Time Lords in Equestria

by Seannetfiction

Rating: everyone
Tags: Random, My Little Pony: Friendship is Magic, Doctor Whooves, Main 6, Queen Chrysalis, Other, Adventure, Derpy Hooves, Crossover
Length: 9930

The Doctor and Derpy get word of chaotic disturbances in Ponyville and Canterlot. While investigating, The Doctor's past comes out of the woodwork - literally. How is this possible? And what force brought multiple doctors and companions together

The Doctor and Derpy get word of chaotic disturbances in Ponyville and Canterlot. While investigating, The Doctor's past comes out of the woodwork - literally. How is this possible? And what force brought multiple doctors and companions together?

Note: The Doctor and Derpy will be written in similar character to PWP's Whooves and Assistant series, but it does not take place in the same universe, so any discrepancies in character can be attributed to the change in universe.

To see the series for yourself, check out Ponies with Pockets Productions at their YouTube page.

For the artist whose designs inspired my descriptions of the Doctor and his companion, go here.

Published 2014-08-19 18:10:03 UTC
Last updated 2014-10-09 17:26:57 UTC

Part 1a

"Wow, the Summer Sun Celebration sure is a lot of fun to see when it's not being threatened!" Ditzy Doo said to the Doctor as the TARDIS was landing. The two had just completed a trip to Canterlot and now were stopping back off in Ponyville so Ditzy could grab the muffins she forgot to take before they went on their next voyage.

"Yes, it's still amazing to think that you ponies have to raise the sun and moon physically. It's quite an impressive sight though."

"Well it's weird for me to see planets that just have the moon and sun move on their own."

"It is how most planets deal with such things."

"So then most planets are weird."

The Doctor had to laugh at such a statement. He knew from experience that his companions would hold their native world and time's customs in top regard, but Ditzy was always so straightforward that it was refreshing to hear.

"In any case, we have landed so you grab the muffins and I'll go pick up plenty of butter," he said.

"Try not to start eating it from the wrapper like it's some kind of salty banana. Again."

"Oh come on now, I only did it that once! It's just of irresis... ti.. ble. What's that?" The Doctor said as screams could be heard from up the hill.

"It sounds like Fluttershy. I think that's her cottage up there and it doesn't sound good."

The Doctor suddenly got serious. "Well, let's see what's causing the trouble. The Doctor is in! Come on Derpy!"

Fluttershy was trying to protect her animals, who had been backed into a corner by a rogue bear that Fluttershy had been taking care of.

"Harry, calm down. Why are you acting this way?" she was desperately trying to appease him now. She had used her stare, but while it had caused him to run away earlier, he was back almost immediately.

"What do you want?!" Fluttershy was getting emotional. She really didn't want to do anything to hurt Harry, but the animals were all in danger if Harry was in a rage.

"Well, looks like I got here just in time! Why don't you pick on someone your own size?" The Doctor said as he and Ditzy walked in through the back door.

Fluttershy looked with complete surprise at this turn of events. "Hello Ditzy Doo, and um, who are you?"

"Nice to meet you, Fluttershy was it? Yes, Fluttershy. Hello Fluttershy! You can call me Time Turner. Now what's going on with this bear?"

"He's been acting strangely all day. He never does this. He's always so friendly"

"Really? A friendly bear?! That sounds amazing!" the Doctor chuckled before calming himself. "Well that's unusual given the bears I've encountered, but I'll take your word for it. Let's see what the damage is."

The bear now approached the Doctor, who pulled out his sonic screwdriver and waved it across his face. "Well this IS fascinating."

"What is, Doc.. um, Turner?" Ditzy asked.

"Well it would seem that this bear isn't really a bear. It's just an illusion. If I could just charge some electricity... THERE!"

The Doctor quickly used his sonic to open the back of a lamp nearby and popped out the two main wires that went into the plug.

"Let's see if this doesn't short-circuit the problem." He took the wires to the bear, who had decided he was a threat and was charging, and after dodging his big left paw, sent a shockwave through the bear's body.

Ditzy and Fluttershy were horrified at what they saw, but were even more surprised when it didn't seem to hurt the bear, instead revealing a black cloth made of some material none of the three could immediately recognize, but inside the material, they saw, were two solid black creatures with teal, insect-like eyes.

