All right, well I got the idea to write a story about Doctor Whooves and Derpy Hooves when I was looking for pictures of Doctor Whooves. The real reason for why I started watching Doctor Who was because of My Little Pony, well mostly. The first thing I noticed was that Derpy was in a lot of the pictures that I was looking at, then I thought, why? I looked through and got to the fanon and that's where I saw that Derpy and Doctor Whooves where together. Then I thought, that's a perfect idea. Both the Doctor and Derpy are two of the strangest characters I have ever seen. They would be perfect together, but I also like Spitfire and wanted to write about her too, so the Doctor will have to choose one of them. The clumsy cross eyed pegasus or the daring and perfectly coordinated pegasus. I really liked this pairing, so I thought, I might as well write about them. This story is really more just something that I just wanted to write down.

Disclaimer: I do not own Doctor Whooves, Derpy Hooves, Spitfire, Soarin, DJ Pon-3, Octavia, Sea Swirl, Minuette, Lyra Heartstrings, Bon Bon, Rose, Amethyst Star, Nightmare Moon, Discord, The Great and Powerful Trixie, Queen Chrysalis, Gilda, or the Diamond Dogs, but at least I can put them in this story.

Chapter 1 Different Body

"I have been alive for hundreds of years. Hundreds of years with a vehicle that has taken me everywhere in this universe, at anytime that something needed changing. I have saved almost every world and a lot more than once. I have fought Daleks, Cybermen, and the Master to name a few foes. After hundreds of years of cleaning up the universe, there was no more trash to clean up. The last battle that I fought was an extremely hard one, but most people made it out alive. I'm not one of them. I managed to save the day for the very last time, but I ended up with a serious wound that will kill me.

Of course I could always just regenerate, but should I? My work was done. This Time Lord had done the unthinkable, but now what? There's nothing else to do here. This universe doesn't need me anymore. Should I just let myself die? Or should I just live my life somewhere else and act like a normal person?" the Doctor stopped thinking to himself when the TARDIS started to shake. The TARDIS had found one more location. The Doctor was surprised by this and pulled the switches and pushed the buttons he needed to too get to this one more place. The destination was in a random part in space at a random time.

When he finally got there, which was about a couple of second from where he was, he realized that something was wrong. The TARDIS had completely shut down and was headed straight towards something. The Doctor couldn't see where he was going because the TARDIS had completely shut down, but he knew it couldn't be anything good. He felt himself grow extremely weak and knew that he was going to die soon. The only way he could prevent this was if he regenerated, but he had no idea why the TARDIS turned off in the first place or if it would turn back on at all. He decided that he should just regenerate and see what would happen with his TARDIS. He tried to let himself be renewed but for some reason he couldn't go through process.

He fell to the floor when he couldn't hold himself up anymore. "Maybe this is what happens when the TARDIS feels the end is near," the Doctor thought to himself. "We had a good run girl," he said out loud as best he could. The Doctors' eyes started to close ever so slightly, but then, his whole ship crashed. He was thrown to the side and hit a railing. He was too weak to do anything except moan. Because his eyes were closed and his senses where going away, he hadn't realized that the TARDIS had turned back on. He heard the noise that the TARDIS makes and opened his eyes to see that his TARDIS had turned on and tried to regenerate again, this time it worked.

His body released massive forms of energy and he could feel himself die and come back to life. He could feel his body change, but when it fully changed he passed out from the use of all that energy.

After who knows how long, the Doctor finally woke up. The Doctor blinked several times and stood up, moaning while he did it. "Uh, where are we?" He lifted his hand to turn the location detector on, but there was one problem, he didn't have a hand. "Aahhhhh!" he screamed as he jumped back and looked at himself. "I'm an animal!" he said. "Bloody hell! I'm an actual living breathing animal!" he said laughing. "That's never happened before." He looked at his legs and he looked at his chest. His cloths had fallen off. "I look like a horse, but if I were a horse my clothes would have ripped off, not just fallen off, which means I must be, a pony!" he said as he headed for the mirror that he kept in a separate room in the TARDIS. He looked at his facial features, and hoped beyond hope that he was, "Darn it, still not ginger!" he said looking at the pony that was staring back at him. "Hm," he said admiring himself, "I still look good though, even for a pony," he also noticed an hourglass tattooed on both sided of his bum. "That's strange. I wonder why I have two tattoos."

