The Secrets of the Factory

by Primary213

Rating: everyone
Tags: Rainbow Dash, Doctor Whooves, Adventure, Derpy Hooves, Crossover, My Little Pony: Friendship is Magic
Length: 3988

The Rainbow Factory and a Time Lord. Should be interesting.

When suspicious activity regarding the weather factory occurs, the Doctor investigates and figures out what the Rainbow Factory is and there is an evil in that factory that the Doctor has seen before.

Published 2013-07-13 06:10:03 UTC
Last updated 2013-07-26 03:41:26 UTC

Cloudsdale's Secret

Cloudsdale's Secret

"Keep him restrained, and prep the machine," a voice had said. There were three scientists inside a dark room with a bright light shining on a single pony. His hooves were tied up and he had a piece of cloth over his mouth.

"All systems operational! The machine is ready sir!" One of the scientists said behind a wall of computer screens. The other two put goggles on and looked at the pony on the table. He was moving around, desperately trying to break the restraints. One of the scientists looked back at the pony behind the computers and gave him a slow nod to start. The machine powered up and the two scientists looked with smiles on their faces as the machine grew closer to the restrained pony. The pony on the table managed to break the cloth on his mouth and yelled something.

"What the hell is that!?!? What are you doing to me?" He yelled as the machine loomed over him. One of the scientists stepped forward and looked at the pony.

"Don't you worry, you are to be upgraded. You won't remember a thing of this. But your brain will be forever alive." He said as the machine continued. A scream echoed throughout the factory, a scream that could not be answered or heard.

"Wow, another day of exploration! Now tell me, where do you reckon we are off to?" The Doctor said as he was working the T.A.R.D.I.S. They just returned from an ancient Equestria. She looked from the other side of the controls to see him staring at her.

"Well, I dunno. We can go anywhere, so I wouldn't be sure." She replied as he smiled when the T.A.R.D.I.S came to a stop.

"Well, you are about to find out, after you." The Doctor said as he ran over and put his tie on. She slowly walked to the door and pushed it open. There was a blinding light, then she saw her destination. Her smile disappeared.

"You took me back to regular Equestria?" She slowly asked the Doctor as he walked out and shut the door of the blue box. He walked up to her and saw some slight disappointment in her eyes.

"Well, I figured you were homesick, so we came back to Ponyville. I mean it shouldn't be for too long. I am only really here so you can see your family and I can get supplies." The Doctor replied as he put his sonic screwdriver in his coat pocket. She sighed and worked up a smile. They both went in town and Derpy insisted that she go to her house first. So the Doctor agreed and they both went to her house. He waited outside as she reunited with her family members. As the Doctor sat on a bench just outside of her house, he heard a scream from a couple houses down. He jumped up and started to run towards the area of the scream. When he turned the corner, he saw a couple of ponies outside and one running out of he house.

"You can't do this! You can't just take him away! He did nothing! Please!" A mare was yelling at one of the ponies. He pushed her aside and continued taking him away. The Doctor ran up and looked at the other two ponies taking the colt away.

"Woah, what is all this about? What is the meaning of you taking this colt from his family?" The Doctor asked one of the ponies. He just looked back and they all became silent. He slowly put the colt down and stared at the Doctor.

"It's none of your business, that's why. This colt is in no way related to you, so you need not worry stranger." He said as he brushed the Doctor away. He picked up the colt again and they put him in a chariot. Just before he left, the Doctor stopped him again and pulled out his psychic paper.

"Actually it is my business. I work for the Princess as you can see, now I demand to know what you are doing with this colt?" The Doctor said as he looked at the paper. He gave out a short chuckle.

"You try to tell me you work for the Princess with a blank piece of paper, you must be crazy!" He replied as they flew away with the colt. The mare ran up next to the Doctor and started to yell. The Doctor looked at the paper, confused on how he knew how to read it.

"Sir, you can't let them take away my husband! Please help!" She said to him as tears ran down her face. He looked at her and put the paper away.

"May I come in? I need to know why this happened." He replied to the crying mare. She nodded and they went inside. He sat down as she was walking back and forth infront of him. "Now, has he been doing anything odd recently? Has he been leaving recently to for no reason or doing anything that may seem different than normal?" The Doctor asked her. She stopped and looked at him.

"He hasn't been doing anything of the sort. He has been acting like he normally would. He just recently lost his job two weeks ago and they just came randomly and took him away." She replied as she started to cry again. "The worst part is, this isn't the first. Ponies like the two you saw have been taking ponies from all around Ponyville. My husband wasn't the first." She added. The Doctor looked up in shock. He stood up and looked at a picture of him.

