Project Tw1l1ght

by Starlight_Glimmer1267

Rating: teen
Tags: Dark, Alternate Universe, Sad, Thriller, Adventure, Human
Length: 4847

Twilight Sparkle. Element of magic, bearer of the element of magic. Gone, one day she just up and dissapeared. No one knows how or why, but one day five years layer she just appears in front of her castle, different.

Twilight Sparkle, Gone. One of the most powerful unicorns in Equestria. This raises the question of where did she go? With her disappearance, she also took a small part of everypony's heart. But when she comes back, will that piece be the same? Or will it be cold and hollow like the shell of Twilight's former self?

There will be a prequel to this telling her adventures.

Published 1970-01-01 00:00:00 UTC
Last updated 2016-05-02 22:05:01 UTC

Reunion

The castle was covered in dust after years of vacancy. Rarity finally decided that no matter how much it hurt to step back into that place, it had to be cleaned.

But she knew that even in one thousand moons she would never get it done on her own. She needed help. Even if it was just a single pony, that would cut the work load in half.

It couldn't be Spike because he left for the dragon homeland in his grievances. He was now Embers life mate. He was of age now considering it had been five to six years after, the incident.

Celestia was devastated, but she could never be as harmed as much as Twilights parents. Even though she wasn't, she knew Twilight even better than her parents.

But than doesn't lighten the load on them.

It couldn't be Fluttershy because she would pass out at the sight of the castle, let alone going inside. Where they laughed, they played.

Rarity quickly pushed that thought to the back of her mind as she felt a tear form in her eye.

'Maybe Rainbowdash?' She thought to herself as she trotted through the streets of Ponyville. Seeing the crusaders run out of sugar cube corner made her think of asking them. Then she realized they still haven't accepted that she's gone.

No one knows what happened. She just disappeared. She looked up and saw Rainbow busting a couple of clouds. Getting rid of the only shade in the ocean of Celestia's sunlight.

She didn't want to bother her. She was working. Maybe Applejack, its her day off. 'Yea, I'll see if she wants to help.' Rarity thought and turned down the road that headed toward Sweet Apple Acres, crossing the wooden bridge on the way out of town.

"What room should I start with first?" She questioned out loud. "Maybe the bedroom. Or the kitchen, or the library."

She walked, not looking. Deep inside her mind trying to figure out how she would ever get that place clean. She could always use magic, but she liked the satisfaction of a job done by hand.

"Thanks fir  the help with roundin up those godstarn parasprites, Pinkie Pie." Applejack said carrying a sack over her back with an exuberant pink pony bouncing behind.

"Oh, Applejack. Perfect timing."

Rarity said turning around and matching pace with them.

"Hey Rarity! Were just disposing of these parasprites." Pinkie said with a bag also over her back.

"Would either of you like to help me clean. You know who's castle." She said as they both stopped.

"Honestly." Applejack spoke up as her and Pinkie stared at the ground. Motionless. "I don't know if I can do it. The castles our only reminder of her, I think we should leave it as it is."

"I know its our only reminder, but would you like our only reminder of one of our best friends to sit there dirty and filthy." Rarity said walking over to the two mares, comforting them.

"I- I guess your right." Applejack said giving in.

"What about you Pinkie?" Rarity asked as she looked over to Pinkie Pie. Her hair was down instead of its usually poofy state. She was crying.

"I-I-I can't!" She yelled. "It's just to much for me, I don't even want to look at that castle." She said falling on the ground.

"Its ok Pinkie, we understand." Applejack said. "If ya don't mind getting rid of these parasprites fir me, so we can get started."

"Ok." She said drying her tears and taking the sack Applejack was carrying.

------------Twilight------------

The pony stood there. One leg made of metal, one wing, a huge scar over her eye and a coat covered in them. Looking down at the body of her fallen enemy, barely alive.

She knelt down and pick him up in her hooves and started laughing. And a light started to cover them.

"Daystar, your time has come." Twilight said pushing her hoof blade deeper and to the soft skin of his neck. "All this death, for what. Your demise. You've sealed yourself a spot in hell."

"Ha, You know what." He said as the light finished covering them. "I think you're right. See you there."

"No thanks, I've already been. Give satan my best regards." Twilight said pushing the blade deep into his throat.

