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.