The Doctor in Equestria

by brilliantblaze

Rating: everyone
Tags: Adventure, Crossover, Main 6, My Little Pony: Friendship is Magic, Human, Doctor Whooves, Princess Luna, Cutie Mark Crusaders
Length: 2855

Just like probably every Doctor Whooves story on this site, except it's Who not Whooves. The Doctor crashes in Equestria and has to find out why.

This is probably like every Doctor Whooves on this site, except he's not a pony. The TARDIS crashes in Equestria destroying some of Sweet Apple Acres along the way. Like any other Doctor Who story he's there for a reason all he has to do is find it.

Published 2013-10-14 17:00:03 UTC
Last updated 2013-10-14 17:00:03 UTC

Ch. 1 Night-mares

Ch. 1 Night-mares

The Doctor stumbled out of the now smoking TARDIS Waving his hand around as not to explode due to dangerous chemicals coming from the TARDIS Then he blacked out only to be waked up by a snarling......The Doctor opened his eyes to see a small brown dog over him.

"Winona get away from that thing," The Doctor heard a voice say, "Any ideas Twilight?"

He closed his eyes again and opened them to see a bright pink creature smiling at him "Ahhhhhhh!" The Doctor screamed and jolted up, only to see more of these creatures standing around him.

The same one from before said, "Do you mind explaining why you destroyed half of our west orchard with that blue box."

The Doctor just stared at them all not able to get a word out. The purple one said, "I wonder if it can even speak."

The Doctor stood up and said, "I can too speak," He coughed still waving the fumes, "I'm The Doctor. Where am I?"

The purple one answered, "Equestria…but what about your box?"

The Doctor turned to look at the TARDIS "Give me just a second." He said jumping into the TARDIS

They stood and watched as the TARDIS slowly vanished before them, then reappear. The doors opened and The Doctor was flung out, his clothes scorched, "Warn me next time will you."

The Doctor stood up and brushed himself off, "Now then while the TARDIS repairs itself I might as well find out about this place." He knelt down in front of the purple creature, "So you have the power of speech and judging by it I would say you're female," He then noticed her horn, he laughed, "No way you're a unicorn!" He looked at the others, "A pegasus, ponies, and another unicorn!" He said still excited.

The blue pegasus dashed at him, "So you know all about us, now who and what are you?" She demanded.

"Rainbow dash," The purple one said, " Calm down."

The Doctor sat on the ground, "Like I said I'm The Doctor, and I'm a Time Lord." He chuckled, "May I know your names?"

"I'm Twilight, that's Applejack, Rainbow dash, Rarity, Pinkie Pie, and that's Fluttershy in the shaking bush." She said.

The Doctor got back up, "I'd love to see more of this world," He said, "Is there a town nearby?"

"Yes Ponyville is that way." Twilight pointed

"Great," He said and began to walk off, but something was pulling on his collar.

"Wait you can't go there every pony will freak out." Twilight said pulling him with magic.

The Doctor turned around, "Now that is amazing," He said, "You can manipulate your bioelectric aura to use telekinesis."

"Did anypony else not understand a word of that?" Rainbow dash asked

"Did you just say anypony?" The Doctor asked smiling

"Yeah so what?" Rainbow Dash asked

"This is just too great, I have to see more of this world." The Doctor said

"Well like I said before you can't go into town, everypony will freak." Twilight said

"I may have a solution," The Doctor produced a key on a necklace from his pocket, "I use the perception filter so no one will notice me but if I just tweak it," The Doctor pulled out his sonic screwdriver and used it on the key, "There we go." He said

"And what will that do?" Twilight asked

"Just watch," The Doctor said and put the key around his neck. Suddenly he changed into a light brown stallion with a spiky brown mane.

"Wha- how did you change into a pony?" Twilight asked amazed

"I didn't really change into a pony," The Doctor said, "It's just a simple perception filter that makes you think you see me as a pony." He wobbled around a bit on his new hooves, "Ooh four legs, that's going to take some getting used too, now onto Ponyville, allons-y!" He shouted

"What does that even mean?" Rainbow Dash asked

"Why it means let's go in French," Rarity said, "You speak French Doctor?" She asked

"I speak many languages." The Doctor replied

"How many languages?" Twilight asked

The Doctor rubbed his mane smiling, "All of them."

"Doctor," Twilight said

"Yes?" He responded

"What are you?" She asked

"I'm a Time Lord," The Doctor said, "Or maybe because of this dimension, a Time Pony, or a Pony Lord, which sounds better?"

"What's a Time Lord?" Rainbow Dash asked

"Well kinda like Lords of Time," The Doctor said, "Since we have time I might as well explain," They all continued to walk, "My people were masters of time travel, but we only observed time, we were not allowed to interact," He sighed, "I eventually got bored of this and I fled from my people with my granddaughter Susan in a faulty TARDIS. The Time Lords found out that I was tampering with the time stream and I was banished to earth, then eventually the charges were lifted and I continued on my journey, finding wonderful companions along the way." He smiled and a tear rolled down his face, "A Time War broke out between the Time Lords and the Daleks, it killed all the Time Lords."