They were now covered in the light, it was blinding as it reflected off of Twilights metal wing.

Rarity and Applejack had just finished gathering cleaning supplies. They walked up to the front gate of the castle and stared at its majesty. Just then a huge beam of blue light and electricity crackled down from above, slamming on the ground. Making an earthquake like impact.

The two mares could just stand there and watch their now alien friend hold the body of some creature in her hooves.

"TWILIGHT!" She got no response, all she heard was weak sobs.

"Goddammit! Die Die Die!" Twilight yelled, this shocked Rarity and Applejack.

Rarity or Applejack could never see Twilight telling anypony to die.

"Twilight, are you okay!" The two mares now running over to her.

They saw Twilight hugging the thing close in her hooves holding a knife into its throat as it gasped for breath.

"Its been a good run." The thing said gasping for breath, making Rarity and Applejack stop in their tracks.

"Twilight?" Rarity said in a confused tone.

She stood up licking the blood off of her hoof knife, laughing.

"I did it." She said quietly. "Your death was not in vain. Nightingale."

"Twilight, are you okay!?" Rarity ran and jumped onto Twilights back. Twilight didn't even phase. She stood rooted in place like a great oak.

"RARITY!" She laughed a little. "It's over. WE WON!"

"Won wh-" She saw the dead body of Daystar. "OH MY CELESTIA! Why did you kill somepony!"

"I would've asked myself that question to, a long time ago." She turned around and hugged Rarity and Applejack at the same time. "You have no idea how much I've missed you."

She whispered into their ears. They both broke down into tears.

"Twilight!" Rarity said sobbing.

"Where did ya go." Applejack finished her sentence doing the same.

"It's a long story." Twilight said plainly walking toward Ponyville motioning for them to come with her mechanical wing. Wearing the standard UDF commander uniform.

"We have to let everypony know your alive!" Rarity yelled as her and Applejack caught up.

"I know." She said walking over the wooden bridge that marked Ponyville's border.

"Who was that?" Rarity asked.

Twilight sighed and replied. "The devil himself."

He wasn't the actual devil. But he made Twilights life a living hell. She still wasn't satisfied with shoving that hoof knife through his throat. She wanted to stab him over and over again in the chest, and watch him gasp for breath as blood filled his lungs.

"Twilight." Rarity said snapping Twilight out of her trance. "Is everything alright."

"Yea, why wouldn't it be." Twilight said as Rarity gave her a concerned look.

"Your stomping your hooves through the bridge." Twilight looked down and saw her hoof went through the wood.

"Oh, I'm sorry. I just have a lot on my mind." Twilight said. She took her hoof out of the bridge and continued to walk.

"What's wrong?" Applejack asked.

"Huh. I'll tell you when I have all of our friends together." She sighed and continued to walk again. "Wheres Spike?"

"He, left for the dragon homeland when you disappeared. The little guy was so depressed. I just hope he found his happiness with Ember." Rarity told her.

"I hope he is too." Twilight said.

"Wait, ya don't mind?" Applejack asked.

"Why would I, if he's happy I am, if I was gone for five years I wouldn't wait for myself either." Twilight said as ponies started to see her. "What happened while I was gone?"

"Well, like I said Spike left. Celestia almost cried herself to death. Your parents and Pinkie were devastated also. Everypony was." Rarity said as they passed the first set of houses.

Twilight saw something out of the corner of her eye, a Rainbow blur. She laughed and said.

"She's not the fastest anymore."

"What do ya mean, Twilight?" Applejack asked. She soon got her answer.

Rainbowdash came flying in at super sonic speeds. Twilight quickly sidestepped so fast that by the time Rarity noticed she was gone Rainbowdash was eating dirt.

"Twigskidyhanh!" Rainbow yelled with her mouth full of grass and dirt. She spit it out and jumped out to hug Twilight.

"Where were you!?" She asked frantically. Twilight jumped three feet in the air carrying Rainbow with her. A pink blur flew faster than the speed of light underneath them.

'Still to slow.' Twilight though to herself.

"TWILIGHT!" Pinkie yelled grabbing on to her with Rainbow.

"Are you okay, where have you been!?" They asked in unison.

"Lets meet Fluttershy at her cottage and I will tell you the whole story." She said walking as the two ponies still held on, but she still walked like it was no challenge to her.