"Changelings!" Fluttershy immediately recognized. "WHAT ARE YOU DOING HERE? WHERE IS THE REAL HARRY!"

Fluttershy had gone into full-on protective mother mode of her animals, and the changelings were understandably intimidated. The two stumbled over themselves but got out through an open window, running for their lives.

"You knew those creatures?" the Doctor finally said after a few seconds of silence passed.

"Yes, they had tried to take over the kingdom at Princess Cadance's wedding last year and my friends and I had to face them. There were hundreds, if not thousands. I didn't know they could combine to make bigger creatures, though."

"It seems that cloth did that for them. You said they were at a wedding you'd attended, which means I'm guessing they have a history with you and your friends. Has anything else been going on recently that was strange or out of the ordinary?"

Fluttershy was thinking. "Well, Applejack's brother has been acting really angry lately and has been reckless with his work the last two days. Applejack sent him away from the farm yesterday, and she's been getting concerned."

"That could be something. Derpy, we need to get back to, um, my shed. I may have some equipment to help out."

"Ok, let's go. Sorry about all this, Fluttershy. You're so nice that you certainly don't deserve this stress."

"WAIT!" Fluttershy cried out as they were leaving. "If that wasn't Harry, then that means they may have the real one. Please tell me you'll be able to find him.

The Doctor walked up to her and looked her straight in the eye. "I'll make a promise to you, Fluttershy. I will get answers for you about what happened here. I can't guarantee they'll be good answers, but you will know where your friend is and why these creatures are attacking you. Now I need to get to my TAR- um, shed."

She smiled at that. "Ok, then. Thank you Mr. Turner. If you need my shed as well, you're welcome to it. Normally I don't like people going in my shed, but if Harry's in trouble, then you all can take what you need."

"Erm, uh, yes well ok then! Come along Derpy!"

"Well what do you make of it, Doctor?" Ditzy asked as the two walked back to the TARDIS.

"Honestly I'm not sure. It seems odd that a plan of revenge for a wedding years ago would need that long to take hold, especially if their numbers were as large as she said and they can transform into other beings. Something about this time has made them become aggressive, and we need to figure out what."

"So what's our plan of action?"

"Simple, first I get an electric device from my TARDIS that can short-circuit these changelings, then we confront this Applejack's brother and... Well that's different!"

"What is Doc-whoa."

As the duo exited the TARDIS, they were greeted by the sight of yet another TARDIS. It looked virtually identical to the one they were leaving, albeit a little cleaner, and was a mere 15 feet in front of them.

"Um, Doctor? What did you do?"

"Why do you think I did this?"

"Well, you're the only one I know with a TARDIS so unless you're expecting company..."

"NO. I was not. No, no, no, this isn't right. I've never landed in this part of town..." he looked up to double-check his surroundings. He was at the edge of the Everfree Forest, at the bottom of a small hill that shielded the TARDIS from view of Fluttershy's cottage. They were faced away from the cottage while the other TARDIS sat at the mouth of the forest itself. It seems that it landed in a pile of wood that had fallen off the trees and been collected by Fluttershy as firewood. "No, I've definitely never landed here before."

"Well it looks like you've landed here twice now," Ditzy quipped.

"This is serious, Derpy! Future me would know not to land in the same place and time that I've already landed. It would create a paradox if I saw my future self, so why would I land the TARDIS somewhere that I've already been. Well, not exactly where, you see, but still well in my line of sight where I could run into..."

There was no more time to speculate, as the other TARDIS' doors had opened. Ditzy and the Doctor approached cautiously. Whatever was the cause of this would be explained, and there was no turning back.

A pony with a golden coat and nearly pure white, curled hair walked out of the box. He had blue eyes with an aged look, but they bore a more fierce, energetic feeling than the weary ones the Doctor had grown accustomed to in the mirror. His cutie mark had more sand in the top half of the hourglass than the bottom, and to top it all off, he wore an elegant green jacket of fine material with a white, ruffled shirt inside.

The Doctor blinked back a few times out of shock. He knew the look, but had never expected that look to be on a pony. His mind refused to accept what had been presented in front of it.

Finally, after scanning the outside for a few moments, the new pony spoke in a voice that Ditzy did not know but the Doctor recognized immediately. "Well, it would seem we're not the only ones. This whole planet is full of ponies!"

The Doctor, still beside himself, could only reply, "What?"

