Chapter I: The Queen's "Apprentice"

Introduction: It has already been quite some time since Queen Chrysalis' devastating defeat at the hooves of the ponies, to include traitorous members of her own kind. With only a slim few devoted followers left, it'll be even longer before any sense of reprieve comes to the defeated queen. Now hidden away in the desert, she angrily plots her next grand plan in besting the ponies and turning them all into changeling slaves. With the use of a chaotic tome and the essence of two of her greatest enemies, she will finally succeed! If she herself cannot overcome the power of friendship, she shall replicate one who can. Or at least, that was the plan.

Prologue

Deep in the heart of the San Polomino Desert, dark energies stirred beneath a cracked mountain. Hidden within a blanket of raging sand, emerald light emitted from the cracks as devious cackles rode on the winds. The pulsing green flashes continued, cutting further into the shadows as deeper and deeper within, a band of changelings all stood around a runic circle of power. Standing at the center as a grand figure conducting the spell, was Queen Chrysalis herself who only had her head raised upward as she smirked in complete anticipation.

In this vast cavernous ritual ground, one of the changelings still loyal to his Queen was hesitant. "My Queen ... i-is this safe? Hissss!"

Queen Chrysalis acknowledged him with a squint. "Now is not the time for cowardice. We are nearly there in breaking the boundaries that will crush our enemies!" She grinned, looking upward again. "Now each of you release what essence you have gathered from our key ingredients." Queen Chrysalis let off hushed cackles as her horn started to glow. "I will conduct the binding myself."

Soon each of the changelings exuded some form of magic which represented itself in the form of various colors. Gathered was a sphere of violet hue, pinkish hue, and a chaotic candy apple red hue. They drifted aimlessly over the queen, locked within the runic circle of power as it continued pulsing with a nauseating green. The spheres soon began falling into a rhythm and circling over her in a more controlled manner as each of the changelings wearily watched with uncertainty. Eventually the spheres drew closer together, morphing.

Queen Chrysalis was awed as she continued to grin, now letting loose her own magic which better helped the flow of the binding. "This is the peak of true changeling magic. With the very magical essence of Twilight Sparkle and that despicable Starlight Glimmer ... I will show all those wretched ponies the true capabilities of those who've mastered the art of replication." She raised a brow, showing her own uncertainty. "Though this is even my first time experimenting with such things. It matters little." She snarled, growling even as she spread her hooves and could do little to hold back her anger. "They took everything from me! When all they had to do was bow and accept their inferior place in this world! But now they've forced my hooves! And in my greatest act of desperation, I shall overcome them in an instant!"

Each of the changelings surrounding the Queen were still cautious, uncertain about her latest plan. Indeed they had all mimicked ponies for ages, but replication and what their Queen planned was far beyond even their usual antics. Chaotic magic was a realm they were unfamiliar with, and also drew the attention of the extremely frightening creature Discord. Without their old home, stopping such a creature would be near impossible if they drew his ire. Still, their loyalty outweighed their fears. They remained silent and ultimately ... complacent.

Queen Chrysalis broke out into wild laughter as she finished conducting the final steps of the spell and watched her magic go to work. Slowly a radiating light permeated with power as she watched it in eagerness. This will finally be the breakthrough I have so long desired! Never in my peace of mind would I have realized the potential such an experiment could unleash! She grinned fiercely. Now Celestia! You and your meddling proteges will learn what it means to cross me! The now single sphere continued to radiate a blinding light as it slowly morphed and soon began taking the shape of a pony. Queen Chrysalis' thoughts continued to race as her fellow changelings watched in disbelief. I have discovered the means of defeating you! And with this new weapon! I will rain down vengeance upon you and your kind! She paused, howling with now maniacal cackling. The new age has begun! Finally, the Age of Changelings is here at last!

And with a final binding flash, slowly descending upon the ground was Queen Chrysalis' new weapon. A young teenage mare.

But as the weeks rolled by, Queen Chrysalis' beaming happiness would transition into an expression defined by exhaustion. Deep lines hung beneath her eyes as she appeared withered as if she hadn't eaten in months. In the background, dreaded bickering continued.

"I mean truly, what were you expecting Chrysalis? Don't you understand the repercussions of your actions! This is one of the worst possible things you could've done. The very boundaries of chaotic magic are unknown yet you still delved into it without the proper research. Research is very important, especially if you take the actual time to calculate the exact quantities between which you divide each individual school of magic you're planning to utilize. Regardless now we've got a real mess on our hooves, one I've been working day and night to resolve! Not that it isn't much of a feat, seeing as something as dire as this is trivial from my perspective." The mare continued back and forth, non-stop talking as she lectured Queen Chrysalis in a disappointed manner. "If you knew what was good for you you'd just go with the route of diplomacy. But that isn't an option for you is it? You always have to be complicated. Spike! Can you get me my-" she paused as she raised a hoof to her muzzle, "Ah right ... I'm not the actual Twilight, gotta make a reminder for that. Perhaps a scroll? Anyway. So as I was saying Chrysalis this is a very complicated mess we have here. Right right right, to the point, um ... okay! So I think we should-"

Queen Chrysalis' blanked out as she merely stared down at this mare in exhaustion lost in her thoughts. The mare she herself created continued to go on her tangent as Queen Chrysalis just sat, looking down at her still. How ... How did this happen? Why does this always happen to me? Where did I go wrong? Just ... w-what is this? She watched as the mare trotted back and forth lecturing her all the same. How could I have created this? It makes no sense. I ... this isn't what I wanted. Yet at the same time ... it is? Have I gone utterly mad since?

The mare was now in front of a large makeshift rock chalkboard as she used telekinetic magic to diagram her theories. "And that's why if we look at it from these eighteen perspectives we can boil it down to the most efficient solution. Pretty simplistic summary overall."

