The Pony Protection Program

by ChessyKat01

Rating: teen
Tags: Romance, Adventure, Human, Main 6, My Little Pony: Friendship is Magic, Dark, Alternate Universe
Length: 4829

When something tries to bring harm to the bearers of the Elements of Harmony, Celestia sends them far away. To the one place no pony has ever heard of. A world ruled by humans.

When something tries to bring harm to the bearers of the Elements of Harmony, Celestia sends them far away. To the one place no pony has ever heard of. A world ruled by humans.

Hope you guys like this. I know this has been done so much, but I'm still putting this up here! Please don't get mad at me for being slow at updating. Things might get dark later, so I'll put up the dark category just in case.

Published 2013-11-10 03:50:11 UTC
Last updated 2013-12-14 05:07:21 UTC

Prolouge

Celestia sighed as she finally signed the last of the paperwork for the night. With barely a thought, the scroll rolled up on itself. Five other scrolls joined it in the air before they were tied together with a silky ribbon. The alicorn then tucked the scrolls into a near-by saddle bag that was decorated with suns. With her magic, it gently floated onto the princess. It had been a long time since she last wore something like a saddle bag, and she couldn't help but feel a bit like a rebel for wearing it. Apparently, it was "against the rules" for royalty to wear dresses made from the finest materials or jewelry made from gold and diamonds.

Going through a mental checklist, Celestia gasped when she realized she almost forgot something. Again, the princess grabbed something with her magic. Six individual envelops, each with a different seal, floated off of her desk and into the saddle bag. A small red book followed them, and a little click! was heard as the bag snapped shut.

Taking on a more serious air, Celestia stood and took in a deep breath. As she exhaled, her body began to tingle all over. A quick spell of dizzyness then overcame the alicorn as her magic "jumped" her to a different location. Her hooves finally touched solid ground. A sigh of relief escaped her lips and she opened her eyes. The first thing she saw was a steel blue mare who was kneelling on her front legs.

"Please, you do have no need to bow down to me here." Celestia said with a faint smile on her face. "I have finished the last of the paperwork, Cosmeta."

Standing back up, Cosmeta nodded. "We shall procede with the rest of the preparations then. If you don't mind, your highness, please follow me." The mare instantly turned around and began to trot down a long narrow hall.

Celestia followed her obediantly. As they walked, all she could hear was the sound of their hoof steps. The building was eerily quiet, but it was quite late when she had arrived. Everypony else who worked there must have hit the hay earlier. The princess felt bad for not finishing the paperwork sooner, and she examined the unicorn infront of her. She swayed just slightly that it would have gone unnoticed by most ponies. She couldn't see her face, but she didn't expect to see any bags under her eyes. Cosmeta always had to be presentable before meeting with others.

Finally, she spoke up. "I apologize for making you stay up late."

"Oh, it's fine." Cosmeta assured the princess as they finally arrived at their destination: her office. Pushing the door open, she explained, "I would still be up because of all of this commotion. Our division rarely has any work to do, so we're all a bit rusty and we're trying to catch up with the work." A hoof flew up to her mouth. "Please forgive me, Princess, for I sound like I'm complaining."

"Rest assured that I did not think that you were." The alicorn smiled as she sat in a padded chair that looked like it was made for foals when compared to her. Using her magic, Celestia sat her saddle bag on the desk infront of her and emptied out its contents. "Here are the papers," she explained, pushing them towards the other pony.

A magical aura surrounded her horn as Cosmeta carefully untied the ribbon and unrolled one of the scrolls. Her silver eyes scanned the paper and she nodded. She did the same to the remaining scrolls. "Everything seems to be in order.... We will start immediantly tomorrow." Her eyes then fell on the envelops and the little red book. "Are these for them?"

Celestia nodded. "I was hoping that you would hand them out once they were ready. The book will give them a bit of insight for this new challenge."

"A book of folktales will?"

"It's not just folktales. That book is full of history." Cosmeta observed the princess. She seemed extremely serious about this.

