Prologue
The lavender unicorn galloped as fast as she could, weaving through the startled crowd at breakneck speeds. Gasps of astonishment and surprised faces surrounded her as she almost collided with ponies left and right. She felt more than saw another green flash behind her and dodged to the right into a tight alley, almost bowling over a thin earth pony that was scrambling to get out of her way.
Just in time it seemed as a chunk of the alley corner she ducked into exploded into a green splatter. She was breathing heavily as she ran. This alley was more of an abandoned route, which she supposed was a good thing as there were fewer innocent ponies to be hurt. But it left her almost no options to dodge the incoming fire.
The unicorn's eyes scanned the alley ahead of her in moments, noting that there were some possibilities. If her memory served correctly it did open out into another major thoroughfare at the end of it. Her horn developed a glow around it as she concentrated.
Several beams of bright purple light lanced out in front of her as she ran. A large dumpster and several smaller discarded containers exploded into the air, flying behind her as she ran underneath them. A few more green blasts of light left none of her improvised flying shields even recognizable. Debris scattered violently through the narrow alley.
Her tactics were successful as she darted out into another large and pony-packed street, dodging into and through the crowd. Her breathing even heavier now with the expenditure of magic. She tracked the movement of the crowd and saw the opening she had been looking for. A small window at ground level behind a number of vendor stalls. Her horn glowed again as she grit her teeth together. This was going to take absolute precision. Bright beams of light shot from her horn as she cast several spells at once.
Approximately a block up the street an entire family of pegasi were knocked to the ground away from another alley by a purple magical glow, two young pegasi screaming in terror. At that exact same moment, the ground in front of the vendor stalls exploded with cobblestones flying into the air surrounded by a similar glow. Several more green beams of energy, launched by those pursuing the unicorn were aimed at the alley. Everypony was screaming in fear. No one noticed the fading sparkle of teleportation hidden inside the cloud of cobblestone.
The unicorn tumbled into a dirty basement surrounded by boxes. She froze in a defensive position with her horn glowing softly aimed at the window she had just teleported through. Trying to calm her heavy breathing she listened carefully, trying not to move. If her ruse had been discovered, it would all be over soon anyway.
She could not help it as her thoughts reached back through her memories. The unicorn's mind delved back to the actions that had set her on this road of life and death...
~~~~~-----~~~~~
***** Eight months prior *****
Twilight Sparkle stood up and faced Nightmare Moon, looking her directly in the eyes. "Do you think you can destroy the Elements of Harmony just like that? Well you're wrong! Because the spirits of the Elements of Harmony are right here!" The shattered pieces of stone surrounding the dark alicorn began to glow and rose up into the air. A nearly whispered “what?” slipped from Nightmare's muzzle as she stared incredulously at the glowing shards around her.
"Applejack, who reassured me when I was in doubt, represents the spirit of Honesty!” Twilight exclaimed as several of the shards spun through the air to swirl around the Earth Pony.
“Fluttershy, who tamed the Manticore with her compassion represents the spirit of Kindness!” Fluttershy gave a worried glance to the glowing pieces of stone that followed her up and circled around her.
“Pinkie Pie, who banished fear by giggling in the face of danger, represents the spirit of Laughter!” The mare's smile seemed larger than life as more of the glowing Elements joined her.
“Rarity, who calmed a sorrowful serpent with a meaningful gift, represents the spirit of Generosity!” Rarity simply closed her eyes as she watched the same magic enveloping her.
“And Rainbow Dash, who could not abandon her friends for her own heart's desire, represents the spirit of Loyalty!” All of the ponies standing behind Twilight were now surrounded by glowing and sparkling crystals.
“The spirits of these five ponies got us through every challenge you threw at us!” Twilight challenged the immortal goddess, standing with a smile on her face.
“You still don't have the sixth element! The spark didn't work!” Nightmare Moon rebutted, stomping a hoof down in frustration.