He went to the home screen and tried to find out where he was, but something odd happened. The TARDIS said that it was in an unknown location. "What! But we've traveled to every single spot in the universe! How is it possible that…" the Doctor could only think of one thing that could have happened. There was one thing that was nearly imposable for the TARDIS to find because it had hardly ever happened and because it wasn't supposed to happen. "The TARDIS had found a crack in the universe!" the Doctor said out loud. "We have gone to a parallel world!

Oh, that's why the TARDIS turned off! Last time it went through a crack while it was on it completely lost all power, so this time it knew that if it turned off it would be able to turn back on after we crossed through the barrier." Then the Doctor thought about the possibilities that this could be the world he left Rose on. "Oh, don't be stupid! What are the odds of me traveling through to another parallel world that's the exact same one I traveled through before?" he said as he looked at the door. "Well I was going to go out there anyway," he said to himself as he grabbed his key that had a thread around it, put it around his neck, and walked outside. Before he opened the door he thought, "Man I really hope I don't need clothes in this universe, or I'm going to be the laughing stalk of this entire raise." He could hear it now, "Oh look the Doctor landed on this planet with no clothes on, let's not take him seriously! Well they might not take me seriously anyways, so whatever!" he said as he opened the doors.

The sun was rising almost directly ahead. This world seemed to have more color, but seemed to have pretty much the same elements that earth had. "Hm, seems perfectly normal," but then he saw some type of grey pony's head with blond hair pop out of a nearby tree and quickly pop back in. "Hm," the Doctor thought back, "never seen that color on a pony before. Why is she staring at me?" then he remembered that he was a pony, maybe those where the dominant species on this planet. "Oh! That's why I regenerated into a pony! There are probably no homo sapiens in this universe, so the TARDIS communicated with my mind, like it always does, and I turned into the dominant form in this universe, or at least in this world," he said to himself.

"Excuse me," he called out to the grey pony behind the tree.

The pony stuck her head out again to see him, "Who-who are you?"

"I'm," he thought about it for a moment. Nobody in this universe knew who he was, so he could choose an actual name for once, "Doctor Whooves, with a w," he said surprised by the little joke he had thought of and started walking towards her, "It's ok. I won't hurt you. I just want to know where I am."

Even from that far away he could see that her eyes weren't looking in the right direction. She looked scared, but she didn't run away from him. She studied him to see if he was trustable or not. "Well he did just fly out of the sky, why should I trust him?" she thought to herself. "He doesn't seem dangerous. He is quite handsome too, but where the heck did he come from, and what was that blue box he came out of?" She decided to talk to this pony after all. She walked out from behind the tree, but prepared her wings just in case she had to make a quick getaway. "You don't know where you are?"

She had the most beautiful golden eyes he had ever seen, "No, I must have landed on the closest planet from wherever I entered this universe. Are those wings on you?" he said when he noticed her slightly spread them open.

"What?" she said puzzled, "are you ok?" she said as she started backing up when the Doctor was several yards away.

The Doctor stopped moving towards her when she started backing up. "Yes, well mostly, but I have never seen an actual pegasus before. Next thing you're going to tell me is that unicorns are real too," he said slightly laughing.

"You've never seen a pegasus or a unicorn?'' she asked slightly surprised by this. "Did you hit your head or something mister?"

"Well ya, but that's not the reason for all of this," he said looking at her. He was feeling something, something strange, but he just pushed it away. "So, can you take me to one?"

"Um, sure," she said as she looked at the blue box.

The Doctor noticed this, "You want to see inside?" he asked her.