"Well, if you say so, Princess." The mare yawned as she levitated the envelops and the book into a file cabinet before locking it. "This must be serious if we are sending them away."

Celestia nodded and said, "Well, their safety comes first. They are the only ones being targetted after all. I try not to use the Elements of Harmony when me and my guards can take care of it. Plus, they might learn something important about friendship."

Cosmeta chuckled. "You're always about friendship and the lessons that you learn from it."

"This kingdom was based on friendship, and everypony must remember that. We don't want to make the same mistakes again."

"Yes, we've all heard the story before." The blue mare waved her hoof. "I'm sorry, but is that everything?" She yawned again. A hint to the princess that they should wrap things up.

"That should be everything." A slipper-clad hoof touched a white chin. "Though I do have a feeling like I'm forgetting something...." Celestia closed her eyes as she thought for a moment. "Hmmm.... Maybe it wasn't that important after all. Anyways, when should I bring them here?"

Cosmeta pondered that for a moment before answering, "As soon as possible, I suppose. Give them about half a day to get ready, but they shouldn't be packing their things. They may only bring very important items with them.... Oh, but they'll need others to watch over their homes and businesses...."

Celestia smiled. "Do not worry about that. I have already hired a few respectable ponies for that job. That was one of the first things I made sure to get done before doing the rest of the preparations. That's one reason why it took me so long to get the paperwork done." The regal pony stood. "Well, I should take my leave now." She bowed her head. "Sleep well tonight." A flash of bright light engulfed her as she teleported back to palace.

Once she was back in the safety of her room, Celestia let herself yawn. She took a step towards her bed when something crackled. Lifting up her hoof, Celestia paled when she saw another page of paperwork.

Author's Note

Sorry, this is crappy. The later chapter will be better though, because that's when we get to the good part!

Mane Six

"Ugh!" Twilight groaned as she stopped pacing. "Where exactly is everypony?!" Ever since she had received a note from Celestia earlier that day, the unicorn had been quite impatient to leave. It was a slow day at the library and her friends were busy getting ready, so she was forced to wait at the train station with nothing else to do.

Now, there were only five minutes until their train left. Didn't her friends know how important it was that they were all on time? If Twilight could do a group teleportation spell, it wouldn't have mattered all that much. She couldn't though. A spell like that took a lot of focus and was hard to do properly with one other pony. Canterlot was also far from Ponyville. Usually, Twilight could only teleport a few yards away and she had to be able to see her destination. She was getting better though.

A crash interrupted Twilight's near-mental breakdown. She instantly turned around to see a familiar rainbow mane spilling out of a box. "Rainbow Dash! What took you so long? The train will leave in four minutes!"

The cyan pony groaned, rubbing her head. "I'm fine," she said, answering a question that was never asked. "Sorry, but I had to wait for Thunder Lane and show him what Tank eats."

Twilight gave her friend a questioning look. "Exactly how long do you think we'll be gone?"

Rainbow Dash jumped to her hooves and stretched her wings. "I don't know, but we usually don't go to Canterlot for just a visit. Unlike yours, my pet needs to be fed by somepony or he'll starve. Spike just grabs himself something to eat. Besides, Tank eats champions food!"

The unicorn glared at her friend, offended for her assistant. "Excuse me, but Spike is not my pet. He's more like a little brother who's also my number one assistant. And what would 'champions food' be for a turtle?"

Rainbow was about to say something when she felt the platform tremble as hooves pounded on it. She immediantly jumped into the air and called out, "Yo, AJ! Slow down! It feels like a stampede here!"

A panting Applejack slowed down to a halt when she neared her friends. "So-sorry fer... bein'... late...." She took a deep breath and exhaled slowly before attempting to speak again. "I lost... track o' time while tryin' to finish the chores.... Whew! Glad I made it in time!" She began to look around. "Now, where are the others?"

Twilight shrugged. "I dunno. But they better hurry or we won't make it to Canterlot!"

Rainbow tapped her friend on the shoulder. "Don't sweat it, Twilight. You know Rarity. She's slow, but she tries to be on time. Same with Fluttershy. And Pinkie? She'll show up at the last second from nowhere!"