“But it did, a different kind of spark,” Twilight said, turning around to look at the ponies facing Nightmare Moon with her, “I felt it the very moment I realized how happy I was to hear you. To see you. How much I cared about you. The spark ignited inside me, when I realized you all are my friends!”
Twilight turned around to face Nightmare once again as she finished her admission to her friends. A bright light beaming from above caused all the of the ponies present to look up. A new stone had appeared, carved with a six-pointed star. It slowly lowered to hover over top of Twilight Sparkle, “You see, Nightmare Moon, when those elements are ignited by the spark that resides in the heart of us all, it creates the sixth element, the Element of Magic!”
The beams of light coming from above Twilight gained in intensity, and the dark goddess had to turn her head and shield herself with her wing. The floating shards swirling around the five ponies increased in brightness as well, and joined with each of the ponies at their necks. The stone floating above Twilight Sparkle also changed into a jewel encrusted tiara, crowned with a star amethyst in the same shape as Twilight's Cutie Mark.
Twilight Sparkle's eyes began to glow white as she hovered up to join the rest of the ponies. The six ponies gathered together in midair, the bright glow around them intensifying as Nightmare Moon crouched defensively in front of them. "NO!" shouted the ebony alicorn goddess as brilliant beams of light swirled into a huge rainbow that arced it's way down on top of the dark goddess.
Twilight felt mental connections forging inside her own mind as the rainbow beam spun together. Time seemed to slow down. Something else was happening that was far more profound than when she had just realized that these ponies she met just recently were now her friends. White light surrounded her and her friends as the magic of the Elements of Harmony coursed through their bodies.
Twilight noticed something very strange that seemed to be faintly spun into the magic rainbow flowing through her being. Even though time appeared to have almost stopped, she could barely comprehend whatever it was she was "seeing" before the power of the Elements of Harmony blasted down and surrounded Nightmare Moon in a spinning rainbow tornado. The dark goddess screamed as the power twisted around and consumed her. Twilight and her friends floated to the ground as the power left them.
The rest of her memories of the day were blurred and distant. She vaguely recalled Princess Celestia arriving and her reunion with her younger sister, Luna. Twilight felt disconnected during the following celebrations. Even the elation she felt at Celestia's proclamation that her new home was in Ponyville with her friends was as though it was happening to somepony else. Something seemed slightly twisted and wrong with the world, but she couldn't quite put her hoof on it.
The only time Twilight's perceptions lifted from the fog she felt she was in was at the library later that evening after the town-wide party. The Royal Sisters were both present still, as well as Spike and all of her new friends. Princess Celestia's joyous and loving expression had fallen from her face, and even Princess Luna wore an indecipherable look. Both of the Sister Goddesses were waiting expectantly on the group.
"If'n ya feel that's fer the best, then," Applejack said, bowing her head down and letting the gorgeous necklace with her Cutie Mark in sparkling emeralds slide to the floor in front of the alicorns.
Pinkie Pie's smile almost, but not quite faded from her face as she followed Applejack's example. Her hair didn't straighten out though as she deposited her gem-laden balloon necklace in front of the Sisters.
"I don't mind," Fluttershy whispered softly, letting her butterfly necklace fall gently to the ground next to the others.
"Aaaaawe, this necklace is just too awesome! Do we have to?" whined Rainbow Dash. It only took Celestia glancing at her for Rainbow to snap her muzzle shut and drop her necklace on the ground with the rest of them.
Rarity just sighed, her horn glowing softly as her necklace raised from around her neck. She stared longingly at the jewels representing her Cutie Mark as her magic gently lowered it into the pile of the other Elements of Harmony.
Twilight Sparkle bowed low before the Princesses. "I don't understand," she spoke softly.
"My faithful student, the Elements of Harmony will be perfectly safe in Canterlot. We will take care of them until they are needed once again. Fare well."
The tiara still resting on Twilight's head began to glow, along with the other five necklaces. The glow spread to both of the alicorns standing in the library until it reached a near blinding crescendo, then with a flash the two Princesses and all six of the Elements of Harmony were gone leaving six pony friends and one baby dragon alone in the library.