The other pony then looked to him. "Well, it seems they can talk, which means they're one of the main sentient lifeforms on this planet. Hello there!"

"What!?"

"Oh, I suppose I should introduce myself. I'm the Doctor." the golden pony said.

WHAT?!" the Doctor and Ditzy said simultaneously.

The pony was looking a little miffed about these reactions. "Is that all you can say? Why do you keep..."

His thought was interrupted by the second TARDIS which had been at an angle he had not yet looked. He didn't even notice the pile of wood he was parked on as he stumbled down the pile. After staring for a moment, he let out an exasperated sigh and said, "Oh no. Well, it looks like the Time Lords have done it again. I am once again they're galactic yo-yo!"

***1972 theme music - Following title crawl: 'Time Lords of Equestria', then 'Written by SeanNetFiction', finally 'Part 1'***

"Oh this is just brilliant." the Doctor (the brown one) said just loud enough for the others to hear.

The other Doctor scrunched his face as the brown pony in front of him looked like he might try to lunge at him with some gusto.

"Yes, well in any case, as I said I am the Doctor," he finally said.

"Oh yes. Yes you are 'Doctor,' the brown doctor (to be referred to as Time Turner from here on in) said before bursting into laughter.

"And what is so funny about that?" the new doctor asked.

When Turner calmed down after a good 20 seconds of solid laughter, he finally said, "I never thought I'd hear that voice coming out of a pony hahahaha. My goodness this is incredible! Well, I shouldn't say 'incredible.' This is actually quite a serious situation - whole sections of existence blowing up all around us kind of serious, but... ah, I can't keep a straight face for this. This is amazing!"

"Now calm yourself down!" the new doctor said, clearly flustered by the reaction. "You there, grey pony! What is the problem with this maniac?"

Ditzy shook herself out of her gawking to reply. "Oh he does that a lot when he sees things that are funny to him. I don't really get it. He's like this any time he sees a word that refers to ponykind."

"AHAHAHAHA ponykind! Derpy, you can't be adding to the silliness or I'll never keep a straight face," Turner said through the laughs.

The other Doctor looked at the brown pony slamming his hoof on the pavement and walked past him, clearly insulted, and approached Ditzy. "Well, it would seem you're the one to talk to of this group. If I heard correctly your name is Derpy. Pleased to meet you, I am the Doctor."

He offered his hoof but she just stared at him. "Um, my name is actually Ditzy Doo. He just calls me Derpy. And you are not the Doctor."

"What are you talking about? Of course I'm the Doctor! Do you know any other people who refer to themselves as the Doctor?"

"Yeah. Down there."

The other Doctor followed her hoof, which pointed at the laughing maniac behind him. He stood there, about to tell off Ditzy, but then he looked back to the other TARDIS. After looking back and forth at the two for a few moments (during which even Turner had restrained himself long enough to see his reaction), the other Doctor brought his hoof to his face and dug his face into the joint.

"Oh no," he said through the leg, prompting Turner to laugh all over again.

He eventually got back to a standing position and calmed himself enough to say, "I'm afraid so, old friend! I hope you're enjoying the equine body because you're going to have it one day!"

"Ugh," the other Doctor said. "Being a pony would be an issue no doubt... but I'm far more concerned about the sheer incompetence I seem to be showing in this time."

"Hey! You'd be wise to be more like me now. But that always was you - oh so serious about time and space travel, being all prim and proper. Clearly you mellow out in your old age so maybe down and dirty is the way to go!"

"There's a difference between 'mellowing out' and going barking mad, and I think it's clear which way you, or should I say, I have clearly gone!"

Ditzy was now completely lost with what was going on. The two now seemed to know each other and were arguing about stuff that was going over her head.

"Um, hey, Doctor?"

"Yes?" they asked at the same time.

"She meant me, oh high and mighty one. She does travel with me after all," Turner told his counterpart.

"By all means, be my guest."

"What exactly is going on. Who is this pony? And why does he keep calling himself the Doctor too?"

"Well, let's see how I can explain this to you..."

"Perhaps you should let me. I'm not confident you'll get it right the way this conversation is going."

"Hey! Home dimension advantage to me. You stay silent. Anyway Derpy..."

"That's another thing. She just told me her name is Ditzy Doo. Now that name may sound silly,"

(HEY!),

"but the fact is she has a name, so why are you calling her Derpy?"

