The Horrible Chimera Laboratory: Tragic Reconstruction

by SecretPerson

Rating: mature
Tags: Tragedy, Crossover, Human, Dark
Length: 3525

One does not wake up in the Chimera Labs without fear of what will happen to them. As Fluttershy opens her eyes, she sees her friends in separate cells, and the horrible creations of the Pig King, Porky Minch. This is a dark Mother 3 crossover.

Equestria is gone.

A man by the Name of King Porky Minch has destroyed everything. Canterlot it burning, Fillydelpia is ruble, ManeHatten is filled with desolate buildings empty of live. And Ponyville is a charred valley. What became of the Mane Six?

One does not wake up in the Chimera Labs without fear of what will happen to them. Numerous cells will surround them, filled with many creatures filled with fear and pain. Some already having been tortured and tested upon. Then, when the men with Pig Masks on come, you will shiver as they open your cells, and tie you onto a wheelchair.

Soon enough, you will be brought through multiple corridors to see the terrifying improvements on other creatures. Some mixed with metallic parts, some even crudely attached together, filled with fear and rage as they attempt to break loose of their new bodies.

Then, once your shoved into THE room, under the monitoring of the Pig King himself, surrounded by scientists and engineers, and many machines. You will wish they would knock you out, but they won't.

What will become of Fluttershy and her friends?
___________________________________________
I decided to try something dark.

This is a crossover with Mother 3, if Porky had won. And it will include things such as torture, depression, grief, and pain.

It won't be as bad as things like cupcakes, but I would't read the whole thing if your queasy.

Published 1970-01-01 00:00:00 UTC
Last updated 2013-03-11 01:02:19 UTC

Prologue: The end of Equestria came and went.

Everything was going to be just fine.

Why wasn't it just fine? What happened? Why now? Why couldn't we stop it?

All I remember is that tune, that damn tune.

Then, everything was gone.

Why after such a happy event? Why at all? Is this a nightmare? Is it just a dream?

Why do I feel cold? Why do I hear screaming? What is happening?

Were is the Princess? Can't she help us? Can't the elements help?

This must be the end.

It is finished. We are finished.

_____________________________________________

Fluttershy began being able to hear sounds again. Everything sounded like gibberish, and there were odd noises mixed in with talking. She twitched a bit, and realized she wasn't in her normal bed. The ground was hard, felt smooth, and pretty cold.

She slowly opened her eyes and everything was blurry. Fluttershy then felt her head, noticing some bandages there. She blinked repeatedly, and began being able to see and hear more clearly.

"Fluttershy!" said a voice, it sounded like Applejack

Fluttershy blinked, and slowly stood up. With a look to the side, she saw she was in a small glass cage. The room outside was larger, consisting of multiple of these cages. Then she looked at the one across from hers, and saw Applejack.

"Applejack...?" muttered Fluttershy wearily.

Applejack had a very gloomy look, but she smiled slightly to Fluttershy, "It's alright girl, how are yah feeling?"

Fluttershy rubbed her eyes, and tried to think, but it came with a very bad headache.

"My head..." said Fluttershy.

Applejack frowned, "Ah know girl, you took one to the head real hard. Ah'm glad your alright though."

Fluttershy looked at the walls, and saw some signs. Most notably, on large on above the door into the room said 'Chimera Lab unfinished chimera cells'.

"What... why?" asked Fluttershy, having trouble thinking.

She heard another voice come from her side.

"Those damn pigs." said Rainbow Dash, "Those god forsaken Pigs."

Fluttershy looked to see Rainbow Dash sitting in the cell beside hers. But, she was covered in bandages, and her eye had an eyepatch over it. From it she saw a bit of blood, only hinting at what Fluttershy worried happened.

"Rainbow Dash, just stay calm. Yah don't want to hurt yourself now." said Applejack,

Fluttershy looked more closely around, and saw Rarity was in the small bed behind Applejack in her cell. although, she was very bad looking, and covered in what looked like third degree burns and bandages.

"I just wish the party was still going..." said Pinkie Pie.