"But you survived," Twilight said

"Not by choice, I continued anyway trying to forget, but it still haunts me," His frown immediately changed to a smile, "So anyway here I am now."

"I'm sorry for asking Doctor," Twilight said

"It's alright, as the last Time Lord I have to carry their legacy," The Doctor said, "So this is Ponyville?" He asked as they arrived

"Yes, everyone is friendly here and I know everyone in town and I always throw a party for a new person in town," Pinkie said then paused, jumped up, gasped and bolted of at lightning speed

"What was that about?" The Doctor said

"It's best we not say." Applejack said

"Okay…well anyway the TARDIS didn't crash here on accident, I'm here for a reason." The Doctor said

"How do you know for sure?" A small voice asked

"Hm? Oh Fluttershy, I forgot you were even there," The Doctor said, "Well Fluttershy, my TARDIS brings me to places I am needed, so wherever I go danger follows."

"Well you came to the right place," Twilight said, "Something always happens in Ponyville."

"Brilliant now I need to just find it." The Doctor produced his sonic screwdriver from thin air and began scanning the area

"How did you do that?" Rainbow Dash asked

"Remember," The Doctor jingled the key around his neck, "Just a disguise."

"Oh, right."

The Doctor finished scanning, "Nothing I can detect, anything unusual happened in Ponyville lately?" He asked

"Nothing out of the ordinary Doctor." Rarity said

"Nothing at all?" He asked, "Even the smallest thing?"

"Well Sweetie Belle and the crusaders have been trying to figure out the strange nightmares." Rarity said

"That is something to work off of, knowing this world there must be some figure that watches dreams." The Doctor said

"Well yes, Princess Luna watches everypony's dreams and nightmares." Twilight said

"And how long have these nightmares been happening Rarity?" The Doctor asked

"For a few weeks now but we never really thought about it." Rarity said

"Why can't I ever show up when the problem starts, I always get here in the middle," The Doctor face hoofed, "Where are these crusaders now?"

"In their clubhouse as usual." Applejack said

"Then we have no time to lose, allons-y!" The Doctor shouted and bolted off

The rest of the group just stood there as he stopped and came back with his head down, "Which ways is it?" The Doctor asked ashamed

"This way, c'mon." Applejack said

"Now can I say allons-y?" The Doctor asked

Twilight sighed, "Yes."

"Allons-y!" He shouted and they all ran

………….

"So what are they crusaders of anyway?" The Doctor asked with Pinkie now part of the group again

"They're trying to get their cutie marks." Twilight said

"Cutie mark?" The Doctor asked

"Oh I forgot that your new to this world, a cutie mark is a symbol everypony gets when they find their one special talent." Twilight explained

"Doesn't seem that hard to achieve." The Doctor said

"Not really," Rainbow Dash said, "Even you have one."

"I do?" The Doctor examined the hourglass on his flank, "Would you look at that I do! And it's an hourglass, how fitting."

"Here we are." Applejack said as they arrived at the clubhouse

"They built that whole clubhouse?" The Doctor asked

"Well it was actually my old clubhouse, they just fixed it up." Applejack said and knocked on the tree trunk and the drawbridge was released. The group climbed up into the clubhouse to find a small orange pegasus in a bed and two other ponies on both sides of the bed.

"Are you asleep yet Scootaloo?" The one on the left asked

"No not yet Apple Bloom." Scootaloo said opening one eye

"Well how are we going to investigate the nightmares if you can't fall asleep?" The other on asked with a squeaky voice

"I don't know Sweetie Belle, it's hard to fall asleep with you two over me." Scootaloo said

"Sorry to interrupt," The Doctor said, "But she is right, it's hard for her to fall asleep with you two there."

"Who are you mister?" Apple Bloom asked

"I'm The Doctor, and I'm here to help," He said, "Now is it just the three of you that are having these nightmares?"

"As far as we can tell, nopony else at school has nightmares." Sweetie Belle said

The Doctor came up to the bed, "If we're gonna find out what's causing these nightmares, first we need you asleep." He said to Scootaloo

"But how are you going to do that?" Scootaloo asked, "We've tried everything."

"By doing this," The Doctor began whispering something into Scootaloo's ear. Her eyes began to cross, almost as if she was in a trance, then she collapsed on the bed fast asleep.

"What did you do to her?!" Rainbow Dash said about to pummel The Doctor

"Relax, I just put millions of scientific theories into her head at once, instant sleep." The Doctor said

"Will she be alright?" Rarity asked

"Of course all I did was put her to sleep," He said as Scootaloo began shifting around moaning, "Oh looks like the nightmare just began." The Doctor put his hooves on the sides of her head.

"What are you doing Doctor?" Twilight asked

"Just a simple mental link so I can see her nightmare." The Doctor said closing his eyes and focusing. The Doctor began moaning with Scootaloo then he was thrown back against the wall breaking the link. Scootaloo's eyes shot open and she was fully awake

The Doctor rubbed the back of his head, "Whatever is in there is very powerful and very dangerous."