"Because it sounds better. Now hush!" Turner said bluntly to his counterpart. "As I was saying, Derpy, this pony is calling himself 'the Doctor' because he is, in fact, the Doctor. Me."

"... What? Doctor, how does that make sense? Is this like that time when that Doctor from another dimension came and..."

"No, Derpy. In this case, this Doctor is actually me. A past version of me, but me nonetheless."

"I don't understand," Ditzy said, clearly trying to process the information. "You two look and act nothing alike. How can you be the same pony?"

"Well if you remember, I said when we met I'm not really a pony. You see, my kind is able to change its shape when we're about to... well, when we're in serious trouble and are really hurting. The Doctor you see over there was what I used to look like a long time ago. Though that does not explain how you," now addressing the other Doctor, "are in Equestria when I have no memory of being here before, or how you are a pony."

This comment earned a scoffing sound from the other Doctor. "Well if you must know. I was sent on a mission from the Time Lord council. I'm sure you remember them."

Turner's eyes darkened a little at this statement and he had to turn away from his counterpart. "Yes, I remember," he said, his voice barely holding any volume.

The other Doctor noticed the shift in demeanor but chose to continue. "Yes, well, while I was traveling, I felt the TARDIS losing control of itself and being sucked into the abstract plane. The turbulence knocked us unconscious, and when I had awoken, I was a pony. I was left a message by the Time Lords that indicated they did not know where exactly I was being sent, only that I was being sent where there was a serious disturbance that threatened both this and my original universe.

"As for why you don't remember, I've was informed that the trip indicated that my being sent here was causing the TARDIS to give off waves that indicated I could be causing trans-dimensional paradoxes by coming here. I had assumed that meant whatever threat that came here had already embedded themselves into the world's history, but as it turns out it was my own history that was causing the problem. Either way, my memories of this world will peter out of our memories as we go back through the barrier."

Turner had been listening closely and had perked his ears up about halfway through. "That's all well and good, but you mentioned the words 'we' and 'our' in your speech. Did someone come with you?"

"Well of course! I was not traveling alone when I got the call, so naturally-"

"AHHHHHH! DOCTOR! COME QUICK!!!" a voice screamed from inside the other Doctor's TARDIS.

"Uh-oh. It would seem Jo has discovered she's a pony now," he said as he turned and hurried back into the TARDIS.

Turner was suddenly back to being excited himself. "Oh, Jo's here?! This is turning out to be quite the day!"

"Jo? Doctor, who is Jo?" Ditzy asked, but it was too late as Turner was following his past self into the TARDIS. "*sigh* I guess I should follow. At the very least I want the full picture of what's happening. This has become a very confusing day."

Ditzy could only shake her head in utter frustration and confusion as she walked along after the pair of Doctors.

Author's Note

Yeah! A little tribute to one of the top Doctor Whooves series in honor of 12's debut this week! So a little backstory: Doctor Whooves and Assistant, as well as Doctor Whooves Adventures were big into getting me into the revived Who series. But in the time I've been here, I've noticed a limited number of crossovers with the Classic Who series. Most Whooves stories that feature a Time Lord Doctor in pony form use a new, future incarnation or use a revived series Doctor. When I do see a Classic Who Doctor, it's usually 1 or 4. I notice a severe lack of Jon Pertwee and Patrick Troughton stories, so rather than wait to see someone write a story, I decided to do them myself! (The crossover with DWA and the Second Doctor is being fine-tuned right now too. You'll see it soon.)

Anyway, yeah, I've seen all of the Third Doctor's episodes and he's a personal favorite of mine, so this should be fun. As I said, this universe isn't a perfect replica of the DWnA universe, but I think I come pretty close and at least have their approaches pretty solid. For those wondering where Tick Tock is, he's not here. You can chalk it up to him already departing the show, dying, being sick, etc. Either way, I won't be addressing him in this story. This is strictly Third Doctor and Jo meet Turner Doctor and Ditzy.

My descriptions of the Third Doctor and Jo will come from the images created by LissyStrata's DeviantArt page. Check her out at http://lissystrata.deviantart.com/. If you look at Jo Grant's design and listen to DWnA, you'll probably guess the joke that sparked this idea.

See you for the rest of part 1 where Jo is introduced, the group visits Applejack, and I try my hand at a Classic Who end-of-episode cliffhanger!