Pinkie was in the cell next to Applejack, she looked pretty fine at first. Then, Fluttershy saw something was wrong with her left fore-leg. It wasn't normal anymore, it was metallic, and had numerous lights on it.

Fluttershy was already shaking and tearing up as she asked "What happened? Why is everypony hurt?"

Applejack sighed, "You must've lost some of your memory... Ah hate to say it.. but were done. We've lost all of our homes, and Canterlot it likely still burning."

Fluttershy gasped, "How?! I remeber the coronation! we were all having fun! Twilight was a Princess!"

Rainbow Dash growled slightly, "A couple days after that, Canterlot was attacked. Twilight is probably dead. The princesses vanished. We only began to react before ponyville began being bombed."

Rainbow dash groaned, and heled her stomach.

"Careful Rainbow, your still very weak." said Applejack.

Fluttershy was in tears now, "T-This can't be happening... It can't!"

Applejack looked sadly at Fluttershy, and began tearing up too. "Ah wish it weren't... Ah've been awake in this here cell for days now. They only let us give yah slight medical attention before keeping ya'll over there... Mah brother was here to... But they took him."

Fluttershy dreaded to ask, "W-Were?"

Pinkie answered "The room with the knives and machines." before she began crying, "They took me there to, but they said they were out of something, so they just left this on me."

Pinkie lifted her mechanical arm, and teared up more, "They didn't even bother to knock me out, or give me anything. They just drilled it on!"

Suddenly, the door opened, and a strange machine entered. It looked like clay, but was moving on it's own and was shaped like a golem of sorts. It was pushing a cart filled with small amounts of food. Then with haste it took each tray and sent it into each of their cells.

Fluttershy wiped her tears, and asked "P-Pease let us go s-s-sir. W-We just want to..."

The Clayman groaned, and ignored her as it slide a tray of food into her cell. Fluttershy just cried more, and felt her head as it walked away ignoring her.

"Those bastard don't say anything. They just listen to their king and destroy homes." said Rainbow as she glared at the Clayman leaving.

Applejack picked up her tray and walked over to Rarity. "Come on sugarcube, they gave us some food, yah need to eat."

Rarity opened her eyes and groaned, she really didn't looked well. Appeljack helped her sit and and set the tray infront of her.

"Just eat, yah need it." said Applejack.

"D-Did, did they say anything of my s-sister yet?" asked Rarity in a quavering voice.

Applejack sighed, "Not yet. But ahm sure she's fine. They want to test on the stronger ones, I doubt they'd bother with some fillies. Fluttershy woke up though."

"Fluttershy?" asked Rarity, "How nice... I was w-worried about her."

"Ahm more worried about you at the time being," replied Applejack, "your wounds aren't healing well, yah need to try and get as much food in yah as possible."

"But I'm not hungry right now..." responded Rarity as she laid her head down.

Pinkie looked over with a worrying eye, "Come on Rarity, listen to Applejack, please don't just give up."

Fluttershy tried to wipe away her tears as she ate to processed salad she received, but tears kept falling into her food. She still just wanted to believe this was a nightmare, and to just wake up.

Rarity replied to Pinkie "Why should I? I-It's all gone. Were not getting out, unless we are made into on of, them.. I'd much rather not be one..."

Applejack looked at Rarity sternly, "Don't talk like that girl, we'll figure something out. Yah just need to get better so we can get out."

Fluttershy set down the tray, and asked "Who would do this?!"

Suddenly, the door opened again, and multiple men wearing pig masks walked in. They weren't ponies, they were something else, and had hands like monkeys. Leading the group of six pink uniformed ones, was a green uniform one.

"Alright, were ready for another subject! Now which one should we chose?" asked the grean one as if this was a test for the others.

"Why don't y'all just leave?! and stick those fancy weapons of your up your asses!" said Applejack furiously.

The groups just laughed and snorted, as Rainbow Dash said "How can you live with yourselves?! Destroying everything we had? Locking use in these cells! Cutting animals and ponies into pieces and reworking them together! What could be so wrong with your sick minds?!"