This pegasus kept looking at the blue box then at the Doctor, Should I? she thought to herself. A complete stranger, who came out of the sky, who hasn't seen any 'real' unicorns or pegasus, whatever that meant, wanted to show her his strange blue box, "Ok."

"Ok," he said leading her to it. She still stayed a few yards away from him but followed. "Don't be surprised," he said as he opened the door and motioned for her to go in.

At first she was surprised, but she had seen several unicorns make something that was small on the outside bigger on the inside. "I thought you had never seen a unicorn before."

The Doctor was surprised to hear her say this instead of asking a bunch of questions like almost everyone does, "I don't understand why you're asking me that."

"Well this is obviously the work of unicorn magic," she said looking around at the strange blue box with equipment that she had never seen before.

"Unicorns here have magic too?" he said smiling, "Well it's not real magic, but to you guys that's what it looks like, but wow! I have never visited a world as exciting as this one! How do you guys survive when somepony with magical powers can simply just pop in and steal something important?"

"Well, what good would it do to steal?" this grey pony said looking at him now.

"That's what I always think, but some people just can't help it."

The pony looked at him confused, "What's a people?"

"Oh," the Doctor said remembering that there were no 'people' in that universe, "um, it's a long story," he decided to say, "Don't worry about it," he said as he looked at here. She was extremely pretty. "Why am I thinking about this!" he thought to himself, "This is a pegasus, and I just met her. Well we are the same species now. No! I can't fall in love! I'm just over whelmed by all of this. Ya. I'm in a new universe with strange new creatures. Who wouldn't over react to all of this?"

"Oookkaaayy? Well what is this thing? It looks like an alien space ship," then a thought came to mind, "Oooohhh, are you and alien?" she asked with excitement. She had heard of aliens from other ponies. They also said they were fictional, but she didn't know what that meant. "Aren't you supposed to be green, and have three eyes?" she asked getting into his personal space and started checking him over.

The Doctor felt weird being inspected by this strange pony, but in a way he liked it. "Well yes I am, but I changed form to look like you do."

"You can change form?" she asked surprised. She seemed to be really interested in his mane.

This tickled him slightly but he just kept talking. "Well no. Only on a very special occasion. That's how I got here," he couldn't help but stare at the tattoo on her bum. "Hey, what's this tattoo that apparently all ponies have on either side of their bum?"

"Do you mean our cutie marks?" she asked looking at her own. "You don't know what they are?"

"Why no, and apparently they are all different, since I have an hourglass and you have," he looked at her cutie mark and squinted trying to figure out what hers was. It looked like, "bubbles?"

"Ya, well, um, we get our cutie marks when we discover what makes us different from other ponies."

The Doctor seemed impressed, "Hu, so that's why I have an hourglass, but what do bubbles mean?"

The grey pegasus looked embarrassed, but said, "Um, I don't really know," she said honestly. "Why do you have an hourglass?"

"Well, I think it's safe to say, seeing that you guys have magical ponies anyway, that I'm a time traveler, and what you see here is my spaceship."

"Um, I thought you where a time traveler?" she said looking at him confused.

"Well yes, but I can also travel to other worlds, and through space," he paused looking at a screen on the TARDIS, "but by the looks of it, I think I won't be able to do anything with the TARDIS for at least two years! What am I supposed to do for two years!" he said as he hit the screen. "It's going to take two years for the TARDIS to scan the whole universe. Until the TARDIS knows what the universe is like, I'm not going anywhere."

The grey pegasus didn't know what he was talking about, but she didn't want him to leave, "You could live in Ponyville with the rest of us ponies."

"I guess I'm going to have to," he said thinking, "but I have no money. Where am I going to live? The TARDIS is going to have be on its own for the whole two years if it's going to get accurate readings."

The pegasus didn't know what else to say, "You could live with me," she said sheepishly.

The Doctor was slightly shocked to hear this, but it was probably the only thing he would be able to do. At least until he got a job. He just hoped beyond hope that his emotions wouldn't get the best of him. "Ok. But only until I have enough money to live by myself."