The orange farmpony nodded. "Jus' relax, Twilight. They're yer friends, as well as ours. They won't be late unless it's somethin' important that slowed 'em. They know how well ya admire the princess, and they won't let ya down."

Twilight sighed. "... You're right. Sorry, girls but I've just been so stressed since I got the letter from Princess Celestia. She said that it was urgent, and I don't want anything bad to happen because we were late."

The pegasus mentally facehoofed. "If it was really THAT important, then she would've teleported us to her or she would've sent for guards to escort us. Or maybe she would've came to us instead."

The librarian could feel her face grow warm. 'She's right,' Twilight thought. 'I really shouldn't be stressing out like this. I'll die at a young age or my hair will start to fall out. Okay. Deep breaths.'

"Oh, dear. So sorry for being terribly late." A calm voice said as its owner walked up to the group of friends. "I know she said to pack only very important items but...."

Rainbow's and Applejack's jaws dropped at the sight before them. A very large bag, looking like it was about explode, was levitating behind Rarity. "What the hay is in there?! ... Oh. Hi, Fluttershy." The yellow pegasus waved.

Rarity looked at her friends as if they were crazy. "It's just my make-up, dear Rainbow. I would have brought my hats and scarves, but I restrained myself." The white unicorn smiled as she proudly said that. Her friends had to give her a pat on the back for that. "I never leave home without a little touch-up make-up."

Twilight rolled her eyes. That was her "touch-up" make-up? She knew that looking good was important to her friend, but that was a ridiculous amount of make-up. Rather than trying to lecture her though, Twilight decided to leave that be. The train was going to leave soon. "Well, it looks like we're all here then."

"Aaallll aboard!" a stallion called out, telling ponies that it was time to leave Ponyville.

Twilight took the lead as they all entered one of the passenger cars. Rarity was close behind with her make-up bag, which struggled to fit through the door. Applejack headbutted the large bag to help get it in, complaining that the unicorn could have put it in with the other bags and suitcases. Rarity shot back a reply, saying that she wanted to look her best for the princess when they arrived. The farm pony still continued to grumble.

"Sorry for almost missing the train," Fluttershy apologized as she took a seat behind Rarity. "My animals were upset because I had to leave so suddenly. I also had to break up a fight between a cat and a mouse."

"Oh, my Opal was upset because of the very same reason." Rarity used her magic to take out a compact mirror so that she could study her make-up job. "Thursdays are her brushing and special breakfast days. I do that because I feel so bad for not being able to play with her because of work."

Rainbow flew in and dived for a seat next to Applejack. "Glad I'm not a fashion designer. I hate being stuck inside when I can go outside." She shuddered. "I hated being stuck at the hospital when I hurt my wing."

Twilight turned in her seat to look at her friends. "I still can't believe they sicced a... mentally unstable pony on you for stealing a book," she commented. "Sure, stealing is wrong and I do love books, but that seems a bit harsh."

The train gave a loud whistle before lurching forward. The sound of the departing train filled the air as they began to leave Ponyville behind. Applejack waved furiously as they passed by Big Macintosh with a cart hitched up to him. "Now, I wonder why we were called t' Canterlot."

Rainbow yawned. "She probably wants to tell us how awesome we are in person!"

The lavender unicorn shook her head. "Who knows? Anyways, where's Pinkie?"

Before any of them could answer, the door leading to a different car swung open. "Here I am!" the pink mare exclaimed behind a pile of candy. "I was here the whole time!" She dumped the sweets in an empty seat. "Well, not here, in this car, but I was still on the train. And I bought snacks from the snack car!"

"This train has a snack car?" Rarity asked.

Pinkie hopped over to Fluttershy with a lollipop with a pink marshmellow butterfly attached to it. "Here! Oh! I also saw a royal guard on my way here."

"You did?" Twilight asked. "That's weird. Well, maybe he was visiting some friends or relatives on his vacation? And he's on his way back to Canterlot?"