"What happened to you?" Rainbow asked as her and Pinkie let go.

Twilight started to sing.

"There was a time, when I was alone, nowhere to go and no place to call home. My only friend was the pony in the moon, and even sometimes she would go away too. Then one night as I closed my eyes, I saw a shadow flying high. He came to me with the sweetest smile, told me he wanted to talk for a while. He said, Nightingale thats what they call me, I promise that you'll never be lonely. He sprinkled me in fairy dust and told me to believe, believe in him and believe in me. We'll fly away in a cloud of green toward your beautiful destiny." She finished, all the mares snapped out of the trance induced by Twilight sweet voice.

"That, was the sweetest song I have ever heard." Rarity said.

"Thanks. It helped calm my mind when I was knee deep in bodies." Twilight said as all the mares stopped and looked at her with open mouths. Rarity and Applejack not so much, considering they've seen her do it, still no less surprised.

"You killed!" Rainbow yelled.

"Yea. Is there something wrong with that." Twilight said turning toward Rainbow.

"Yes! The whole concept!" Pinkie yelled.

"Ok, TELL ME IF ITS WRONG IF YOU HAVE TO DO IT TO SURVIVE! THAT IF YOU DON'T ALL YOUR FRIENDS WILL DIE!" She finished and calmed down. "I-I'm sorry. I just,"

Rarity walked over and put a hoof over her shoulder. "Its ok, you must've been through a lot, dear. We understand."

"Thanks, I'm so happy to be back." Twilight said as they rounded a corner and Fluttershys cottage came into view.

"AHHHH!" They heard Fluttershy's scream from around the corner. They all started to run. Twilight moved so fast even Rainbow couldn't see her move.

Twilight rounded the corner and saw timberwolves moving in on her friend.

Twilight drew her hoofblade and flew so fast it cause wind of around twenty five miles per hour behind her. She moved her hoof up as she came near the timberwolves. She stopped on the other side, twisted her hoof so the blade would contract, and the wolves exploded into splinters as the other four ponies came around the corner.

"Fluttershy, are you okay?" Twilight asked as she walked toward Fluttershy. The timberwolves started to form into one behind her. Dragging in trees from the nearby forest.

Fluttershy was speechless pointing behind Twilight's back as they made the wolf shape and converged. It was now one giant angry wood wolf.

"Fluttershy?" Twilight asked as the wolf tried to step on her, everypony gasped as it seemed like Twilight was crushed.

"I wasn't. Done. TALKING!" Twilight yelled picking the wolf up by the same paw that he just tried to use and crush her. She slammed it into the ground and spun around and threw it as far as she could. Which was a good distance considering the size of the lumberwolf.

The four ponies around the corner of the house were staring at her with wide eyes, Fluttershy with closed eyes because she passed out.

That look on Fluttershy's face brought back a memory.

"TWILIGHT! Hold off the Desperado! I'm kickstarting the engine now!" Sgt. Riley yelled over the comms.

"You got it!" Twilight yelled firing potshots at the approaching Desperado from the Starships cargo bay. The Desperado were a band of aliens led by their leader, Daystar. He looks to enslave the entire universe for profit. All he sees is the business in everything.

They are some of all species. Ragnar, who are bug warriors, humans. You name it.

Twilight was paying attention to the far side and wasn't watching close by the bay doors. A Ragnar spider scouts crawled into the hatch, this wasn't the average spider, all Spinar are at least ten times bigger that normal bugs, so a little bit larger than Twilight.

The ship started to take off as Riley ran out of the cargo hold with his rifle blaring. The Ragnar saw this and dogged and shot a spike right through his face.

"RIILLLLLLLEY!" Twilight yelled turning and tackling the Ragnar out of the ship.

The spider used one of its legs to rip off Twilights wing. She screamed as she fell through the air with the spider. She stabbed it directly through the heart. It screamed also, fell back, and floated away from Twilight. Twilight fell for another second or two thinking this was it.

The ship flew under her with cockpit open and caught her.

"You can't get away that easily, Ms. Sparkle." The AI, Monday, told her.

Twilight crawled over to Riley's body. "RILEY!" She screamed over and over again. Seeing one of her only friends in this horrid wasteland called reality.

"RILEY!" Twilight screamed and all her friends could do is watch as she had that horrible nightmare. She shot up.