"We get ALL of our orders from King Porky himself!" said one of the pink suited pigmasks.

"Your not supposed to tell them anything!" scolded the green one.

"Well, I say we take this yellow one, she seams pretty fine." said a pink pigmask as he tapped on the cell Fluttershy was in.

Fluttershy just pressed against the wall in fear, "P-Please leave us alone!"

The green suited one laughed "It appears this one has finally come out of her coma. Other than the head injury she is pretty healthy.

"DON'T THINK ABOUT IT!" yelled Rainbow Dash.

"You just leave Fluttershy alone you bullies!" yelled Pinkie Pie.

The group of pigmasks just laughed again, and the green one said "I just love how you all act like you can do anything about it. We are in control now, deal with it!" He then turned to Fluttershy, "Open this cell, were taking the yellow one."

Chapter 1: The one in charge.

Fluttershy pressed against the cold metal wall as the Pigmasks were about to open her cell. Then suddenly, the green uniformed major's phone rang. He picked up it, and after a few seconds of listening he put it back on his belt.

"Alright, move all of them to the king P's playroom!" said the Major.

Rainbow Dash glared with her one eye, "What does your king want? I won't talk to him!"

The Pigmasks ignored her, and each opened the cells.

On grabbed Fluttershy and began dragging her to a wheel chair of sorts.

"Please! J-Just let u-us go home!" she cried as they thre her onto the chair, and strapped her in.

Rainbow Dash made a fuss as they grabbed her, "DON'T TOUCH ME YOU JERKS!"

One of the Pigmasks then pulled out a large stick, with electricity visible on the end. It then jabbed Rainbow Dash causing her to spaz out of control. Rainbow made grunting noises as she was visibly in a lot of pain already.

"STOP IT!" yelled Pinkie Pie, "She's just upset!"

One of the pigs grabbed Pinkie and tied her down to another wheel chair. The others then stopped electrocuting Rainbow Dash, and threw her wheezing, mostly limp body onto the wheel chair. Then two came into Applejack and Rarity's cell, and forced Applejack up and toward a chair.

"Leave here!" said Applejack, "She's too weak, just let her rest!"

The pig's ignored her, as one Pigmask came up to Rarity and forced her up.

"Get moving!" it scorned, as Rarity tried to stand up.

Rarity coughed, and fell to the ground. The Pigmask began getting annoyed and kicked her in the back, resulting in a groan of pain.

"Come on you lazy horse!" said another one, as the two picked her up and dragged her to a chair and strapped her down.

"Your all just a bunch of monsters," said Applejack in a few tears, "I can't hardly understand why you would do this!"

The Green one replied, "You should have chosen to just follow the kings wishes and be nice. If you had been nice, all you would have gotten would be a nice relaxing bath in a tube. Then you would be a nice person who can come to LOVE King P and live in his utopia!"

Fluttershy was continuing to cry, as the green one came up to her and yelled, "SHUT UP! I will have your limbs twisted off if you continue this nonsense!"

Fluttershy closed her eyes and tried desperately to stop crying. But, the tears kept coming, this whole event was too emotional. She was scared, sad, and empty feeling. Was it true her home was gone? How did these guys take over? Why couldn't she remember all of it?  Fluttershy just wanted it to end, to be able to go home and cuddle with her Angel bunny and sleep in her own bed.

By the time she opened her eyes again, they were moving down a long hallway. To the sides they could see multiple odd testing rooms. Some had machinery, some had diagrams of odd creatures, seemingly plans for creations in the future. All of that threw chills down Fluttershy's spine, especially when she saw a design that looked to be a pegasus with it's wings replaced with dragon wings, and mechanics on it's head and legs.

Suddenly, another door opened, and they were brought up an elevator. Rarity groaned slightly in pain, and one of the Pigmasks kicked her chair and scolded "Shut up!"

Rainbow Dash growled, "Leave her alone you bastard! she's hurt! Can't you see that through your stupid mask!?!?"

Then one of the Pigmasks hit Rainbow Dash in the side of her head with the bandage, and she just groaned in pain.

