Equestria Origins- Twilight's Story

by Isolox4

Rating: teen
Tags: Dark, Tragedy
Length: 3396

Since the dawn of time, pony-kind has wondered; who are we and where do we come from? Well that's just about to be answered.

Ponies are missing and Twilight intends to find out why. But when she comes face to face with an other worldly being, everything she believed in is about to change. For good.

Published 1970-01-01 00:00:00 UTC
Last updated 2013-08-14 05:00:02 UTC

Prologue

A dark figure crawls through a metal corridor. It moves toward a large monitor surrounded by several devices and machinery. The figure opens it claw and begins to chart a of Equestria on its desk. "Where are you, you little bastard?" the figure muttered through two fang-filled jaws. It crossed out every location except one: Ponyville.

The Visitor

"As of yesterday, 12 more ponies were reported missing." Twilight read when she saw the newspaper headline. "This follows another 6 ponies having gone missing the previous day." Twilight kept reading with a worried look on her face. "The citizens of Ponyville are advised to keep careful watch when leaving their houses." Where in Equestria is everypony going?" Twilight said to herself. She trotted downstairs and saw Spike looking through a pile of books. Spike ignored twilight as she walked out the door and headed towards the meadow to see Fluttershy (whom she had promised to help earlier in the day.) But then, Twilight heard a loud scream coming from the east near Applejack's farm. Twilight hurried towards the farm and saw smoke rising into the sky. The whole orchard had been destroyed. She turned her head and gasped when she saw a large beast cornering Applejack. The beast has a large fin running down its back, a horn like that of a unicorn, several tentacles hanging from its upper lip, hoofs like a pony and was oozing yellow slime. The strange creature began to mumble at Applejack as if it were trying to speak.

"Twilight, help me!" screamed Applejack. The beast turned its head towards Twilight and charged. Twilight's horn began to glow as she produced a bright light that blinded the creature. The beast crashed into the door of Applejack's barn with its head stuck in the wall.

"What in the name of Celestia happened here?" Twilight asked Applejack.

"I was just tendin' to my crops when I saw that somethin' was knockin' over all of the apple trees. I saw this varmint thrashin' round screamin' gibberish." Applejack told Twilight. Twilight turned to the trapped monster that continued to speak in some alien language. Twilight's horn glowed as she put a spell on the beast. The monster's gibberish became fluent english.

"GRAGRAWhere are you? I know you're here!" The monster was still strongly blinded. "You've caused this planet enough trouble, Celestia!"

"Celestia?" Twilight exclaimed feeling very confused. "How do you know Celestia?"  The monster turned toward Twilight.

"Who said that?" It said. Twilight had forgotten that it was still blinded. She removed the spell so that it could see clearly. The beast looked around first at Applejack, then at Twilight. It didn't attack them but instead asked again, "Where is Celestia?"

"What do you want with Princess Celestia?" Applejack asked.

"Princess? That freak of nature is no princess!" The monster said in a very furious tone. Twilight was ticked off. Nopony badmouthed Princess Celestia especially in front of her. Before Twilight could say anything Applejack stopped her. Twilight didn't understand, but decided to keep her mouth shut.

"Maybe we just got off on the wrong hoof." Applejack told the monster. "My name is Applejack and this is my friend Twi-"

"I know who you are." said the monster. Twilight and Applejack were even more confused. "I was specifically sent to you to retrieve information on the whereabouts of Celestia. I wrecked your facility because you would not respond when I ask you where Celestia was and I suggest you do so immediately."

Twilight said to the monster,"Before we tell you anything, we want you to tell us who you are, why you're here, and what the hay is going on!" "Alright then I'll talk. You may want to get comfortable, this will take a while." they monster responded as it wriggled into a more comfortable position.

"My name is PX-2. I am the second failed experiment of Project Plasma." PX-2 pointed to a sun shaped symbol imprinted on his rear. Twilight was astonished. The symbol was perfectly identical to Princess Celestia's cutie mark. PX-2 continued to speak.,"That is the symbol of Project Plasma, a plan to create the ultimate galactic super-soldier." Twilight interrupted PX-2. "But if that is the symbol of Project Plasma then Celestia is-" She was cut off by PX-2,"That's right. Celestia is the third failed experiment of Project Plasma."

Twilight began to cry. "All these years... NO! I won't believe you!" Twilight ran home crying. When she got home, she didn't notice that Spike was missing and there was a hole in the wall.