"Can you tell me where they have been taking them to?" The Doctor asked as he kept looking at the picture of him. She slowly stopped to cry and was taking short breaths.

"My husband was saying that there is this Weather Factory in Cloudsdale. That's where they have been taking them to." She replied as she started to cry once more. The Doctor went over to comfort her and remembered Derpy.

"I promise, I will bring your husband back! I will find him and bring him back!" He said as he walked to the door and left. He ran down the street and saw Derpy waiting outside her house. He walked up to her and told her about the situation.

"That makes sense, cause my parents told me some ponies took a pony from their neighbors house." Derpy replied. The Doctor looked around the street they were on and was confused.

"Somepony is taking innocent ponies put of their houses. But the question is, why?" The Doctor said. He looked at Derpy and she was just as confused as the Doctor was. "Well, I think it's time we give the Weather Factory a visit. Shall we?" The Doctor asked. Derpy thought for a little bit and a problem occurred.

"Wait, only Pegasai can actually walk and fly to Cloudsdale. How will you get there Doctor?" Derpy asked. The Doctor stopped and looked back a Derpy.

"We can get a ride up there, and Couldsdale has very compact clouds. I can stand up there as long as I don't hit any softer or less compact clouds. Those are only located on the outskirts of Cloudsdale. Now lets get going Derpy." The Doctor replied as he waved down a Chariot. They both got on and were on there way to Cloudsdale. When they had arrived, the city was busy with Pegasai flying and walking around busily. The Doctor got off the chariot and became overjoyed.

"Why are you so happy now Doctor?" Derpy asked as she got off and walked up next to him.

"Look at this! Your species is amazing! Able to build cities in the sky, I love it!" He said as he looked around in amazement. He looked back to Derpy and continued to smile.

"Well, since you are from here. Can you point us in the right direction to the Weather Factory?" He asked Derpy. She looked around the city for a couple of seconds and started to look confused. "Do you know where that is at?" The Doctor said to break the silence. Derpy then flew directly up and the Doctor just watched her. She stopped and was looking around. She then flew back down and reunited with the Doctor.

"It's over this way! We should see it after we make a left over there." She said as she pointed to their left. He smiled and started walking toward the factory. The more closer they got to the factory, the less ponies there were on the streets.

The Rainbow Factory

"Here we are, the Weather Factory." Derpy said as they both turned the corner to see a gray building with smoke stacks on the top of the building. They were spewing out black clouds of smoke. There was nopony around the factory, just the factory itself.

"Ah yes, this is the place. Also known as the Rainbow Factory. Interesting." The Doctor said as he walked up to the front of he factory. "Thing is, why would a place like this make beautiful rainbows? You think they would make the place a little more friendly on the outside." The Doctor said as he reached inside his coat pocket and got out his sonic screwdriver. The tip of the screwdriver lit up blue and the Doctor was slowly pointing toward the factory.

"What are you doing?" Derpy asked from behind him. He still kept his eyes on the gray building and listened for a distinct sound from the screwdriver.

"Scanning the area for unusual amount of energy, if the screwdriver goes solid blue and the buzzing is constant, than that means there is something else then rainbows being made in there." The Doctor replied as he kept scanning. Just as Derpy was going to say something back, the screwdriver went solid blue and the buzzing was constant. "I knew it, there is something else happening in that factory. It's not just the production of weather, there is something more happening in there." The Doctor said as he ran behind the building, searching for an entrance. Derpy followed him, but was still confused. They both made it to a metal door in the back and the Doctor unlocked it with the screwdriver. Before he opened it he looked at Derpy and smiled. "Time to see what all the fuss is about." He said as he opened the door. They both walked in to be surrounded in darkness with nothing but machinery all around them. The door closed behind them and they just stood there watching.

"What is happening in here? Why do they have ponies being kept in line by guards?" Derpy asked as she pointed toward them. The Doctor looked in shock. He saw the line moving one by one and heard screams coming from the other side of the factory.

"What the hell is this place?" The Doctor whispered to himself.

"Beautiful isn't it? This is just the beginning." A voice had said above them. They both jumped back and saw a pony fly down to them with a bloody lab coat and yellow construction hat. When she looked up, it was Rainbow Dash. "Welcome to the Rainbow Factory. It's my own little creation that I love to share with others as you can see." She said as a smile broke her face.

"What the hell do you do here?" The Doctor said as he became angry with her. She laughed and walked closer toward them.

"Why don't you come with me and find out?" She said as four guards flew up behind the Doctor and Derpy. Derpy looked behind at the guards as the Doctor just stared at Rainbow. They all walked over to an elevator that took them up to the highest floor in the building. "Our mission was clear. We were to build a machine that could generate clouds and other necessary weather items and distribute them accordingly throughout the land. But this was a tough task." Rainbow said as the continued to move along the walkway.

