Equestrian Dreams

by Zaehlas

Rating: teen
Tags: King Sombra, Crossover, Dark, Alternate Universe, Doctor Whooves, Main 6, Lyra, Changelings, My Little Pony: Friendship is Magic, Adventure
Length: 4541

Twilight feels there is something wrong with the world. Incredible adventures ensue.

Twilight has a strong feeling something is wrong with the world. By following this feeling she starts an adventure that is beyond her wildest dreams.

Published 2012-11-30 07:50:01 UTC
Last updated 2012-12-05 18:28:26 UTC

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.

Conspiracy

Twilight glanced at the stack of books that surrounded her as her heart rate approached normal. She noticed the glaring hole in the air that used to contain the note to her. Magic to cause a note to disintegrate after it was read wasn't particularly difficult, but wasn't known by many unicorns either. The second things she noticed was the discarded envelope had disappeared as well. She clambered out of her stacks of books, knocking over several stacks in the process to join Spike on the other side of the library.

“Spike!” she called out, as she skidded to the shelf he was cleaning. Of course he was on a ladder cleaning the top of the shelf, so he had to grab the shelf in a hurry before he fell down, dropping the dust cloth while he recovered from being startled. “What is it Twilight?” he asked, looking down at her, frustrated.

“Who was the pony that dropped off that letter for me? Do you know her? Have you seen her around before?” the questions came pouring out of her while Spike shook his head. He climbed down from the ladder while answering.

“I've seen her around town before, but this is the first time I remember seeing her in the library. A lot of ponies come through here, so I could be wrong. She's a uuuuh light blue? Um, light green? Argh, light colored something unicorn, and, um...” Spike wrinkled his forehead and closed his eyes while thinking. After a moment he pumped a fist into the air, “that's right! Her Cutie Mark is a musical instrument.”

Twilight nodded and her eyes went distant as she was thinking. “I've seen her before, as well,” she shook her head then smiled down at Spike. “Thanks so much. I think it's getting late, so we can worry about anything else tomorrow.”

Spike nodded at her before yawning and heading to the kitchen. Twilight locked the door with her magic. They both settled with a quickly made dinner before heading to their respective beds. She tossed and turned in frustration before drifting off to an uneasy sleep. She couldn't get the letter out of her head.

~~~~~-----~~~~~

The next day was relatively normal for the both of them. Almost no visitors to the library which let both of them get some cleaning and organization done. The pantry was still well stocked, and although Twilight glanced at the organized remains of what was her recent research, she couldn't quite bring herself to jump back into reading through the books. There weren't any plans for her to visit her friends at the moment, and they were all busy enough with their lives that they had no need to drop by the library that day.

Evening was quickly approaching, and Twilight was getting more and more nervous about how she was going to get to this meeting. She wasn't sure yet if she trusted this unknown pony, but it was the first indication that someone might understand her feelings and even more importantly, she was promised answers! As she busied herself idea after idea ran through her thoughts and were quickly discarded. Her eyes then roamed across one of her portable telescopes. Perfect!

“Spike? Do you think it's time for dinner?” she asked loudly across the library. She received an affirmative grunt, and knowing the little dragon assumed he would be busy in the kitchen for a bit. She headed to the Astronomy section of the library, pulling down a few random books to make her excuse rock solid. After spending some time making sure she had the right books that wouldn't make the little guy suspicious, she joined him in the kitchen.

Spike was already setting out a large salad for her and a plate full of gemstones for himself when she sat down, levitating the books onto the table with one of them open in front of her. They both quietly attended their separate meals. It was a little awkward for both of them. Spike knew that Twilight was hiding something from him, but she was his big sister, maybe even almost his mother. He didn't want to be devastated if he questioned her and was wrong. Twilight hated lying to Spike, even if she hadn't overtly said anything yet. It was wrong. But at this point she didn't know what else to do.

She calmly finished her meal and put a smile on her face, hoping that the duplicity that she felt wasn't showing through. “Spike, I'm going to go out for a little Astronomy research tonight. You look tired and can go to bed. I'll be fine.”

Spike sighed and nodded. He tried to suppress the yawn he felt shuddering through his little body, but it was a losing battle. “OK, Twilight. Try not to stay up too late, K?”

She gathered her things with magic, trotting out of the front door with her telescope and books following her. After she shut the door, Spike sighed again, busying himself with cleaning up the kitchen before heading to sleep. The scrunched up look on his face betrayed that he really wasn't fine, but there was little he could do. He simply planned on not sleeping, unless he heard her come back in, for what good it would do him.

~~~~~-----~~~~~

Twilight could feel her heart hammering in her chest as she trotted towards the park in the center of town. She stopped near one of the benches, pulling the telescope over and setting it up. The dumped the books unceremoniously on the park bench and busied herself with adjusting the telescope for a few moments before growling to herself. “What am I doing,” she mumbled to herself. “I'm not going to use it anyway.”