~~~~~-----~~~~~
Twilight Sparkle settled into her new life, although she still perceived that something seemed fundamentally wrong with the way things were. Over time she became used to the antics of her new friends and the general atmosphere of Ponyville. She had several adventures that as crazy as they were, her new home really started to feel like a home. Through the arrival of the tickets to the Grand Galloping Gala, the visits of Gilda and Trixie, the invasion of the Parasprites, and even the Winter Wrap Up that turned out great in the end, Twilight felt like she belonged.
Spike, on the other hoof was worried about his caretaker. She had changed a lot more then most ponies realized since her move from Canterlot. Her old research projects were gathering dust or completely forgotten. Twilight wasn't obsessing over details as much as she used to. Nopony other than Spike noticed these differences, and he didn't have anypony to confide in. He could tell she was looking for something, but had no idea what it was. With no idea how to help her, he followed her orders as usual, and clasped his claws in worry when she wasn't looking.
Twilight was looking for something. If she could share her thoughts with Spike, he would be amazed to know that she really didn't know what she was looking for either. For the past several months she had been feeling that something was simply wrong. It was nothing she could directly sense nor anything that any of her scientific instruments could detect. It was nothing she could even put into words so she kept it to herself for the most part. She had tried a few times to talk with her friends and a few others in Ponyville about it, but she had kept her questions so vague that she only ended up worrying those she was trying to ask. She fell back on telling everyone that she was OK and retreated to her books in the library for comfort.
At first it had just been a way for her to take her mind off what she was feeling. However, when she was reading an old manuscript that delved into the court records during the Changeling Treatise of 974 one of the recorded statements of a Canterlot unicorn Noble read "These creatures are not natural. Anypony can tell that just being around them is wrong." The rest of the manuscript was damaged, but it got her thinking, what if somepony else had the same feelings she did? Her research expanded from there. Most of the court records from the time were excised. The argument over the Changelings was something that had been settled for years, however. Very few ponies had actually seen or encountered the Changelings since then. It was generally assumed, as the Treatise dictated, that the Changelings were to be trusted as they reported to the Princess and the Royal guards. The resentment over them stemmed from the Canterlot Nobles not appreciating anypony that wasn't under their hoof, so rumors would abound.
Another snippet of information led to her current research project. A pegasi historian had written concerning Sombra, “This unicorn is said to have been able to see beyond sight. The unusual abilities of his led to his lordship in the Crystal Empire.” Other than that, most of what Twilight was able to find was negative propaganda about Sombra and his banishment. There was very little information about the Crystal Empire as well, other than it's disappearance. Once again, she seemed to be running into a case where the history was written by the winners. Real information about the day to day life of Sombra just didn't exist, and nopony had heard about or seen him for years.
It was at this point in her research, surrounded by every volume that held any snippets of Sombra or the Crystal Empire, when she was interrupted from her focus by a sealed envelope drifting down and landing on the page she was reading. She looked up to see the smirking face of Spike as he stood on the other side of the stack of books she was in the middle of.
“I've been watching the library like you asked, and there was a pony in here that looked like she wanted to talk to you, but she also seemed a bit shy. Before she left she asked me to give that to you,” Spike turned and walked to another section of the library, dust cloth in claw.
Twilight looked at the envelope. It appeared to be plain with no writing on the outside. Her horn lit up softly as she raised the envelope in front of her, opened it, and removed the single folded sheet of paper that was inside. The envelope drifted back to the ground next to her, unnoticed.
There was only a few lines on the paper and Twilight scanned them very quickly. The color seemed to leech out of her fur as it looked like she froze. She felt her heart stop momentarily, and puzzled out to herself why the words on the paper affected her so.
I know who you are looking for.
I know why you are looking for him.
If you want answers, meet me at the confectionery shop after sun fall tomorrow night. Tell nopony and do not be followed.
The Matrix has you.
While Twilight was still locked in confusion at the note written to her, the paper glowed and disintegrated into dust.