"Creating weather, that takes a lot of energy, you must have an abundant power source." The Doctor said as he looked down at the factory.

"We couldn't find anything with both mass amounts of energy and an abundant source until recently." She said with a smile. The Doctor was thinking for sometime. He looked down at the line of ponies and he took in a deep breath.

"So you are using the one thing that has those both. Your using ponies! How dare you!" He yelled as he grabber her lab coat. The guards quickly jumped behind him and restrained him. "You sick being you! Your ending innocent lives!" The Doctor yelled as Rainbow turned around to look at him.

"It is for the greater good of all ponies in Equestria! This is not all we do with the ponies!" Rainbow yelled as he was being restrained. The Doctor stopped fighting the guards holding him and looked at her confused.

"What do you mean by that? What more are you putting them through? Answer me!" The Doctor yelled as Rainbow looked down at the ponies being killed in the factory.

"You see, I recently had my scientists working on experiments that could further enhance the Rainbow Factory to a world wide scale." Rainbow replied. Derpy jumped forward and was staring angrily at Rainbow Dash.

"Equestria only needs one rainbow factory, why create others?" Derpy said as a guard brought her back next to the Doctor.

"Only certain ponies will know that there only needs to be one factory. What they won't know is that these new factories won't be factories after all. Just storage." Rainbow continued as she walked along the walkway. The Doctor and Derpy were forced to walk along with her.

"Storage? For what!?! You've been killing ponies for the weather! Why would you need storage?" The Doctor yelled as they continued walking. They all turned a corner to a new part of the factory and Rainbow stopped.

"Storage for my creations! For all of my scientists success!" She yelled as they all looked down in horror. There were millions of metallic silver ponies standing in line and some walking around them. The Doctor's eyes grew wide and his mouth opened. "With these new creations, there will be no classification! No segregation! Only unity and, eventually peace." Rainbow said as she burst out laughing.

"What are those things? They look like ponies!" Derpy said to the Doctor. He slowly turned his head towards her and looked at her.

"Another species has made the same mistake. Derpy, those are Cyberponies!" He said as she looked at him with a blank face. "They are the brain of a pony, but the body of pure metal and electronics. They feel nothing, and each one is exactly the same as the last one." The Doctor said to her to clarify. Derpy looked down at them again in absolute horror.

"Canterlot is a bug waiting to be squashed! The Princess would never agree to this, so she must be removed! First her, then all of Equestria will belong to the Cyberponies!" Rainbow said as she continued to look down at the machine and her slaves.

The Cyber age

Rainbow looked back at the guards behind the Doctor and Derpy. Coming from behind them were two Cybeponies.

"Guards, you are relieved from duty," Rainbow said as she smiled at the Cyberponies. The guards turned around an saw the metal ponies standing there. They put one of their hooves on a guard and electricity flowed through the guards. They screamed and fell to the floor. They did the same to the other guards and stood behind Derpy and the Doctor. The Doctor looked at Rainbow infuriated.

"You didn't have to kill them! You could've let them go!" He yelled.

"They were impure. They contained errors. Therefore, they were deleted," one of the Cyberponies responded in a monotone robotic voice. The Doctor turned and faced the Cyberpony.

"Cold and lifeless, that's all you are. Just programmed to do whatever she says in mere milliseconds," the Doctor said lightly to the Cyberpony.

"That is correct, why must we need difference when we could all be the same? I already have a squad of Cyberponies on their way to the Canterlot Castle as we speak. The age of war and ignorance is at an end. The age of Cyberponies is at hand!" Rainbow said to the Doctor. "Now take these two down to the ground level, I think they require the upgrade." Rainbow said as she turned and walked the other way. The Cyberponies pushed Derpy and the Doctor the other direction towards an elevator.

"You won't get away with this! I will not let this happen! So help me, I will make sure all these ponies that died are avenged!" The Doctor yelled at Rainbow as he was pushed again by the Cyberponies. They were taken to the ground level of the factory and the regulars guards were now replaced with Cyberponies. Next to the Cyberponies feet, lay the lifeless bodies of the guards that once stood there. Slowly they walked toward a row of five small empty rooms that were shrouded with cheap fabric. The machines lay dormant on the roof of each room.

"You will now get to witness first hand, the birth of a new Equestria. You will be upgraded." One of the Cyberponies said as he pushed the Doctor forward. He took a couple of steps forward and looked inside the room. It was empty and smelled like fire and one would get the sensation that death stalked this factory, especially this room. The Doctor looked back and saw Derpy. She was very worried and was looking right back at the Doctor. He then turned around and faced the Cyberpony behind him.