Part 1b

"DOCTOR!"

The pair of Time Lords came barreling into the TARDIS, Turner following his younger counterpart, and Ditzy used her wings to glide through the doorway moments later.

Jo Grant was seated on the ground staring at her the hooves that had taken the place where her hands had been. Above her was a piece of reflective metal she and the Doctor had picked up at the end of their last trip. If suddenly seeing purple hooves in place of her hands and being a quadruped hadn't caused her to flip out, then looking down at the metal and seeing a pony in the reflection definitely did. Just about the only thing she hadn't noticed at this point was that a small, purple horn was poking out of her blonde mane.

"It's ok, Jo. I'm here. Not to worry."

"Doctor?! Oh, not you too. What's going on? How did we end up like this?"

"We've just crossed into an alternate world so we just have to get used to the bodies long enough to figure out what's going on..."

"JO GRANT! It's been far too long since I've seen you... are a UNICORN! A PURPLE UNICORN!" Turner said as he became absolutely giddy at this turn of events.

By contrast, Jo was now incredibly uncomfortable and was now very aware that two ponies had entered the TARDIS and were gawking at her. She looked back and forth between them and her suddenly ponified Doctor and looked like she was about to hyperventilate.

"Doctor, what's going on? Who are these horses and does that one have wings?! Where are we?!"

"Now calm down, Jo you're clearly seeing things. What you're describing is a pegasus, and the ponies here are... oh my word, you are a pegasus," he said, finally getting a good look at Ditzy's side. "Incredible. This is a world where pegasi are true creatures and... and... you are a unicorn. There is a genuine unicorn horn growing in your hair."

"What?" Jo reached up to her head and felt around until she found the hardened appendage protruding from her head. "I'm a unicorn. I don't believe it. I mean, I had wanted to see one when I was a kid, but I never wanted this! Oh what is happening Doctor? We've gone through some wild times in the past but I don't know if I can wrap my head around this one."

"I think I can explain that," Turner, who had been giggling and making 'squee' noises in the background for the last minute or so, finally said. "You see, the TARDIS has the ability to adjust your mind so that you may understand whatever language is being spoken by the native species whenever and wherever you go - a gift from the dear TARDIS, you might say.

"Now. If you were sent here across a universe where the native species of dominance was ponies, and a Time Lord already present - hello there! - is a pony, and the TARDIS detects that she already exists in the same frame of space with a pony Time Lord controlling it, then she should be able to automatically reroute the tool to temporarily alter your atomic structure while you're occupying the universe. Plus the fact that you're on a mission from the Time Lords practically guaranteed that if all else failed, they would ensure the change be made personally, so that no paradoxes occur in a new universe because a species was introduced before its time. Did you get all that?"

The room had gone dead silent during all of this, as the room just stared at Turner.

"I don't think he, or rather, I took a single breath during that entire exchange," the past Doctor finally said.

"You get used to it," Ditzy replied.

"I'm sorry that was a lot to take in. And just who are you. I think during that, you said you were a Time Lord too?" Jo asked.

"Oh I'm far more familiar then that, old friend," Turner said.

"All right, that is enough!' the other Doctor said. "Jo, look at it this way. Do you remember the situation with Omega where you met my two previous selves?"

"Of course, what does that have to do with..." Jo's eyes widened with understanding. "You mean this, this pony is another version of you?"

"Yes, I'm afraid he's a regeneration yet to come. What regeneration are you, by the way?"

"Thirteenth."

"Oh, that's impossible. You know as well as I do that Time Lords are limited to 12 regenerations. Are you suggesting you received another regeneration?"

"Not just one. A whole new cycle! Isn't that great?"

The younger Doctor considered this prospect for a moment. "Well, regardless of that I'd rather not know how that happened. In case some memories of this event somehow seep through, I don't want to have to deal with any paradoxes within myself. I suppose I should be thrilled you are part of a new cycle. I'd hate to think that this was how it was all going to end."

"I'm beginning to get tired of your attitude. You're more of a stick in the mud than that other world's Doctor."

"Not to interrupt, but didn't we have something important that we were doing?" Ditzy spoke up.

"Oh you're right! See what you did?" Turner suddenly looked at his counterpart. "I have to deal with a changeling invasion and you've got me wasting time with your nonsense."