Queen Chrysalis finally interrupted finally interrupted with a screeching roar. "That's enough!"

The mare rolled her eyes as she huffed. "Here we go again." She lowered her rear to sit in a patient manner.

Queen Chrysalis got in the young mare's face as she pushed a hoof against her chest, prodding her angrily. "I created you! Yet all you do is sit here and complain and lecture and tell me to do research! You theorize theorize theorize yet you never actually accomplish a single thing you useless pony! I did not create you to sit here and be lectured like a child! Now go out there and actually accomplish something! Destroy the ponies, anything! But this is beyond tiresome! I refuse to tolerate such insolence from one of my subordinates! Understand!?"

The mare gave Chrysalis a crooked frown as she rolled her eyes again. Her horn started to glow as she immediately seized a nearby scroll and unveiled it to the mare. "Chrysalis ... listen. I understand where you're coming from, I do. Which is why I've considered my care for you in significant fractions. You are my caretaker after all, and without you I wouldn't even exist." She rose to all fours and patted herself off, "But allow me to also remind you how unstable your ritual was and without a master's touch, the result can also be pretty unstable." She placed a hoof over her chest, "My memories are in shambles and infused with both Starlight Glimmer and Twilight Sparkle's. Thankfully I'm smart enough to realize this and categorize each of their memories without much difficulty. But I must also consider my mental health before disembarking on whatever you're planning, seeing as everything I've ever known and love actually isn't mine. Get it? As to your actual plans themselves, they are all poorly done. We have a lot of preparation to do if you even want the slightest chance at succeeding, simply put."

Queen Chrysalis hissed. "And let us say I do entertain your nonsense longer. If what you say is true, how can I even trust you?"

The mare lightly sighed as she turned back towards her chalkboard. "Because if I were going to blatantly betray you I would've done it in a far less invasive manner. We're in a cavernous mountain Chrysalis ... pretty sure I can think of some means of escaping you."

Queen Chrysalis' nose wrinkled as she immediately seized the mare with telekinetic magic before glaring at her fiercely. "Now you listen here young pony, you best watch that tone with me. I am a Queen and I expect to be respected as such. Don't test my patience."

The mare smirked a little. "Pretty sure Thorax stripped you of that title when you were booted from your home but okay."

Queen Chrysalis gasped as she gritted her teeth with a snarl. "Don't you dare mention his name to me! A traitor is all he is!"

The mare raised a brow then. "But if he became the current ruling body of your general population, doesn't that make you the traitors for deserting his newfound decrees?" She turned back towards her chalkboard. "Kidding ... only messing with you Queen Chrysalis."

Queen Chrysalis began trembling with rage as she was about to seize the pony once more, before a loud abrupt explosion rang out within the cavern. It shook the entirety of the mountain as Chrysalis stumbled a few feet back before snapping. "What was that!?"

The mare flinched as she also nearly stumbled but muttered. "A breach in the defenses?" She immediately turned to face Chrysalis in a hurry. "Chrysalis, are you certain nopony knows of this place?" She frowned, "Because that didn't sound awfully friendly you know."

Queen Chrysalis glared back at the pony. "Do you truly think I would not ensure my hiding place is kept secret!?"

The mare began brainstorming hastily for answers. "Well here we are okay! There's no time to bicker about this. If you're that certain it means one of the other changelings was tracked here by somepony. You said you stole magic from Twilight, Starlight and Discord?"

Queen Chrysalis nodded simply down at the mare, getting irritated by such stupid questions. "Yes ... what of it?"

The mare continued. "Did your changelings simply hide as they're supposed to? Or did something go wrong?"

Queen Chrysalis rolled her eyes then as she lowered her head to eye level with the mare. "Fine! A complication is all it was, that meddlesome being Discord only exudes magic near that Fluttershy pony! So we impersonated her after ponynapping her briefly."

The mare ran a hoof slowly down her face as she shook her head in passive frustration. "So ... you angered Discord."

Queen Chrysalis shook her head at the mare. "There is no way we could've been followed! Not even by him!"

The mare sighed as she turned towards one of the exits of the cavern. "Then who else could it possibly be?"

Soon a changeling grunt rushed into the room as he huffed, catching his breath. "M-My Queen, we've been attacked!"

Queen Chrysalis approached the changeling as she demanded answers. "I am aware, but by who!?"

The changeling was sweating profusely as he gulped. "The Night Princess my Queen! She and her sister are here!"

Queen Chrysalis flinched as she took a few trots back. "But how is it possible ... we remained utterly discrete."

The mare cut in then after a brief moment of silence. She had came to a conclusion. "M-Memories, of course!"

Queen Chrysalis glanced back at the mare she'd created again, in confusion. "What're you going on about now?"

The groaned as she rolled her eyes in irritation. "They didn't come for you Chrysalis." She paused, "They came for me!"

At the entrance of the cavern, Princess Celestia and Princess Luna stood together as blocking their path was a path of changelings. Princess Celestia was fairly serious as she looked upon them. "Changelings? Luna ... you made no mention of this earlier."

Princess Luna shook her head. "That is because I didn't expect to find changelings here dear Sister."

Princess Celestia glanced over at Luna. "And you are certain the dreams you witnessed belonged to Twilight and Starlight?"

Princess Luna continued. "Yes and no ... the memories were authentic but something was off. They were in distress."

Princess Celestia pressed forward. "Then I guess it's best we not waste any more time." She glared ahead. "I spoke to them myself and know they are alright. But you are right, even destiny is in flux due to whatever has happened here. We must find the cause Luna."

And following behind the two princesses, were a band of Celestial and Nightmare guards, all adorned in glistening armor.

Princess Celestia finished. "Seeing the changelings means can only mean one thing as well. What have you done ... Chrysalis?"