Isolox

Fluttershy was wondering why Twilight had not come to help her. She knocked on Twilight's door but no one answered. She turned and saw smoke rising from a massive hole in the side of the library. Fluttershy looked through the hole. "Twilight? Spike? Are you home?" No one responded. Fluttershy trotted upstairs and heard Twilight crying. "Umm... Twilight? Can I come in?" Fluttershy said through the closed door.

"No! Go away!" cried Twilight, her face in her pillow.

"Ok. But you might want to know Spike is gone and the floor is on fire. I'm going to go now." Fluttershy told Twilight as she flew out through the missing ceiling.

"THE FLOOR IS WHAT?" Twilight burst out of her room, grabbed a bucket of water, and put out the fire. She looked around for Spike but he was nowhere to be seen. She did notice a note nailed to the door written is strange cryptic symbols. Twilight used her magic to translate it and it read;

''If you ever want to see your purple friend again, you will come to 3276 Everfree Forest Trail. P.S. We also have the blue one, the orange one, and the weird pink thing. Come unarmed."

Twilight couldn't believe this. Somepony or something had taken her friends captive. She took off towards the Everfree Forest without making any preparations. She wondered what horrible things that could be happening to her friends. She then decided to think positive and look on the bright side. Maybe they were still okay. She snuck through the Everfree Forest very carefully to avoid contact with Manticores, Cockatrices, and Dragons. Twilight wandered into a clearing that contained nothing she had ever seen before. She saw large glowing buildings made of shining metal unlike any known to pony-kind. She read the numbers on each building. "3273... 3274... 3275... well, here it is, 3276 Everfree Forest Trail. Twilight was worried. Would she make it out safely with her friends? She built up the courage to knock on the large metal shape she assumed was a door. Nopony answered the door. Twilight heard something walk up behind her but when she turned around, a tall figure had knocked her out cold.

"Hello there Ms. Sparkle." said a cold voice. Twilight opened her eyes and found herself strapped down to a cold steel chair. She looked forward and saw the most unruly creature she had ever seen. It had six horns, four legs, crab-like claws, two fang-filled mouths, compound eyes, wings like a beetle, and a thorax coated in a protective metal.

"Who- what are you?" Twilight screamed.

"It doesn't matter who I am. What matters is my plan." said the creature. "Let us go for a ride shall we?" The steel chair Twilight was in was moving along a track as did the chair belonging to the creature. They entered a dark room. All Twilight could hear was snarling and growling. The creature turned on a switch and the whole room lit up. The sight was horrifying. Twilight saw Discord, Chrysalis, Diamond Dogs, Gilda, and many others. But these were not the monsters she used to know. These were savage, snarling animals. In their eyes, she saw nothing. Just darkness. "Oh, I hope you don't mind." said the creature. "We did some experiments on your planet's native species. We were able to remove all mutated pathogens to revert these organisms to their former selves. Twilight was speechless. She responded with only a tear dropping from her left eye, dreading what were to become of her friends. "Let's move on."

Explainations

The chair began to move once again. Twilight looked up and saw Spike. But, this Spike was 50 meters tall and being held down by two chains, "What have you done to him!?!" Twilight was now crying so hard that she was unable to see.

"What have I done to him? You are the one who managed to stunt the growth of an endangered species." the creature told Twilight. "At this rate all of the unused energy inside of him would have built up and he would've exploded!" the creature continued,"This is indeed a rare species. Where did you find it?"

When Twilight opened her eyes she blurted out,"Celestia gave him to me when I was a filly." she continued to cry.

"Oh, Celestia. It seems as if it were only yesterday she were growing in test tube. But that was 3000 years ago."

"3000 years! That's impossible!" Twilight responded.

"Maybe for a simple organism like yourself, but my race can life up to a solid 10,000 years." "Ah! That reminds me. I haven't introduced myself." the creature remembered. "My name is Herbert Isolox IV, but you can call me by my surname, Isolox." The chairs began to move again as Twilight turned her head to see Spike say softly in a low voice,"Twi... Light..."

"You're going to like this part. You get to be with your friends." said Isolox. This room was different. It was filled with green pastures.

"Where are my friends?" Twilight asked breathing heavily.

"What do you not recognize them?" said Isolox

Twilight did not see her friends but horses. Not colorful ponies, but regular horses. "WHAT THE HAY DID YOU DO YOU MONSTER?!?" Twilight screamed frantically.

"What are you talking about? I haven't done anything yet." Twilight turned her head farther to the right and saw Applejack, Rainbow Dash, and Pinkie Pie hooked up to large machines.

"Hi, Twilight!" shouted Pinkie Pie "Isn't this fun? Wee!"