"Twilight what happened!" Fluttershy asked as Twilight slowed her breathing when she realized it was a nightmare. "Just a nightmare."

"Just a nightmare." She said again.

Chapter Two

"So uh, how'd ya end up like this?" Applejack asked.

"It's a long story." Twilight told them sitting up on the bed.

"Well now is a good time as any to start." Pinkie said.

Twilight huffed. "I guess your right. But like I said we will be here for a while."

Twilight was walking out of her castle with her saddle bags ready to go meet Celestia and Luna for their monthly tea.

"Almost ready Twi! Hold on!" Spike yelled from the bowels of the castle.

"Ok, but hurry! I've only been late once, I don't want to be again!" Twilight yelled her response through the door.

--------5 Minutes Later--------

'Come on were gonna be late, were already late for being early!' Twilight yelled in her mind. Stomping her hoof of the ground.

After she did that a white light started to cover her and she started to float into the air. She flapped her wings frantically.

"I'm sorry Equestria!" She yelled as she floated higher. "I didn't mean to hit you!"

She stopped in the air and said "Phew."

Then she started to dissipate into nothingness. She could still fell her hoof and move it even though it wasn't there.

A few seconds later all that remained was her head. She took in one last breath with no lungs and then poof. Nothing left.

Spike ran out the castle. "Twilight, I'm ready!"

He yelled to nopony.

"She must've left without me. Can't blame her. I swear I heard her a second ago though." He said locking the castle door and running to the train station.

Twilight found herself standing in a plain white room. Nothing but white in all directions.

"Hello!" She yelled and the sound echoed off of everything and came back to her.

"Hello Ms. Sparkle." A voice from out of nowhere asked. It was encrypted and sounded mechanical so Twilight couldn't recognize who or what it was.

"Where am I? How do you know my name!?" Twilight started to panic.

"Don't be afraid. I'm not here to harm. I'm here to help. I am merely a guide." It said.

"What do you mean guide." The know calmed down Twilight asked.

"That is not important, neither is where you are. Not at the moment anyway. What is is where you will be." The voice said. "Don't be overwhelmed by the technology."

Twilight started to disappear again.

"Oh great, not this again." She said as she fully disappeared.

-----Planet J-19 Sector 12-----

"No, I won't leave you!" She heard a male voice yell.

"You, AHHH! You have to. Save yourself!" Twilight could see now and what she saw left her speechless.

Lying on the floor was a creature cut in half. Next to it was another one holding the top half in his arms.

"I can't just leave you!" The other creature was now crying.

"If you don't leave. Ahh! Now you won't make it. When that device blows it will take this entire sector with it." The other one said writhing in pain. "It's to late for me. But you still have a chance."

Twilight looked over and saw another creature dead on the ground. This one was dead and had a sword in his chest.

"Five minutes until detonation." Twilight heard a robotic voice over the intercom.

"I can stop it!" The other one said.

"No! You'll only make it worse." He said.

"SHUT DOWN!" He yelled at the device as Twilight stood there in awe at the giant contraption in front of her.

"Voice recognition failed! Time until detonation: fifteen seconds." *Beep*

"Damnit! See what yo- Ahhh!" He said.

"I'm sorry!"

"10!"

"9!"

"8!"

"I thought I could help!" He said.

"7!"

"6!"

"5!"

"4!"

"3!"

Twilight saw what was happening. She didn't know much about this technology, but she did know that, that machine was imploding on itself. She started to run toward the two on the ground. The world around her almost slowed to a stop.

"2!"

Twilight jumped right next to them.

"1! Have a nice day!" The machine was like a nuclear explosion. It destroyed everything, everything except Twilight and those two things. Twilight cast a force field around the two and herself as the energy pushing off of the machine threatened to destroy the only safe haven on that planet.

"What!" The thing yelled. Noticing he was still alive.

The building was crumbling around them and the ceiling collapsed. Putting more strain on Twilight using every drop of her magic to keep them alive.

Soon after Twilight blacked out at the use of all that magic.

-------Some Time Later--------

"Is she going to be alive?" She heard the same male voice ask.

This time the voices were faint, Twilight being on the edge of life or death. Barely able to hear or see.

"We don't know, the second her horn fell off, her vitals dropped. But we have her stable now, so only time will tell." She heard a female voice followed by a pair of footsteps leave the room she was in.