"You know, maybe I don't want to be upgraded. What happens if I say no?" The Doctor bravely said as he took a step closer to the metallic pony. It looked down at him and didn't respond for a solid minute.

"Then you will be deleted," the Cyberpony replied. "Now, into the room or you will be deleted."

"Well, I think I need to take some time on this deci-" the Doctor stopped halfway and pulled out his sonic screwdriver. He ran to the side of the Cyberpony and used the screwdriver right behind the earpiece of the robotic being. The two both let out a loud robotic screach that pierced the ears like knives. They then stopped and fell to the floor, lifeless.

"Come on! We have to get back up to the top floor and stop her from taking over the Castle!" The Doctor yelled to Derpy as she ran over to him. Other Cyberponies witnessed the death of two of their own and moved to intercept them both. Derpy stopped running and pulled the Doctor's coat to get him to stop as well.

"We can take the stairs! The elevators will be too easy to trap us," Derpy said as Cyberponies were starting to make their was close and closer to them. The Doctor held the door to the stairs open to let Derpy in. After she was in, he closed the door and locked it with the screwdriver.

"Incoming transmission from Canterlot. It is from unit 05580," one of the scientists said to Rainbow. She turned around and walked to the center of the control room. There were screens covering a whole wall of the room.

"Patch him through, I want to see my progress," Rainbow replied as the scientists went to their keyboards. Suddenly, a big center screen lit up and there were three Cyberponies on the screen. They all saluted Rainbow and one of them stepped forward. "I require a status update on the situation in Canterlot," Rainbow demanded as the other scientists stared at the screen.

"All hostile targets have been deleted. The Princess is under our command. We have captured her and cealed her in a room with no possible way out," the Cyberpony replied. A smile began to appear on Rainbow's face.

"We are moving faster than I expected. Good work my ponies. Bring her to me, alive," Rainbow said. She began laughing as the three one the screen saluted her once more and the transmission ended. She turned around and left the room.

"Ok, we can go from here to the fifth floor. That is where the main operating room is. From there I can use the screwdriver to override the Cyberponies. Now, Allons-y," the Doctor said as he grabbed Derpy's hoof and ran up the stairs. The Cyberponies on the ground floor had broken the door open and looked up to see the Doctor and Derpy already on the second floor. One of the Cyberponies put a hoof on his chest and spoke. The center piece on the chest acted like a speaker to all Cyberponies.

"Cyberponies will engage the Doctor and his companion. Delete them on site, they are in the Northeast stairwell." It said as the two rushed up the stairwell. Cyberponies from all over the factory were converging to the Northeast stairwell. When the Doctor and Derpy arrived at the fifth floor, the only stairway was blocked by Cyberponies. They all reached one hoof out toward the two of them. The Doctor grabbed Derpy and they both retreated to the stairwell again. The Doctor locked the door and looked down to see more Cyberponies. He reached into his coat pocket and pulled out the sonic screwdriver. He put it in Derpy's hoof.

"Take the screwdriver, it has a preset to teleport to the T.A.R.D.I.S. you go and stay there," The Doctor said to Derpy. She took a step back and put the screwdriver in the Doctor's hoof.

"I'm not leaving. Not without you," Derpy replied as the Cyberponies grew closer. The Doctor walked up to her and put the screwdriver in her hoof again.

"Derpy I'm not telling you. It is my responsibility to make sure you are ok. Now please go!" The Doctor replied as Derpy was still not taking the screwdriver.

"You have to trick me to make me take that thing! I am not leaving you Doctor." She replied as she put her hoof on the ground. The Doctor looked at the Cyberponies one story down and climbing. He was searching for a way to make her take the screwdriver. Then, he looked at Derpy with his eyes wide open.

"Fine, you won't take the screwdriver without a trick. Then I will have to trick you!" The Doctor said as Derpy looked confused. She was about to say something when the Doctor grabber her and kissed her. Her eyes were wide open and she wasn't moving. She was taken over by the kiss and her eyes closed shut. The Doctor put the screwdriver in her hand and clicked the button on the side. He then moved back and watched her disappear. She opened her eyes just before she was gone and looked at the Doctor. Once she was gone, the Cyberponies reached the Doctor and surrounded him. "Ok wait, wait, wait! Don't you think your master should decide if I die or not? Maybe turn me into one of you?" The Doctor said as the Cyberponies grew closer and closer. As they were about to go in for the kill, a voice was heard from the outside of the stairwell. They Cyberponies moved aside and Rainbow Dash walked up to the Doctor.

"I'll take him from here, there is something I want out little guest to see." She said as he was forced to move behind Rainbow to the operatong room.