"I swear, there is something wrong with that pink thing." Isolox whispered to Twilight. "It broke at least $250,000 of equipment."

"Please! Let them go!" Twilight cried.

"You really have no idea what's going on do you?" Isolox shook his head. "Looks like I've got some explaining to do." He pulled a lever releasing Twilight's friends from their machines so they could hear his story.

"It all started 3,000 years ago. During Project Plasma, which I am sure PX-2 has old you about already, we decided to take DNA from the three most powerful creatures in the Solar System. The Horned Corona Slug from our planet, the Electric Death Swan from Jupiter, and what we wanted to be Earth's Giganatosaurus. Unfortunately, our close allies, the humans, were preserving the Giganatosaurus so they offered us a species that was populous and had also served them well during their course of evolution. After splicing the DNA of all three specimens, we were able to create four results. Three of which were incomplete but still strong enough to be useful. PX-1 contained DNA dominant from the Electric Death Swan. PX-2, whom you met earlier today, contained dominant DNA from the Horned Corona Slug. But, PX-3, whom you know as Celestia, contained DNA dominant from the Earth's horse. PX-4 was a pure mixture of all three and an unstoppable fighting machine. We treated all of our creations as equals, but Celestia wanted more. As our ship left for our home planet, Celestia escaped and went to seek control of the Earth."

"But, how come Earth horses don't look as cool us?" asked Rainbow Dash.

"Well, you see, that blasted monstrosity um... how can I put this, "interbred" with the Earth's native horse population, creating unicorns, ponies, and pegasi. The humans where overpowered by the "Plasmic Energy" you unicorns call "magic." We sent one of our creations to help but..." Isolox pulled out an old photograph as a tear came from his eyes.

"There's somethin' you ain't telling us." said Applejack. "Who was it that you sent to Earth?"

"That would be NX-3 of the Dark Matter Project. She was my first creation after Project Plasma had ended. They let me keep NX-3 as a pet because the experiment had not resulted in what they were looking for. I raised her from a single-celled amoeba until she grew into what she is today. I named her Luna after the latin name for Earth's moon." Isolox had a look of grief on his face. He was softy weeping.

The Invasion

This was too much for Twilight to take in. She had a hard time believing it all but then, Rainbow Dash spoke."What if we were to say that we might know where she is."

Isolox grabbed Rainbow Dash by the shoulders and said gleefully, "She's alive? She's safe? I demand you tell me where she is!"

"Why don't we make a deal?" said Rainbow Dash.

Isolox's smiles became frowns. "Yes of course. If you tell me where she is, I will leave your leave your friends unharmed and return all fifty-nine of the stolen ponies. Now start talking!" Rainbow Dash told Isolox the location of Luna. "Canterlot?" said Isolox. "Where is that?" He scuttled over to his map of Equestria. "Computer, scan for Canterlot!" The computer's screen turned green with wavy lines moving across.

"No matches found Error:404 "Canterlot" not found." responded a deep metallic voice. Isolox grabbed Rainbow Dash by the throat.

"If you lie to me again, you can say goodbye to your friends."

"Leave her alone!" said Twilight.

"Would you like to tell me where Luna is, weakling?"

"She's not lying! It's not our fault your stupid hunk of metal can't detect floating islands!" Twilight protested.

"Floating islands? Of course!" Isolox hurried back to his computer. "Scan for level 100 electromagnetic waves!" The computers screen showed a large silver sphere floating above Ponyville. "She thought she could hide from me? How could I be so ignorant? We're leaving now!" The whole building began to rumble and vibrate.

"Wheee! This is fun!" said Pinkie Pie as she moved across the floor. The building left the ground as several rocket thrusters moved it through the sky. The ship landed in Canterlot and as the ship's door opened, the ponies ran away screaming looking for cover.

"Twilight, where are you going?" said Applejack.

"Sorry Applejack, but I have unfinished business to attend to." Twilight ran towards Celestia's castle. She charged through the doors and confronted Celestia.

"Twilight, what's going on?" said Celestia

"You know very well what's going on, you fraud! You don't raise the sun! Luna isn't your sister! Magic isn't real! You aren't even a pony! Everything you told us is a lie!" said Twilight, feel betrayed.

Celestia's eyes widened. "Twilight I-" "Shut it you freak!" Twilight said. "Twilight! Don't come any closer!" said Celestia's guards.

"Get out of my way!" Twilight's magic threw the guards against the wall and then caused them to burst into flames."

"Stop this right now, Twilight!" ordered Celestia. Twilight had never felt so furious in her life. Electricity moved through her veins, her mane began to glow as bright as a fire.