"Wait, you lost your horn?!" Rainbow yelled.

"She couldn't have. Its right there on her head." Applejack said.

"This horn isn't real. It's only purpose is to keep me alive. It's connected to my dimeridium skeleton." Twilight told them.

"What is dimeridium?" Rainbow asked.

"Its a type of metal." Twilight told her.

"So you have an artificial horn?" Rarity asked.

"So you can't do magic?" Fluttershy asked.

"Nope. I burnt out my magic supply which caused my horn to fall off." She told them shaking her head.

"You have a metal skeleton!?" Pinkie yelled.

"Well it was either that or continue living with destroyed bones." Twilight said.

"Oh right, like we're supposed to believe you have metal bones." Rainbow said sarcastically.

"RAINBOWDASH! Stop being so rude! She's telling the truth. I have a knack for this sorta thing being the element of honesty and all."

"Can you just continue the story now!?" Pinkie moaned.

"Actually. I think there is a few peop- I mean ponies who should know I'm alive." Twilight told them. "Wouldn't you agree?"

"Why yes of course!" Rarity said ecstatically. "Who should we start with. Most of Equestria thinks your dead."

"Wait, like who?" Twilight asked.

"Well, everypony." Twilight heard Rarity say. In her head the word everypony just didn't sound right anymore.

"I guess we should start with the ponies of Ponyville." Twilight said.

"First ya should start with the CMC." Applejack told her. "Look y'all I'm really sorry, but I have to get back to work."

"What time is it?" Rainbow asked.

"I think around fourish. OH SUGAR COOKIES, I have to get back to Sugar Cube Corner." Pinkie and Rainbow both raced out the door.

"I forgot about work! My boss is gonna kill me!" Rainbow yelled.

"I wish I could come, but I have to many animal friends to take care of." Fluttershy told them.

Twilight turned to look at Rarity.

"I suppose, I could shut down the boutique for a day or two." Rarity told Twilight.

"Sounds like a plan to me." Twilight said as her and Rarity walked out of the cottage and started down the road.

They walked for about fifteen minutes until they reached the outskirts of Ponyville. Everypony there started to notice Twilight immediately. She didn't really blend in much for two reasons. One, she was an alicorn. Two, half her body was metal.

As Twilight and Rarity walked past the ocean of staring eyes they heard faint whispers.

"Is that princess Twilight?" One asked.

"Is she really back?" Another asked.

"Their just, surprised you back. To say the least." Rarity told her as they trotted through the now empty streets. All the ponies moved out of the way to let the long lost princess walk through the normally bustling town center.

"Where do you think the CMC are?" Twilight asked.

"Well, they were supposed to be trying to help me clean up the boutique last time I talked to them. They came out of Sugar Cube Corner on the way there. Why don't we check there first." Rarity suggested.

"Sounds good." Twilight said as the two turned off of the towns main street and headed into a smaller part of town. It wasn't a less active area. Actually it was the most active area in Ponyville. Just smaller.

They heard a very loud crash from the boutique all the way on the street. They quickly rushed and burst through the front door.

"SWEETIE BELL!" Rarity yelled.

No Mercy

"Oh, hey Rarity!" Sweetie yelled rolling by on roll of fabric.

"What did you do?!" She asked. Twilight couldn't help but laugh.

"Whats so funny, the boutique is a disaster!?" Rarity asked with the same tone as Twilight continued laughing.

"Things never change!" Twilight said, sill laughing.

"Twilight?!" Applebloom asked from up the stairs. Rarity started laughing along with Twilight.

"Is she really back!?" Scootaloo asked flying down the stairs.

"We told them you would come back!" They all yelled in unison. They were older than when Twilight left. They were all about half a foot shorter than Twilight. Scootaloo's wings finally developed. And Sweetie Belle can do adept magic now.

"Still, I would still like to know how this happened?" Rarity asked.

"Its not that bad. There may just be an ocean of fabric upstairs. But other than that its 'fine'." Scootaloo said putting emphasis on fine.

"I told you it would be okay. Nothing a little tlc and hard work cant fix." Twilight said.

"I guess your right. But, like I said. I that doesn't excuse this." They all ignored her and ran to hug Twilight.

"You were gone for so long." Sweetie said.