"Silly! He's a pegasus! I'm sure he would've flown back! I mean, sure it's far from here, but its not that far! Pegasi have pulled the carriages when the princesses came to visit us after all."

"Pinkie dear.... Have you ever thought that maybe he wanted a rest from flying such a long way? I know I would if I could teleport back and forth. Long-range teleportation spells do take a great deal out of you."

"But you know what's weird?"

Twilight sighed. "No, Pinkie. We don't." Already, she was wishing that the conversation could take on a different route.

"There was another one! But this one was a unicorn!"

"Maybe he's in the same boat with the other one?" Applejack asked inbetween bites of her caramel apple. She scratched her head. "But ya know what? I don't remember seein' two new ponies in Ponyville. An' I'm sure that Pinkie woulda thrown them a party."

"I tried, but they would run away whenever I saw them! They wouldn't even come to their own welcome party!"

Rarity lit up with surprise again. "That was what that party was for? I heard that it was a welcome party, but nopony knew who you were welcoming!"

Rainbow grabbed a blue cupcake, which was filled with a cherry filling. "Sweet!" she squealed, squirming in her seat. "Anyways, maybe they're on some secret mission. I mean, if they really were sneaking about Ponyville, then it's because of a secret mission.... Maybe they were checking out the Rich family and their friends the... whatever-their-name-is family."

A groan came from her earth pony friend. "Rainbow, the Rich and Silver family ain't part of some grand conspiracy."

"What conspiracy?" Fluttershy asked hesitantly.

Rarity rolled her eyes. "Believe me, Darling. You do not want to know. Let's keep you innocent for a little while longer." She looked out the window. "Tunnel up ahead, girls!"

"Oooh! I love tunnels!" Pinkie squealed as they passed through the dark tunnel. "That means that we're almost there! Then we'll be in Canterlot and see the princesses and see what they want from us! Maybe they want us to throw a HUGE party for them! But it's weird that we got to the tunnel already. Maybe they want to speed this up?"

"I don't think that the train is going that much faster. Anyways," Twilight shook her head, trying to get back on track. "The Princess said that this was urgent. You know. It's important. Sure, a party may be important to you, but a party isn't that important for the Princess to send for us. Unless it is for Princess Luna, but her birthday was about two months ago...."

"An' a party, a good 'un, fer royalty takes lots of preperation. She'd have told us t' pack 'bout fer a weeks stay at the most. Princess Celestia might be sendin' us somewhere else to do somethin' similar to that dragon quest when we had t' get it t' stop smokin' up Ponyville. That's why we were told t' pack lightly."

Smiling, Twilight looked out the window. Light blinded her eyes as their car exited the tunnel. Sitting in the mountains was Canterlot, the center of Equestria. The palace where the princesses lived could be seen from miles and miles away. It was easily the tallest structure in all of Equestria. The palace from the Crystal Empire was the only thing that was bigger than the Canterlot palace. Or maybe it just seemed like it because a lot of it was hidden underground.

'Applejack's right,' she thought. 'It's probably another dragon thing. Or something similar to that. It's nothing that we can't handle as long as we work together.'

"Princess!" Twilight exclaimed as she galloped towards her mentor. "What do you need us for?"

Celestia, who she had expected to smile upon seeing her and her friends, looked down at them with a serious expression on her face. The smiles melted off of their faces, except for Pinkie Pie, who continued to smile.

After a long uncomfortable silence, the sound of hoofsteps gained the princesses attention. She looked up and gave a small forced smile and nodded. Twilight followed her teacher's gaze to see two royal guards; one a unicorn, the other a pegasus.

"Oh, I do not need anything from you six.... I want you to be careful." She sighed, feeling her heart starting to act up. "I will not sugar coat this," which seemed more like a command to herself rather than to the small band of ponies. "... We have discovered that somepony is out to take your lives."

Author's Note

I know this sucks! Please, don't yell at me! This was mostly conversation and longer than the prolouge! The next will be better though!

