely managed to block it, stumbling backwards in the process.

Nightwing stopped the session with a flick of his hoof. “You’re improving, but you still hesitate. In a real battle, hesitation will get you killed. Fight with purpose. Fight with anger.”

Shadow Wing nodded, her breathing heavy, determination glinting in her eyes.

After hours of intense combat practice, Nightwing led Shadow Wing into a darkened room with a single holoprojector at its centre. The hum of the Sky Destroyer outside was barely audible, but the oppressive atmosphere within the room was unmistakable.

“Not all battles are fought with blades,” Nightwing said as he activated the holoprojector. Images of maps, guarded facilities, and strategic outposts appeared. “In the shadows, there is power to be gained. Espionage is an art, one that requires patience, precision, and secrecy.”

Shadow Wing watched, fascinated by the shifting projections. She had never considered the value of such tactics, but her master made it sound as though this was the most vital skill of all.

“You will be trained in infiltration, subterfuge, and sabotage. You will learn to gather information and strike at our enemies from within,” Nightwing continued, his tone low and dangerous. “A true warrior must also be a spy.”

He gestured to the holoprojector, bringing up an image of a heavily guarded Equestrian base. “Your first lesson begins now. Study this. Memorize the layout, the guard rotations, and the weakest points. When the time comes, you will be ready to slip past their defences and deliver the killing blow without them ever knowing you were there.”

Shadow Wing's wings fluttered nervously, but she nodded, staring intently at the projected image. She didn’t want to disappoint him.

The training continued late into the night, with Shadow Wing learning the subtle arts of deception and sabotage. Nightwing taught her how to blend into the shadows, how to lie convincingly, and how to remain unseen even in plain sight.

By the end of the session, she was exhausted, physically, mentally, and emotionally. Yet there was a growing power inside her, a darkness that pulsed with each new skill she mastered.

As she retired to her quarters, her mind swirled with conflicting emotions. She wanted to impress Nightwing, to grow stronger, but at the same time, a small voice deep within her whispered doubts. Could she truly embrace this path, or would it consume her?

But for now, Shadow Wing silenced those doubts. She would become powerful. She would become strong.

She would become a weapon.

The metallic halls of the Sky Destroyer echoed with the steady hoofsteps of Emperor Nightwing and Shadow Wing. After a gruelling day of training, her body ached, but her mind was sharper than ever. The weight of the lessons she had learned still pressed down on her, combat, espionage, and the dark powers of the aura, but Nightwing had promised her that this would be the most important lesson yet.

They stopped in front of a large, reinforced door marked with the symbol of the Imperial Empire. Nightwing’s crimson eyes gleamed as he placed a hoof on the door’s scanner, and with a soft hiss, it opened to reveal a vast war room. It was dimly lit, the walls lined with holographic displays of troop movements, starship formations, and key locations in Equestria.

"Leadership," Nightwing said as he stepped inside, his voice resonating with authority. "The final piece of your training. The power to command is not simply about strategy or intellect. It is about control. You must inspire fear, loyalty, and absolute obedience in those who serve you. There is no room for mercy."

Shadow Wing followed him, her magiscaber clipped to her side. She had never commanded before, never been in charge of anypony but herself. Her heart raced at the thought, but Nightwing's presence gave her a strange sense of confidence.

Nightwing strode toward the centre of the room, where a group of officers stood at attention around a central command table. He gestured for her to join him at his side, the officers’ eyes darting toward her with curiosity and suspicion.

“These officers are among my most elite,” Nightwing explained. “They have been tasked with leading our forces, but even the most skilled commanders must bow to true power.”

He turned his gaze to Shadow Wing. “Today, you will learn how to lead with an iron hoof. Leadership is not about fairness or kindness. It is about domination. You will instill fear in your subordinates, so they know that failure will not be tolerated.”

One of the officers, a dark-coated stallion with a sharp jawline, stepped forward. "My Lord, if I may—"

Nightwing silenced him with a raised hoof, then turned to Shadow Wing. "You see, Shadow Wing, this officer questions my authority. He believes he can speak out of turn. What do you think should happen to him?"

Shadow Wing felt a cold chill down her spine as the officer looked at her, his expression unreadable. She knew what Nightwing expected her to say, but the idea of giving an order that harsh felt unnatural to her. Still, she couldn’t falter now. She had to prove her strength.

“He should be punished,” Shadow Wing said, her voice steady though her stomach churned. “Failure to obey should not be tolerated.”

Nightwing's eyes gleamed with approval. "Correct."

With a flick of his hoof, he motioned to one of the guards. In an instant, the officer was seized and dragged toward the side of the room. His protests were drowned out by the hum of the energy restraints clamping down on his hooves.

Shadow Wing watched in silence, her heart hammering. She had seen such displays before, but now, she had given the order. Her words had made it happen.