She sighed and took in a deep breath, trying to calm herself. She stopped fiddling with the telescope and closed her eyes, feeling the cool night air wash through her mane. “Get a grip, girl.” Twilight stood back up, reoriented herself and started trotting straight towards the candy shop. She knew that when the letter had mentioned “confectionery” that it wasn't Sugarcube Corner that was being talked about. The little shop was on the other side of town, in an area she had rarely frequented. It wasn't far though, and before she knew it, she was walking up to the small building. The door and windows were shut, but she could see a little light peeking around the edges. Someone was there, at least.

As she slowed down and was within a few paces of the door, she saw it open partially, and the head of a pony stick out. She was sure she recognized this pony as the one who ran the candy shop. A white or nearly white earth pony with a dark blue and pink mane. Although given the light out here it was more difficult to recognize her. The earth pony swung her head around, eyes darting and scanning the entire area behind Twilight before locking her gaze on the unicorn. “Get in,” the candy shop owner said abruptly, her eyes resuming scanning behind Twilight. The unicorn's horn glowed briefly as she opened the door fully, hesitatingly taking steps through the doorway as the earth pony backed up, never facing away from the door. “Hurry.”

Twilight let the door shut behind her, even more nervous than she was before. The earth pony stared at her, her eyes seeming to bore into her. Twilight only just noticed that the owner of the shop had raised her right foreleg, pointing it straight at her from the moment the door had closed. “Did anypony follow you?” the owner asked, almost no emotion in her voice. Her right leg and hoof appeared unadorned which confused Twilight even more.

“Um, no. I'm pretty sure nopony knows I'm here,” Twilight stammered out.

“Stop scaring her, Bon-Bon,” came another mare's voice from Twilight's left. She barely kept a gasp from escaping her throat as her head whipped towards the voice. A mint colored unicorn with a similar mane and strikingly golden eyes stood calmly to the side. She slowly started to walk towards us, the quiet clopping of her hooves almost deafening in the silent shop. Twilight glanced back and forth between the two ponies. Her legs felt frozen and her mind was racing in circles.

“I am Lyra Heartstrings. I am assuming you got my note?” she asked, walking between Twilight and Bon-Bon, continuing to the other side of the room.

Twilight was barely able to squeak out a “Yes.” She took in a bit more of her surroundings during the lack of conversation after the one question. Bon-Bon had backed up against a counter that stretched most of the length of the room, with enough of an opening on the far right end for somepony to walk back to the “employee area”. The counter was shoulder height, made of glass, and filled with an impressive array of different candies. The front area all three ponies were standing in was decorated sparsely, with no furniture. Lyra was facing away at the moment, while Bon-Bon kept constantly glancing at the door and visible windows, rarely actually meeting Twilight's eyes.

Lyra never stopped her slow walk, turning around at the far right side to continue pacing back between the two ponies.

“I know that you are probably confused and aren't even sure why you are here. I know you are probably expecting answers, ones that I can't give you right now,” she finished this statement glancing at Twilight and holding her gaze before continuing her back and forth pacing. “We needed to be sure about you, and I am. I need you to understand that you are now in more danger than you have ever been in your life. I... we believe you and know what you are going through,” Lyra stopped her pacing to stand off to the side of Twilight, facing her directly.

“I will arrange a meeting for the one you are looking for,” she broke off when she saw Twilight's eyes go even wider. In a softer voice she continued, “he's been looking for you too, and he's not as evil as the books paint him to be. But he's the only one that can give you the answers you seek.”

Lyra lowered her head for a moment, then raised a hoof and put it on Twilight's shoulder. “I need you to understand. Our safety depends on you. Tell nopony. Not even your friends. You might be gone for a bit, so you'll also need to make up an excuse as to why, and it might be short notice. Please trust me on this.”

Twilight nodded, still trembling. Both Lyra and Bon-Bon then tilted their heads to the side for a moment, as though listening for something. The fact they did it at exactly the same time caused the mane on the back of her neck to prickle and shivers to run up her spine.

“You have to go, now.” Lyra said abruptly. “I will be in touch. Remember, keep all of this a secret. Your life depends on it.”

Before Twilight could even react she was being pushed back out the door into the night air. She never even looked back as she slowly walked then trotted back to the park. She gathered up the things she had left, still undisturbed and headed back to her library, mind swimming. She dumped all of the stuff she had been carrying with her magic on the floor as soon as she entered, walking up the stairs to her room without even looking at it. It wasn't until after crawling in her bed that she realized her heart was still pounding and she was shaking uncontrollably. Sleep did not come easy for her either.