Mane Six 2

Twilight's jaw dropped. "... D-did you just say that... we're in danger?" Her eyes widened. 'Oh, no. No. No. No! This cannot be happening! It's just a cruel joke! Celestia is too polite and all that to know any good jokes.' The unicorn spun around, expecting to see her friends in a panic. They weren't though. Their faces showed fear and surprise, but they weren't panicking.

Applejack swallowed a large lump that had been forming in her throat. With as steady as a voice as she could muster, she said, "... I-I'm sure that it's nothin' that we can't handle. I mean, we've all been through so much.... We've restored the Elements of Harmony, defeated Discord, learned valueable lessons, fought changlings, and...." She looked back at Fluttershy, who was peeking out from behind Pinkie. "Fluttershy faced a... minotaur? She was also the only one willin' to befriend Discord! An' we also faced an army of Pinkie's. And.... I was almost a Timberwolve's lunch once!" Applejack chuckled nervously. "Point is, Princess. We can handle jus' about anythin'!"

Twilight began to calm down after hearing Applejack's words. Soon, something like courage replaced her fear. She still felt a little uneasy, but that was to be expected. 'Of course Applejack would be the most calm in a situation like this. She's right, we can take care of this situation as long as we work together.'

Celestia's gaze softened. "I am sorry, but this is different from most of those situations. As far as I know, most of the foes you have faced did not want to actually... kill you. Hurt you, both physically and mentally? Yes. Rule over and torture you? Most likely. The point is that this new foe wants to kill you, and only you six."

"Only us?" Rainbow Dash asked, walking up next to Applejack. "Well, that's unusual. I mean, when something attacks us, it also attacks everypony else!... Why are we here? Shouldn't we be taking care of the bad guys?"

The alicorn princess opened her mouth as if to say something, but nothing came out. Instead, she glanced over at the old grandfather clock that seemed a little out of place in the throne room. It was ten past noon. She whipped her head back around to stare at the little ponies infront of her. They looked up at her with scared, pleading eyes.

The tip of her horn began to glow brightly. "I think it would be better if I showed you," she stated, taking a long stride towards them. She lowered her glowing horn, which was shining so bright that they all had to close their eyes tight, and gently touched them all with it. She started with Applejack, then Rainbow Dash, Rarity, Pinkie Pie, Fluttershy, and left Twilight for last. A white string connected them all to each other, and to the surprise of some of them, they began to feel like they were falling. All too suddenly, their hooves touched solid ground. It was like the floor beneath them had just fallen, and they fell down to the floor below. Only, they weren't hurt.

After a few seconds, Fluttershy slowly opened her eyes. Both she and Rainbow were a few feet above the others, having instinctively opened their wings and started flying. Applejack and Rarity looked quite frazzled and were a little uneasy on their hooves. The only ones who didn't even seem to blink at the feeling of being teleported were Twilight, Princess Celestia, and Pinkie Pie. Pinkie was unusually quiet though.

"Oh... my," the yellow mare whispered as she softly landed on the tiled floor. "Did we just...?"

Applejack leaned against the wall. "Whew! I... don't think I was one o' those who believe that they were supposed t' be what they weren't. I'm 100% Earth pony!" She gently pushed off against the wall, having regained her balance, and slowly turned towards Twilight. "Twilight, how can ya do that all the time?"

She shrugged. "I guess I'm just used to it. But the first time I tried a teleportation spell, I was sick for the rest of the day." Twilight looked around her surroundings to see that they were in a large round room that was painted white. There were no windows, nor where there any doors. Other than that, it looked like a normal waiting room with a receptionist desk, chairs, and tables with magazines resting on them. A chandelier hung from the ceiling, which was the main source of light. A couple of lamps were placed at some of the darker edges of the room. "This is strange," she whispered to herself. "No doors or windows. Looks like only unicorns can get in."

A loud gasp was ripped from the throat of a certain unicorn. "This is the. Worst. Possible thing! All my make-up isn't here! It must still be in the throne room back at the Canterlot palace! Oh, if only I could do a conjuring spell!"

"What's a conjuring spell?" Pinkie asked, hopping around everypony else. She didn't give them time to answer her though before asking her own questions. "So where are we? And why aren't there any windows? Are there any snacks here?"