"What do we do then?" Twilight asked

"We all need to enter Scootaloo's dreams and stop whatever is in there." He said

"We?" Fluttershy asked cowering

"Yes all of us, I can't do it alone." He said

"What can we do Doctor?" Apple Bloom asked

"You have the most important job," The Doctor said, "You stay here and make sure nothing bothers us while we do this."

Apple Bloom and Sweetie Belle nodded, "Cutie mark crusaders dream watchers!" They both shouted

"Good, now we need Scootaloo asleep again," The Doctor said and did the same as before, "Now we need to enter the dream." The six all gathered around The Doctor and put a hoof on him. The Doctor formed a mental link with Scootaloo again and the all collapsed to the ground.

……….

The group awoke in a dark forest, "Quite a strange dream world," The Doctor said, "But none the less, where are the nightmares."

"HELP!" They all heard Scootaloo scream

"It came from that direction," Rainbow Dash said and pointed

"Then we have no time to lose, c'mon." The Doctor said and they all ran in the direction of the scream

"Where is Princess Luna?" Rarity asked, "Shouldn't she take care of this."

"Maybe she doesn't know." Twilight said

"It would make sense," The Doctor said, "Since it is only the three of them having these nightmares."

"Think again." A voice said

They all stopped as a figure landed in front of them. It was Princess Luna!

"As Princess of the night I can sense all nightmares." Luna said

"But what is causing them?" The Doctor asked

"Night-mares." She answered

"Night-mares?" The Doctor asked

"Yes they are creatures of the night and attack dreams and feed off fear." She said

"That is why only the crusaders are having the nightmares, no one has more fears than children." Twilight said

"That is correct Twilight Sparkle, I can not detect them they are only shadows." Luna said

"Oh good I have a setting for that." The Doctor produced his sonic screwdriver and began scanning

"Who is this stallion anyway?" Luna asked the group

"He's The Doctor, he's not from around here." Twilight said

The sonic screwdriver began to buzz louder, "I've got them, c'mon!" They all ran behind The Doctor as the screwdriver got louder, "C'mon were getting close."

They came to an opening in the forest and saw Scootaloo being held by the Night-mares.

"Scootaloo, we're here to help." Rainbow Dash said

"There is no need to worry Rainbow Dash, it is only a dream." The Doctor said

"Actually it is much more dire Doctor," Luna said, "If the Night-mares continue to feed off of Scootaloo's fears they will have enough power to invade all of Equestria."

"Well then we can't let that happen now can we?" The Doctor said and approached the Night-mares, "So you feed off of fears don't you?"

"Yes," One Night-mare said, "And we can sense your fears Doctor."

"I would hope so, I've got 900 years worth of fears," The Doctor said

"Doctor, I'm scared." Scootaloo said

"Are you scared Doctor?" The other Night-mare asked

"No I'm not scared," The Doctor said and pointed his sonic screwdriver at them, "But you sure should be."

"Why should we fear you Doctor?" The Night-mare asked

"Because whole armies turn and run at the very mention of my name, I have fought things that anyone would fear and they are nothing compared to you," The Doctor used the sonic screwdriver and the Night-mares began to scream, "Now fear me, that should be enough to feed you for a long time." The Night-mares disappeared and Scootaloo was freed.

"Now, thats settled, you just need to wake up Scootaloo." The Doctor said

"I believe I can take care of that." Luna said and the dream world began to fade

…………

The group woke up exactly where they were before, The Doctor said, "Now I don't think those nightmares will bother for a long time."

The crusaders cheered and hugged The Doctor, "Thank you Doctor."

"You are very welcome," The Doctor said and he felt the key on his neck getting warm

"Doctor that was amazing," Twilight said getting up, "You just landed here minutes ago and you just saved Equestria." Twilight looked for him but he was gone, "Doctor?"

The Doctor was already running to Sweet Apple Acres to meet his new TARDIS. He came to the crater in the field and found the TARDIS standing in the center all brand new. He took the key off his neck and the disguise faded. He put the key in the lock and was about to turn it when he heard a voice.

"Doctor!" It was Twilight, The Doctor turned to see the group of six ponies standing outside the crater

"Yes?" The Doctor asked

"You just saved all of Equestria and your just leaving?" Rarity asked

"Well yes, it's what I do, no need to thank me." He said

"But your just leaving us." Rainbow Dash said

"Not on purpose, if I didn't unlock the TARDIS it could have left without me," The Doctor said, "You know all of you could come with me."

"You think we can all fit into that small box?" Applejack asked, "And what is that thing anyway?"

"Well it's my ship," The Doctor said, "I can travel anywhere in time and space with it."

"But won't everypony notice when we are gone for a long time?" Pinkie asked

"I did say it was a time machine," He said, "No matter how long we are away I can bring you back to a few seconds after you leave."

"I don't know," Twilight said, "Should we go with him?" She asked the group then there was whispering between the group and Twilight said, "Alright fine we'll come with you." They all came down in front of the TARDIS.

The Doctor opened the doors, "Welcome aboard the TARDIS, next stop everywhere."

Author's Note

I originally got this idea from a Doctor Whooves forum that seemed like it was going nowhere. Only the first few lines are from the forum, the rest is my writing. I love comments and feedback and I may continue this story.