"So there is an issue then," the other Doctor said, wanting to not waste anymore time dealing with his counterpart either. "Well then, Jo, let's be off."

"Are you mad? I'm still getting used to this whole unicorn thing?"

"Oh, you are so lucky, though. Did you know unicorns in this world can do magic with their horns. Like real, actual magic! It's so amazing!" Turner just couldn't contain himself around magic.

"You don't say? And just how does Jo do such a thing? I imagine that could prove quite useful?"

"Hmm, you know that's a good question. I don't think training has ever come up since I'm a normal pony and Derpy here is a pegasus..."

Ditzy interrupted. "You know, there may be some unicorns that could help. Twilight Sparkle is one of the most powerful unicorns in the world. Heck, she's Princess Celestia's personal student and she loves helping ponies and studying magic. I'm sure she could help."

"Well then that settles it. Jo, I think it would be beneficial for us to go down there first to teach you how to use that horn on your head."

"Oh fine! I will admit it does sound interesting to be able to perform real magic," Jo said, though still a tad apprehensively.

Ditzy sensed this and made a suggestion. "Actually, Jo, if you'd like I could take you there. I know the area and I think it would be good for you to get a break from all of this dimension stuff while you're getting used to this new body of yours."

"Oh, I think Jo and I can manage," the other Doctor said.

"And if you think about it, neither of you know anything about this world or where things are or even who Twilight Sparkle is, so splitting up may be a better idea," Ditzy finished, hoping she made an argument strong enough to stop the discussion. Honestly, she liked the idea of being able to talk to this Jo girl mare-to-mare and hoped the Doctors would agree.

"She does make a good point," Turner said.

"Fine. But let's agree that you all will meet us at... wherever it is we're going." He turned to Turner. "So where are we headed?"

"Sweet Apple Acres! Let's go!" And with that, Turner and his past self were off.

Ditzy walked over to Jo, who was beginning to practice walking. Surprisingly (to Jo anyway) it seemed to be coming naturally.

"Jo, are you feeling good to go?"

"I think so. What was your name again?"

"Ditzy Doo, but you can call me Derpy. The Doctor does it all the time."

"Ok then. Lead the way Derpy." And the two left, closing the TARDIS doors behind them.

Deep inside the Everfree Forest, there is a cave. Deep inside that cave, there is a passage created along the stone walls. The path leads downward at least 400 feet, and therein lies a series of chambers where a plan is afoot. Changeling guards can be seen along various rooms near the doorways, but it is largely a quiet, subdued place.

Inside the largest chamber sat a purple baby dragon, who was chained by his hands and feet in the center. He was seated, occasionally trying to expand his fire breath, which fell feet short of the walls of the chamber. The metal he was chained with went unrecognized by him, but he knew it was strong enough that he couldn't break or melt it.

He felt like such a fool. He hadn't even thought to ask why the Cutie Mark Crusaders would need him to join them in at Zecora's place. They only had said they needed a dragon for something and that it wouldn't cause any physical harm. It wasn't until they were out of site of Ponyville that they revealed themselves as changelings and overwhelmed him.

He cast his entering captor an enraged glare as she walked in.

"What are you doing back here? I thought Twilight and the others finished you long ago," he said angrily.

The large changeling chuckled to herself. "That's what pretty much everyone thinks, but you know better now. That arrogance will come back to bite your pony friends. I seek power and a constant food source for my changelings, and I will not be defeated so easily."

Spike looked at her with a smirk now. "Well it doesn't matter what you think because once Twilight realizes I'm missing she and her friends are going to bring the Elements of Harmony and finish you for good!"

The chuckling the changeling queen had been doing switched to full-blown laughter with that. When she got it out of her system, she said, "Oh, believe me, dragon, I have plans to ensure the Elements of Harmony do no harm to me, and you are going to play a huge part in that."

"Well forget about that because I'm not helping you with anything!"

"I assumed you'd be unwilling, but my associate is really skilled at making arguments... well, just make sense. You'll see," she told him from the wall as he launched his hardest breath at her. Still a good 10 feet short.

"You should save that energy, my friend. You'll want all your strength when you're helping me and my dear friend, Queen Chrysalis over here."

Spike turned and couldn't believe who was talking. "A... a pony? A pony did this?"