Nightwing leaned down, whispering in her ear. "This is what it means to be a leader. You must show strength at all times, and never hesitate to crush those who defy you. It will inspire fear, yes, but it will also inspire respect."

He stepped back and addressed the remaining officers. “You will follow Shadow Wing’s commands from now on. She speaks with my authority. And if any of you question her, you will face the same consequences.”

The officers snapped to attention, their expressions unreadable but their bodies tense. Shadow Wing could feel the shift in the room. They feared her now, and that fear gave her a sense of power she hadn’t felt before.

Nightwing led her away from the officers and back to the command table. Holographic displays of starship formations and troop movements flickered before them, casting eerie shadows across their faces.

The next day, Emperor Nightwing summoned her to the command bridge aboard the Sky Destroyer. Shadow Wing couldn't help but look in fascination at the various dials and controls of the Sky Destroyer as various ship engineers worked around the clock to control the massive behemoth, Shadow Wing had never been allowed onto the command bridge, before, she usually only spoke with her master in the training room or a classroom and rare cases, her private quarters.

Shadow Wing bowed before her master, "Rise my apprentice."

Shadow Wing rose and asked, "You called for me, master?"

Nightwing then told her, "Take a good look around you." Shadow Wing looked around her as the ship's captain barked out orders and through the massive front window, she watched the desert of the badlands slowly roll underneath them. "One day you will be in command of an entire fleet of Sky Destroyers."

Shadow Wing's eyes widened in excitement, "Really!"

Nightwing nodded, "Yes, but before then, I have an important assignment, a mission for you to carry out. I hope that you have remembered all of your training because it will have prepared you for this moment."

The concept of her going on her very first mission, filled Shadow Wing with a mixture of determination to make her master proud along with nervousness that she will mess up.

Nightwing then continued, "A new threat has emerged that could destroy everything that we have built." Nightwing then used a hologram to show six, magical gemstones, "These are the elements of harmony, they are powerful artefacts that have a strong connection to the aura. They have recently been used to bring back an old enemy of mine."

Nightwing then switched on a magiscreen, revealing images of six different mares, "These are the bearers of harmony and the ponies that wield these elements. They hold the power to destroy us." The magiscreen then changed to show images of two little fillies, "These are the sisters of two of the bearers, your mission is to infiltrate Equestria and become friends with these two fillies and gather as much intelligence as possible."

Nightwing then gave her a large file, "This is your mission brief, it shows everything that we know about the elements of harmony and their bearers along with your cover story, I want you to study this file, I will be quizzing you in the morning, so I expect everything to be memorized."

Shadow Wing gulped before whispering in a worried tone, "What if they discover my true identity."

"Then you will fail and the Equestrians will torture you and most likely banish you to a godforsaken place, where you will most likely die a horrible, lonely death."

The next day, Shadow Wing arose from her desk, where she had fallen asleep, she had been up all night learning her cover story and every detail about the ponies, she will be spying on. She then walked to the command bridge, where she found Emperor Nightwing waiting for her. "Have you learnt everything that you need to know?"

Shadow Wing nodded with bags under her eyes, "Yes master."

"What is your name?"

Shadow Wing instinctively replied, "Shado-"

Nightwing cut her off, "No, your cover name."

Shadow Wing clenched her eyes shut as she remembered everything about her cover story, "Scootaloo, my name is Scootaloo."

"Where are you from?"

Prepared this time, Shadow Wing replied confidently, "Trottingham."

"Why did you come here?"

"My parents were killed during a storm so they had to send me to the orphanage, here in Ponyville."

"Incorrect."

Shadow Wing's eyes flashed with confusion, "What? But that's what it said in the file."

"What you said, isn't the problem, it's how you said it. You've just lost your parents, so you should be upset and on the verge of tears. You should be afraid, you are in a new place with nopony to talk to. Now try again!"

Shadow Wing then repeated but this time with a deep sadness in her voice, "My, my parents they... died during a storm so they sent me here."

Suddenly Shadow Wing cried out in pain as Nightwing blasted her with aura lightning. Shadow Wing fell to the floor panting with tears rolling down her face as she tried to hide them from her master. "That is much better."

Nightwing continued the session until she had everything completely memorised. After the session, Nightwing gave her a cloak along with a helmet that had a sinister look with sharp edges and a T-shaped visor. "You will wear this, whenever you are carrying out various other side missions, your officers will also accompany you. You are their commander and they should follow your orders with absolute loyalty."

Shadow Wing then followed Nightwing towards the hanger bay, where she would board her shuttle that would take her to Ponyville, "Your officers will be waiting for you, and they will take you to a safe house within the nearby Everfree Forest, there you will find everything that you need to complete your identity as Scootaloo."

With that, Shadow Wing boarded the shuttle, taking one last look at her master, however, he merely nodded, not bothering to wave goodbye to her.