Fluttershy gasped at that, but held her tongue worried of what they might do to her if she spoke or cried.

"Everypony just stay calm..." said Applejack, trying to better the situation.

The group was lead down a more narrow hallway now, and through another metal door into a large room. It was like aholding area, beside a lab room filled with many scary looking devices. Such as a large mechanical saw, drills, and mechanical arms. All of this around a single chair with many restraints. In that room were multiple scientist in lab coats, and a couple blue suited Pigmasks.

Then Fluttershy saw Applebloom and Scootaloo int eh holding room they were in.

"Rainbow dash!" said Scootaloo, before she glared at the Pigmasks.

The Pigmasks finally let them out of their restraints, ann let them off the wheelchairs. Applejack readily hugged her sister tight, and Pinkie Pie helped rarity down.

"Did they do anything to yah? are yah hurt?" asked Applejack checking over her sister.

Applebloom replied "I'm fine, I was so worried about you though."

Applejack hugged Applebloom closer, "Ah'm alright, and I won't let them touch you if it is the last thing I do."

Rainbow Dash checked over Scootaloo, who seemed in good shape. Scootaloo however looked at Rainbows covered eye with worry.

"Rainbow Dash, what happened to your eye?" asked Scootaloo.

Rainbow Dash felt her eye patch, and replied "Nothing, just a flesh wound. But don;t worry, I will think of something..."

Rarity looked around weakly, and asked "Were's Sweetiebelle?"

Applebloom looked down and replied "T-They, took her some time ago, from the rest of us... But ah'm sure they just took her to a different area."

Rarity looked down and said "T-T-They better not have done a-anything to her."

Pinkie replied "Don't worry Rarity, I'm sure she's fine. I measn they only took some of us to this place... I'm sure they took her with the rest of the ponies."

Fluttershy looked over and sniffed, before asking "Were did they take the others?"

Applejack replied "These monsters said that everypony who listened and did not fight would get to have a bath in goo for a little while... Then they would become nice people, who like their King."

"Oh..." was Fluttershy only responce, as suddenly a voice spoke.

"Well well well... WELCOME TO MY LAIR! *Cough Cough*" spoke the old voice.

Rainbow Dash looked up to the ceiling, and asked "Who are you?!"

The voice replied "I'm your great protector and king. The visionary who built this empire. The one who brought the end of my last world! The relentless King who will rule all! Master Porky Minch!"

Pinkie Pie then yelled "Why are you doing this?! Why did you attack us?!"

"Aha.. hahaha.." spoke the king, "Because you all were under the false illusion you wer living perfect lives! I wanted to show you all what true creatures I could think up, many more creative things that you have! And show you the true happiness of fulfilling the deeds of your king! But you all were fighters, so rather then a nice long bath in my 'nice person hot spring', all of you get to become part of my newest line of Chimera's!!! Spankety spankety spankety!"

The group was silent, and Applejack held Applebloom close, while Fluttershy, Rainbow Dash, and Scootaloo stayed close together.

"K-King..." said Rarity trying to stand up, "w-were is my s-sister?"

The speaker sat silent for a few seconds, then Porky replied "Oh? Sweet-liver...? I foresaw her becoming the first of a new race of warriors! *Cough*, she will have the honor of being the precedent for all the younger and weaker ponies in this land! You should be proud of her! Ahahaha! *Cough, wheeze, cough*."

Rarity stood up in pain, and glared at the speaker, and said, "W_Were, IS, SHE?!"

Applejack came up to Rarity and said, "calm down Rarity! Don't hurt yourself."

Rarity coughed, and spat up a small amount of blood, before sitting back down.

"You know, miss Rarity, I understand you have a thing for true style, so let me show you what I thought of for your dear sister." said Porky.

Suddenly, the large metal door to their holding room opened, and a small white robot unicorn walked in. It was Sweetiebelle, but her entire body was encased in metal, and electronics could be heard moving with each step she took. Here eyes were now soul less lights, and multiple other lights flash around portions of her body. And her moath was a large flash plate, as her flank now had a cruel image of a pig nose mark. She walked with a completely obiediant manner, and stopped right infront of the entire group.