But what was clear to Spike almost immediately was that this pony was far from ordinary. He was grey and wore a suit that was an even darker shade of grey. His piercing green eyes gave off this feeling of power and they were hard to ignore. As he forced his face away, though, he noticed the fob watch that was his cutie mark, and realized that despite his age and white stripe through the center of his otherwise black mane and tail, he did not look like he was short on energy.

This was not a pony to mess around with.

The pony started to move in toward the center. "You see, Spike. It is Spike, isn't it? I have designs of my own for this world that cannot be complete with the royal sisters in power. This planet needs beings like Chrysalis, here, who is willing to get her hands, er, hooves dirty to do what is needed. And it needs someone like me, who is more capable of greatness than the sisters could even fathom."

Spike had yet to try to burn him. For some reason he was focused on the piercing, powerful eyes of the pony approaching him. "And just who do you think you are to make those choices?"

"Why I am the solution to your problems. I am brilliant. I am. The Master. And you. Shall obey. Me."

The Master had put his full, focused gaze and pointed it directly at Spike, who could only stare dumbfounded.

"You shall obey me."

"I shall obey you."

The Master grinned before turning with an arrogant smirk at Chrysalis, who was equally impressed and terrified every time he did such things.

"Now, I want you to follow Chrysalis to the mouth of the cave and wait with her for my command. She will tell you what to do from there."

"I will follow and wait for orders," Spike said.

"Excellent. Guards! Unchain our friend here."

Quickly, two changelings came through the doors and unchained Spike, who sat motionless until they were done and Chrysalis waved him over. She decided to speak with the Master before heading out.

"You're sure this won't work to our disadvantage? We could have just used a changeling to do this, though it would have taken some time to train them for dragon mannerisms."

"This plan is our best hand. If this Twilight Sparkly you talk about is as perceptive as you claim, she would know something was amiss fairly quickly, and if this plan is to work, she needs to be one of the first we take out so that the best deductive mind of the team is absent."

"You of course know my guards reported that the one called Fluttershy was growing suspicious of our changeling bear, so I did give the order to attack?" Chrysalis asked.

"Yes, and did they succeed?"

"It should have been completed by now, so we will know shortly, but for some reason I'm concerned it's taken so long."

The Master chuckled. "I assure you, it's of no concern. Regardless of what happens, we will have our success. I have accounted for anything that could stop us, and even if we lose her, we'll get her soon enough."

Chrysalis thought to ask more, but she didn't want to give any more information in front of Spike in case he came to. As she left, The Master looked to the top of the chamber and spoke in a barely audible voice.

"I will defeat you this time. I dare you to stop me.

"Doctor."

"So, you travel with the Doctor? Well, the Doctor of this world?" Jo asked her new pony friend. The two had had a largely quiet walk into Ponyville, but as the two walked and Jo saw the tranquility of this world, she began to settle down.

"Oh, yeah we've had a lot of adventures with and met a lot of new ponies," Ditzy said.

"Does he still do a lot of technical talk that no one understands but him?"

"All the time," Ditzy said with a chuckle. "So, your Doctor is younger, right? How come he looks so much older then?"

"I'm really not sure. I actually met some of his past selves before and some look older, some look younger. It's really odd to think they're all the same person, but when you see them work, you do feel it, like they share something and work well together. When they're not fighting, of course."

"Heh. Yeah I noticed they fight a lot. So you've traveled with your Doctor a lot then, huh?"

"Yes, I was brought in as his assistant after Elizabeth Shaw left UNIT," she laughed at remembering their first meeting. "He honestly didn't want me there, I don't think. He really seemed to talk down to me at first and seemed really uncomfortable when working with me, but he warmed up to me after a while and I really think we've made a great team."

"And you two are... really close?"

"Oh yes, he's a very sweet man, but I'm sure you know that."

"It's just weird I've never heard him talk about you."

Jo shrugged. "That is true, but my Doctor doesn't talk much about his past either."

"That's definitely true. Anytime his past comes up he gets all sad. Have you ever looked in his eyes? It's like there's a lot of sadness there and he never likes to talk about it."

"I don't pick that up at all from my Doctor. Maybe something happened in between my Doctor and your Doctor's times?"

"Maybe, I- oh, hey there it is!" Ditzy said as Twilight's house came into sight.

"Your library is in a tree?" Jo asked.

"You know, the Doctor said something similar when we walked past it the first time. What are libraries made of in your world?"