"Oh, I don't mind," she said with a slight redness coming out of her cheeks.

The Doctor looked at her strangely, "What's your name? I never caught it."

"Oh, sorry, my name is Derpy Hooves, without a w," she said slightly embarrassed that her last name was almost the same as his.

The Doctor laugher slightly, "You're kidding me aren't you?" Derpy shook her head. "Wow, and to think I just made that name up."

"What?" she said confused.

"Well I used to have a name, but it was lost forever, so I was known as the Doctor where I came from, but now that I'm here I guess I can choose any name I want.

"Oh, oh," Derpy said getting excited, "You should be named," she thought about it for a moment, "Time Turner."

The Doctor thought about this, "Time Turner. I like it. Well we'd better be off. The sooner the TARDIS leaves the sooner it will come back," he said as he started heading towards the door.

Derpy followed him out. The Doctor said one last goodbye before he got out. As soon as he did the TARDIS made the strange noise that it made when it arrived, but it left the one thing that he always carried that was in his pocket. His sonic screwdriver! "Oh my! How could I ever forget this!" He said as he picked it up with his mouth. The TARDIS had even put a string around it so he could wear it as a necklace like his key. The Doctor looked sad so Derpy put her wing around him to comfort him. The Doctor let her do this. After about a minute or so he said, "All right, let's get going. I know nothing about this world, so you might as well start telling me what it's like since it looks like it's getting dark."

"Ok, well my house is pretty close by, so we can go there and talk," she said as she started making her way towards her cottage.

"Is Ponyville close by?" he asked wondering why Derpy lived on the outskirts.

"Yes, about 15 minutes away by walking," she said as she turned at a fork in the road. The Doctor could see her house not far away from where they were.

"So, do all the ponies live away from Ponyville?"

"No, not really, but some of us like living in the forest or just away from the noise of everypony."

"So why do you live out here?"

"Oh, um," she started saying slightly embarrassed, "Most ponies in Ponyville think I'm clumsy. So they asked me to move away from everypony so I wouldn't cause any more harm to them than I already do."

"Oh, well, I'm sorry," he said felling bad for this pegasus.

"Oh, it's ok. There's this little filly that I see almost every day that brings me hope and joy."

"Oh, and is she your daughter or niece?" he asked.

"Oh she's an orphan. I would adopt her, but I just can't afford it."

"Well then I really shouldn't intrude on you if you can't afford it."

"Oh no! I can't afford something for too long, but if you're going to get a job then I can survive for a couple of months," she said not wanting him to leave.

"Ok, but as soon as I have enough money I'm be out of your mane," he said assuring her.

Derpy was slightly saddened by this, but she couldn't say anything without sounding too desperate. "Ok," she said softly.

They finally arrived at Derpys cottage. She told the Doctor everything that he needed to know about it, like where the bathroom was. The Doctor was surprised at how nice it was. The pictures she had all over the house had only two different ponies. Her and a little filly that looked slightly like her.

Derpy noticed the Doctor was looking at a picture of the filly and told him that that was Dinky, the filly that she would visit all the time.

"You must really care for her," the Doctor said turning to look at her.

She was smiling while she looked at the picture. "Ya, she's my little muffin. Oh! Those sound pretty good about now," she said as she headed towards her kitchen. "Do you want one?" she asked.

"Um, yes. I'm starving," he said heading towards the kitchen too.

"What kind?"

"Um, banana if you have any."

"Of course. I have all kinds."

He walked in and saw about every single type of muffin he had ever heard of, and more. "Wow! You really like muffins don't you?"

"Ya! They are my favorite type of food."

"Hm, I'm surprised you don't have muffins as a cutie mark," he said as she gave him his muffin. He took a bite, "Oh my gosh! These are good! Did you make these?" he asked.

"Well, ya. This is the one thing I can do without messing it up," she said blushing a bit that he liked her muffins.