"Would you like to see dirt, worms, or maybe the occasional bone when you looked out of one?"

Almost in unison, the group turned around to see a beautiful unicorn with a shiny steel blue coat. Her eyes were silver and sparkled, and her silver mane was styled in a bun. The pony wore a collar and her cutie mark was a detailed butterfly. She gave a small smile, while still keeping her serious demeanour. Most wouldn't have even noticed the fact that her smile was forced. "Nice to finally meet you all," she greeted with a curt nod.

Celestia opened her mouth to say something when two unicorns beat her to it. "You're Cosmeta!"

"Ummm.... Is Cosmeta famous?" Applejack felt dumb for asking that, and it was quite obvious. It wasn't her fault that she didn't know who this pony was though.

Rarity looked offended, raising a hoof to her chest. "Cosmeta was once a spokesmodel for Stable Mare's cosmetics! I remember seeing her in a few of my mother's magazines. I was old enough to remember seeing her in a few commericals shortly after she was replaced by Windy Gossamer. They were obviously soon replaced by newer Stable Mare commericals. Anyways, as soon as I first saw her, I wanted to grow up so that I could wear make-up." A sigh escaped her lips as she smiled in rememberance. "I didn't know that Twilight was interested in Stable Mare's make-up. You should've told me sooner so that we could have traded tips."

Twilight looked at Rarity as if her mane had turned green again. She pointed a hoof at Cosmeta and said, "You must have the wrong Cosmeta, because she is reknowned for her spells. Cosmeta made a break-through in appearance altering spells. She was the one who made it possible for a pony to be able to hide their cutie mark for some reason or another! I also used one of her spells to change an apple into an orange."

"Ya did what?!" It was Applejack's turn to look offended now.

"Well, who is she?!" Rainbow asked, growing impatient. She folded her arms and glared at this new pony, waiting for an answer.

Cosmeta shifted in place, looking a little uncomfortable. "Actually, Twilight.... While I was a model, I was inspired to create new spells that would change ones appearance."

Twilight could feel her face grow warm. She mentally facehoofed. 'Ugh! I should've known that! Even if I'm not interested in make-up, I still feel like I should've known that!' The purple unicorn expected to hear laughter from the others. She was almost surprised that she didn't though.

Applejack, noticing how her friend was embarrassed, said, "Well, that shows ya how different Rarity and Twilight are. One loves make-up, while the other always has her nose in a book."

Celestia smiled at Applejack, who grinned back a little sheepishly. The alicorn then turned her attention towards the mare, and said, "I believe that we are ready."

Rainbow jumped up into the air. "Excuse me, Princess. But I still don't get what's going on. First, you invite us to Canterlot, telling us to only bring what was most important to us. Then you teleport us here after telling us that our lives are in danger. Sorry, but I want to know everything."

Cosmeta gave Celestia a look that would have made a royal guard tackle her and left Twilight apalled. "You haven't told them where we are?"

"I was about to get to that. But I do think that it is best if we show them first."

The blue unicorn nodded. Turning around, her horn began to glow. Before the group's eyes, a door seemed to appear out of nowhere. The door reached all the way to the ceiling, but was only wide enough for one pony to go through at a time. Holding her magic, Cosmeta walked through the magical aura that surrounded the door and pushed it open. Noise came from the other side of the door and not even half of the ponies could catch a glimpse.

Walking through the door, one by one, they found themselves in another, much larger room. Many ponies were trotting in many different directions, and going through countless doors. Every pony, and some other creatures, looked like they had come from all the corners of the Earth. Some looked suspicious, while others looked like celebrities. They all looked nervous though. Especially the minorities, like griffins and diamond dogs and other non-equines. Some pony was pushing a coffee cart, and another was pushing a rack of clothes. One unicorn was using his magic to hand out files to a family of four.

Twilight could feel her jaw hit the floor as she realized something. "Wait. Don't tell me that we're...."

"Welcome, to the Pony Protection Program, my little ponies."