Rarity stared at her, and went up to her sister, "Sweetiebelle!" she said, as she hugged her robotic sister, whom did not budge, "P-Please say something!"

Applebloom and Scootaloo stared in disbelief, as Fluttershy started crying again. Pinkie Pie stared at Sweetiebelle, and to her single robotic arm.

"What did you do to her yah monster?!" yelled Applejack furiously.

Porky laughed over the intercom, and replied "I simply creativly installed some useful modifications, and had my scientists do all of the boring parts! Now I have a new toy! *Cough Cough* you should be proud Rarity, because she is much more obediant now, never talks back, and only follows orders. Being an older sister, isn't that what you would have wanted?"

Rarity began crying over her sister, and replied "No! No! I w-want my sister back!!!"

Porky replied "Oh, your acting like a crybaby who didn't get exactly what she wanted eh? You know what my father would have done to me if I made a fuss over and IMPROVEMENT? *Cough*"

Suddenly, robot Sweetiebelle lifted her arm, and a large knife came out the side. She then stabbed right into rarity's chest, and into her right lung. Everyone gasped with shock, as Sweetiebelle retracted the knife, and Rarity simply held her chest in pure pain. Fluttershy screamed, as Applejack and Pinkie Pie ran up to Rarity who was falling over.

"Rarity no!" yelled Applejack as she lifted Rarity up and held her chest, "Hang on girl, ya'll be alright!"

Pinkie Pie was crying, and held Rarity close, "Please no! Rarity! Don't die!"

Rainbow Dash came around, as did Fluttershy, both in tears. Applejack tried to stop the bleeding, but her pressure was not working, and Rarity was getting weaker.

Rarity then coughed, and said "I-I.. just want... everything to b-be alright... my sister to be h-herself."

Rainbow Dash glared at robot Sweetiebelle, and then to the speaker, "Porky! YOU HEARTLESS MONSTER! Help her! I know you can! Just help her!!!!"

Porky laughed, "Spankety spankety spankety! She was too frail for my experiments anyway! Just lower the surplus population!"

Applejack cried, and Fluttershy just balled up staring in disbelief at Rarity.

Rarity then coughed again, and said "P-Please... d-d-don't let him, have h-his way..."

Rairity then fell limp in Applejacks hooves, and Applejack just yelled "No! NO! Hang on!" as she desperately tried to stop any more bleeding.

Pinkie Pie turned away and held her ears, she began muttering something as if to make everything seem alright. Rainbow Dash just backed away and glared, as she began to cry. Applebloom and Scootaloo were backed away huggin each other crying, they had known Rarity, and were also very upset there friend was nothing but a robot. Fluttershy just came up and hugged Rarity crying, thinking about all of the past spa times they had together, even if they weren't her favorite thing, she regretted not going out more with Rarity.

"Your even more pathetic than humans!" said Porky in disbelieve over the speaker.

Rainbow Dash yelled back "YOU, Are the most DREADED monster I have ever known to exist! DO YOU JUST LIVE OFF OF HURTING OTHERS LIKE THIS?! What does this compensate for?! A life of people throwing you fake love?!"

Porky was silent for a few moments, again, before saying, "You know, I could use spar parts from your friend there one you if that would make you feel better. And that is me being generous, besides, all you are is a freak homosexual flag!"

Rainbow Dash growled, and threatened "Twilight, Discord, somepony will be able to stop you! and when I am out of this cage you will be in the most pain you have EVER felt!"

Porky simply laughed, then coughed, "The most dreaded pain I have is boredom! So if you do that I would be obliged to feel like there is more excitement in my life! But right now I guess, the best punishment for your horrible behavior... would be to start on your close friend there..."

Suddenly, a mechanical claw came into the room, and grabbed Fluttershy. She shrieked in fear and tried fighting, but it was strong, and pulled her through a passage way int the roof, and into the room with he machines. It was somewhat like an old claw machine were a kid would get toys from.

"Shall we get started?" said Porky.