They both ate and talked. Derpy told him about Ponyville and her life while the Doctor told her about some of his more interesting adventures. Even though there haven't been any aliens in Ponyville there have been plenty of crazy things that had happened to them. They apparently had a lot of celebrations too. The next one was the summer sun celebration which was like the summer solstice on earth, except nobody on earth celebrated it.

By the time they were finished they were both extremely tired. Derpy didn't have a sofa or any other beds besides her own which was just big enough for two ponies to sleep on, so she offered him her bed, but he just said that he would sleep on the floor.

"Well the bed is big enough for two," she said nervously, "and I don't mind."

The Doctor was tempted by this, but he just couldn't, "It wouldn't be right."

"I can't let you sleep on the floor."

The Doctor was too tired to argue anymore. He just decided to sleep on the bed. "Ok, but just this once. I'm just too tired to argue about all of this," he said as he got to the far left side of the bed and put the covers over himself.

Derpy got on the right side and couldn't help but smile. "Oh my gosh! He's actually sleeping with me!" she thought to herself.

"Oh my gosh I'm actually sleeping with her!" the Doctor thought to himself too. "This is just for one night. Don't let it go to your head. Why am I even thinking like this? I have never actually fallen in love before. This is just horrible. I'm the Doctor and she's a pegasus," he thought as he let sleep take over him. Regenerating was tiring work.

Derpy was still overwhelmed by this. She really hoped that she wouldn't move around too much that night. She had a habit of being in a completely different position from the one that she started with when she would first get into bed. "Oh well, I guess I'll find out tomorrow," she thought as she drifted off to sleep also.

The very next morning the Doctor woke up when he had a dream that something was squeezing him to death. The Doctor was in the exact same position that he was in when he went to sleep, but something felt different. He looked down at himself as saw that three of Derpy's hooves where holding onto him. When he realized this his face went red. He tried to get up, but Derpy kept pulling him back in. "No, you can't take him from me," she said still dreaming.

Half of him wanted to get out of her grasp, but the other half enjoyed every moment of it. Instead of waking her he just waited for her to wake up by herself. Derpy talked in her sleep, and the Doctor heard everything. Most of what she said where just murmurs, but she kept saying hot, alien, Doctor, and bananas a lot. All the while she just held the Doctor harder. 12 minutes after he woke up Derpy put her lips on his neck. The Doctor twitched slightly when she did this but still stayed where he was. Then she said, "Hmmm, my favorite type of muffin," as she started sniffing his neck, then said, "alien," as she licked his neck.

This made the Doctor jerk violently which woke up Derpy. She noticed that she was licking the Doctors neck and that her hooves where grabbing onto him. She quickly backed up and let him go. "I'm so sorry!" she said as her face turned red.

The Doctor couldn't think of anything to say. "Umm…"

"I forgot that I move around a lot. Sorry. Here let me clean your neck," she said as she wiped the saliva that was on his neck. "H-how long have you been up?" she asked hoping that he just woke up when she licked his neck.

The Doctor didn't want her to know that he had been up for almost 15 minutes. "Oh, just now when you," he felt uncomfortable saying it but that's what she did, "um licked my neck."

"I'm so sorry," she said again, "I thought you were a muffin," she said remembering the last little bit of her dream.

The Doctor remembered what she had said before she licked his neck. He couldn't resist himself, "Hm, what flavor?"

Derpy remembered exactly what flavor she had thought the muffin was and blushed even harder, "Umm, I can't remember."

The Doctor didn't know what else to say so he just got up and went to the bathroom. "Um, I'm going to take a shower now."

"Ok Derpy," still red faced. He got in and closed the door. Once she could hear the water running she said to herself, "Stupid, stupid, stupid! The one pony that didn't think I was the dumbest pony ever now thinks I'm the craziest pony ever," she said as she laid down on her bed again. Then she thought about how he tasted. "He tasted even better than any muffin I have ever had, but now he's probably going to jump out the window and go live somewhere else," she thought to herself.