"Where did ya go?" Applebloom asked.

"How did you get these metal thingies?" Scootaloo asked.

Twilight laughed. "Thats a story for another time. Speaking of another time. Are you going to leave all those ponies at the clubhouse waiting?"

"OH! WE FORGOT!" They all bolted out the door.

"How did you know that?" Rarity asked.

"Bio sonar. I can tell where any living things is anytime if they are within a kilometer of me." Twilight said. "Who do you think we should go see next?"

"We? I have to clean this mess up. But I would go see the princesses next." Rarity said looking at the mess in front of her.

"Ok, I guess I'll see you later then." Twilight said walking out the door. "Oh, and you might wanna take two steps to your left."

Rarity stepped over.

*CRASH*

The light above her fell and smashed right where she was standing.

"See ya." Twilight trotted out the front door.

Twilight shot off of the ground breaking the sound barrier instantly. Leaving a purple trail from where she was to the castle in Canterlot.

Rarity stood there in shock as her ear drums were burning.

"I don't care, we have to be prepared!" Celestia yelled as she walked down the hall. She was speaking to none other that Shining Armor and Cadence, they were visiting Canterlot to spend time with her and Luna.

Celestia's hair was down and in its natural pink state, it has been like that ever since Twilight's disappearance.

"I know, and I'm not arguing about that, but I think we can let up on the patrols. You're working my stallions to death!" He yelled down the hall.

Celestia was in a deep state of depression. She was never in her usual happy carefree state. She was now in seriousness overload. Everything she did was formal and traditional. All by the book.

The type of ruler you would expect to see. Only leaving the castle for royal appearances and other things like that.

"I asked them if any of them had any objections before we started, and they didn't mind." Celestia argued back, turning a corner.

"Do you think they would ever go against what we say, were princess." Cadence said.

"Look, Celestia, we came here to spend time with you. And we haven't spent any time together except for royal duties." Shining Armor said.

"You look, Luna and I are the only ones that can keep this kingdom in tip top shape! I have no time for games." She said bursting into the doors of the throne room.

Twilight smashed through the ceiling with half the changling army following her. They all landed about five feet away with her. Princess Luna walked in between them, filling in the gap.

"This, complicates things." She said walking over to Twilight.

"Sister! What do you mean?" Celestia asked.

"Stay back you bastard!" Twilight barked, causing Luna to jump back.

"I will have to move my plans forward." She said as a green aura started surrounding her, rising up into a pillar of green.

"Luna!?" Celestia asked, confused of the situation. "Twilight, is that you!?"

She just realized who was standing there.

The pillar of green faded, standing there was queen Chrysalis.

"What have you done to princess Luna!?" Twilight demanded.

Queen Chrysalis started to laugh uncontrollably. "I killed her."

She continued to laugh, but little did she know. Twilight would have the last laugh.

She shot forward and buried her hoof deep into the queens chest, wrapping it around her heart.

"H-How!" Chrysalis yelled.

Twilight ripped the still beating heart of of her chest, threw it on the ground, and crushed it.

The queen dropped dead right there, along with all the other changelings. Except one. Twilight rushed over and held it against the wall.

"Why didn't you die with the rest!?" Twilight asked.

"I-I-I" It said.

"Spit it out!" Twilight yelled.

"I am meant to be the next queen! My name is Light Shadow. I am Queen Chrysalis's daughter!" She said.

"Why can't you control the changelings!?" Twilight asked.

"These were all my mothers children, I was meant to leave and create my own hive. I don't have the mental link with all of these!" She said, struggling for breath as Twilight still pinned her against the wall.

"Why couldn't any of the other changelings lead?" Twilight asked.

"Because the hive must have a queen, these are all drones." She said breathing easy because Twilight loosened her grip.

"TWILIGHT!" Cadence yelled running to Twilight with Celestia and Shining Armor.

"Guards!" Twilight yelled.

Two royal guards ran up and saluted Twilight.

"Give her a room and prepare her for me momentarily." Twilight said handing over the new queen of the changelings.

Celestia's hair started to return to its normally wavy state.

"Where have you been!?" Shining Armor asked.

"We've missed you so much!" Celestia yelled running over to Twilight.

"Twilight!" Cadence yelled again, at a loss of words at the sight of her long lost foal sister.