Isolox then broke down the door and Celestia growled in anger. "So we meet again" said Isolox. "Drones, take her away." Two robots entered through the door grabbing Celestia by her forelegs. Celestia tried to fight back. She trashed about in anger, but Isolox just chuckled. "I thought you might do this, so I came prepared." Isolox put a glove over his claw and pinched Celestia. Celestia screamed in agony as she began to grow tired. Her mane was no longer colorful and beautiful, but it turned gray and drooped. Celestia shrank to half her size, weak and unpowered. Isolox's glove was emitting electrical discharges. "Wow, if you had built up any more energy, my glove would have burnt to ashes." Isolox told Celestia. Twilight had fainted from all the excitement.

Luna

"Twilight! Wake up! Twilight!" Twilight vaguely heard a familiar voice. "Twilight! Get up now!" When Twilight woke up, she saw herself face to face with Luna.

"Where am I?" Twilight asked.

"You're on the ship, Twilight. We're going home." Twilight tried to move but found herself strapped down to a cold metal chair.

"Home? Luna, Equestria is our home." Luna was showing a look of disgust.

"Equestria? Equestria doesn't exist. I would never call a land corrupted by her home. When we first met I was on a mission to stop her. I fell for her tricks. I let her trick me into thinking I was her little sister. But then, my creator returned. I didn't believe him, but he showed me pictures. Pictures of who I really was and where I came from."

"But what about me?" Twilight said. "What about my friends. What does he want with me?"

"I think I can answer that." Twilight saw Isolox approach her. "Turn to your left and all will be explained." Twilight turned her head to the left and saw a series of flashing computer screens. Each screen showed a location in Equestria. They showed Discord crushing Manehatten, Gilda tearing apart Cloudsdale, Spike burning Appleloosa to the ground, and Chrysalis devouring Ponyville.

"We had a deal Isolox!" Twilight screamed.

"Why yes, I do recall our little deal. I said I would leave your friends unharmed. Now let us see what's behind curtain number 3!" Isolox lifted a nearby curtain showing Twilight's friends trapped in a plexiglass prison cell with Celestia (who was still unconscious.) "I wouldn't want you all to miss the big fireworks show. Luna, would you like to do the honors?" Isolox asked.

"Gladly." replied Luna with an evil smirk on her face. Luna pressed a large red button that caused a large mechanical weapon to emerge from the bottom of the ship.

The weapon fired a blue laser that vaporized all that was in it's path. Twilight watched as entire cities crumbled to dust. She couldn't stand this any longer. Twilight fired a beam at Isolox's glove. "GAHH!" screamed Isolox as his glove overloaded with energy. His glove burned to ashes along with the rest of his arm. Luna ran over towards Isolox. "Don't worry about me, I'm fine." said Isolox as a new arm grew where the old one used to be. Isolox walked over to Twilight. "You have potential. I might just take you with me after all. Luna, release the others." Luna activated the switch that unlocked the prison cell. Rainbow Dash sped towards Isolox as soon as she was released in an attempt to attack. She crashed into Isolox, knocking him to the floor. "Why you little- GUARDS! SEIZE HER!" Isolox's robots returned and grabbed Rainbow Dash and the rest of her friends, throwing them off of the ship. Rainbow Dash tried to fly back up to the ship but it was too late. Isolox had already escaped with Twilight.

"Well, that's it" Applejack said with remorse.

"We've failed." Pinkie Pie began to cry. There was nothing they could do, no one they could trust, and nowhere they could go.

Isolox and Luna entered a large room with four drones holding Twilight and Celestia. Isolox bowed before a council of extraterrestrial beings. "The deed has been done my liege ,and the monsters are finishing up the job. What shall we do with the prisoners?" Isolox said to the figure sitting in the middle of the room.

The figure began to speak. "Tell your pet to take them to the prison hold. Their trial shall be scheduled for later this week. In the meantime, they are your responsibility." Luna lead the drones carrying Twilight and Celestia to the prison hold.

"I won't let you down, sir" Isolox left the room and returned to his ship.

"Luna! You don't have to do this!" Twilight cried.

"Actually, I kind of have to. It's the law." Luna tossed Celestia and Twilight into different cells. "Enjoy your new cellmates." said Luna as she returned to the courtroom.

"Cellmates?" Twilight said aloud as she slowly turned around. Standing behind her was a creature with 6 eyes, slithering like a salamander, and oozing orange slime.

"I think we'll be great friends." It said. "Heh heh heh."

THE END (for now)