The Doctor just stood in the shower and tried to contain his emotions. "What had just happened?" he thought to himself. "Why am I acting like this? I'm supposed to save the universe, not fall in love. Who knows is she likes me or not, but I can't like her. Of course she doesn't like me. It was just a dream she was having. Dreams can mean anything. She was just being polite by letting me sleep in her bed." He heard a knock at the door.

"Doctor? Are you still there?" Derpy asked.

"Um, yes. Why?"

"Well didn't know if you climbed out of the window or not."

The Doctor was confused by what she had said, "Why would I climb out the window?"

"To get away from me."

He turned the shower off and looked for a towel, but there weren't any for some reason. Oh well, he didn't even where cloths so he just opened the door all wet. He saw that she was standing right outside the door and asked, "Do you have any towels?"

Derpy couldn't help but stare at him. "So what if he's wet?" she thought to herself. It still turned her on slightly. The Doctor waved his hoof in front of her face. She snapped out of her trance. "What?"

"I asked you if you had any towels."

"Oh! Ya sorry. I just did laundry yesterday and I haven't put anything back yet," she said as she went to get a towel from outside.

The Doctor decided to wait for her so he wouldn't get the whole house wet. He heard something crash and then Derpy came flying back upstairs with the towel. The Doctor looked at her confused. "Was that you that crashed?" he said as he started drying himself off with the towel she gave him.

"Oh ya sorry. I tripped on the towel and hit myself on my table. Then I just flew in here."

"Ah. It must be cool to have wings. I hope that next time I regenerate I have them," he said as he finished drying himself off.

"You can't choose what you turn into?" Derpy asked him.

"No, I just turn into something. I can't choose."

Derpy smiled slightly. "What?" the Doctor said wondering what was so funny.

"Oh, you just seem like a really lousy alien."

"What? Why?"

"Well you can change forms, but you can't choose them and you can travel everywhere and anywhere, but you don't have the ship that does it for you."

"Well I can at least still fix anything."

Derpy looked at him confused, how can you do that?"

"With this," he said as he picked up his sonic screwdriver.

"Whoa, at least you can actually do something."

"Oh, now you're just making fun of me," he said as he put his screwdriver around his neck.

"Sorry, it's fun. Well what do you want to do?" she asked him.

"Well I'm going to go look for a job, and I'm going to need your help because I have no idea where I'm going to find it."

Derpy remembered a flyer that the Mayor had put up not long ago on the city hall. She just happened to bump into it on one of her deliveries. Literaly.

"Oh, the mare needs someone to turn hourglasses at special events and things like that."

"Turning hourglasses? Can't anybody do that?"

"Well ya, but she's looking for a permanent," Derpy started laughing, "time turner."

"Oh, sure make fun of my new name, but does it pay well? It doesn't sound like I could make a lot of money off of that."

"Oh sure. You're going to be working for the Mayor. Anyone that works for her gets paid more than the average pony, and you wouldn't even have to work that much. Only on special events that need you."

"Well ok then, let's get going," he said as he and Derpy made their way towards the door.

The Doctor had finally gotten his job and as soon as he could he would get out of Derpy's hair, but did they want to leave each other? What will happen to the Doctor's TARDIS? Will Derpy ever be able to adopt Dinky? Find out in the next chapter.

Longest chapter I have ever written on fanfiction. I will try to put Spitfire in as soon as possible, but the next chapter will be about two years in the future after all of the events of My Little Pony: Friendship is Magic. And I will be putting all the characters that I mentioned in my disclaimer. I wonder who the Doctor will choose, well of course I already know, but I want to make sure that you guys don't know. Oh, and the Mane Six will be in it, but very very briefly for two maybe three parts, but most of it will be the background ponies I mentioned in my disclaimer. Tell me what you think. It's still early in the story so there's plenty of room for me to change things. You can pm me if you think I shouldn't have that many characters or that many villains. Please follow, review, fav, read, anything, please. P.S. notice how this Doctor Whooves story doesn't have Doctor Who villains, but it does have MLP villains. I haven't read a single Doctor Whooves story like that. Tell me if there are actually stories like that, cause I haven't found any.