"Oh they're just buildings. Made of stone or wood and such. But never living trees."

"We have those too, but yeah, this tree works just fine," Ditzy knocked on the door as she finished speaking. The door opened and another purple unicorn came out, this one with a pink stripe in her mane. She looked over the two before speaking.

"Hi Ditzy. It's nice to see you again. I don't think I've met your friend before. It's nice to meet you. My name is Twilight Sparkle."

"Jo Grant. Nice to meet you."

Twilight raised her eyebrow with a hint of confusion. "Jo Grant? Interesting name. And interesting clothing! They remind me of clothes my mom's schoolmates wore in her old yearbooks. Are you a fan of history?"

"Oh, well, I suppose you could say that. I've learned quite a bit about history over the last few years."

"It's amazing isn't it? I see your cutie mark is a lock. Are you a locksmith?"

"My what?"

"On your flank," Ditzy whispered to her. Jo looked behind and saw the mark on her flank.

"Oh yes, that! Um... oh, I studied escapology!"

"Really? I don't know of many ponies who have studied that. It sounds fascinating. You'll have to tell me all about-"

"Actually, Twilight, Jo needs help learning basic magic," Ditzy said.

"Basic magic? But you're fully grown. You seem as old as me. How do you need to learn the basics?"

"Well, I, I... never really had a chance to learn?" Jo was stumbling for a rationale as to how she had no magical knowledge. "But I've certainly wanted to! So do you think you could help?"

Twilight gave her a look that seemed to combine sympathy and excitement. "Well I would like to try my hand at teaching to see if I could do it, and I don't want a unicorn who wants to know magic to be stuck trying to learn from scratch. Yes, I'll teach you."

"Great!"

"But first I need to head into the Everfree Forest."

"Why do you need to go there?" Ditzy asked.

"I was actually on my way out to go look for my assistant, Spike. He left a note early this morning that he was going to help the CMCs with something but he hasn't returned. Besides that, Sweetie Belle already came by an hour ago looking for a book and said she hasn't seen Spike, so I'm thinking he's up to something. It's already midday so I'd like to make sure he's not getting into any trouble."

"Well we'd be more than willing to help you find him," Jo offered.

"Oh, I couldn't impose."

"It's the least I can do considering you'll be helping me,"

"Well, if you're sure. You coming too, Ditzy?"

"Yeah I guess I can join you guys. Jo's new to town so I think it'd be good for her to have some ponies with her for her first trip into the forest."

"If it's your first time here in Ponyville, then I'll tell you a little about the town on the way!" Twilight said.

"That sounds lovely, thank you."

"Well, let's get going then!" Twilight used her magic to levitate her keys into the door and lock it as she said this. She didn't notice Jo's eyes go completely wide upon seeing magic in action.

The key went into Twilight's supply bag, and the three departed for the forest.

"You know, I never realized it until now, but age is really noticeable on a pony. I'm sorry if I sound a little vain but did I really look that old?" Turner asked his counterpart as they walked onto the Sweet Apple Acres premises.

The other Doctor looked offended. "You know as well as I do that my body has been older and younger over time and I'd ask you to show a little more focus. You've been rambling since we left the TARDIS. Besides, I'll take old and distinguished over young and unfocused."

"You know, I could go off on how you're being rude, but why should I? I already know you're rude. I've been you! Just an old stick in the mud..."

The other Doctor was about to respond when he heard arguing just over the next hill. "Looks like we have a direction to head," he said.

"Right."

"I must say, this area is remarkably well-kept. How do ponies manage such things?"

"I've been meaning to ask Ditzy, but there's just so much that fascinates me about this universe. I know nothing of it and that has just sparked my sense of adventure!"

The past Doctor had a reflective look on his face at hearing that. "I know the feeling. I suppose we both know. It's what we felt when we first took the TARDIS. And this world seems so peaceful... These ponies really seem to have something here worth protecting."

"I knew there was something in you I liked. Oh! There's who we're looking for!" Turner said. The Doctors ran up to a brown earth pony who Turner vaguely remembered being called Applejack. She seemed to be fuming about something.

"Hello there! I couldn't help but hear you yelling. Anything we can help with?" Turner yelled to her.

Applejack looked the two over before speaking. One pony wearing a random green tie and the other in... something out of the last century, it seemed like. They certainly looked a sight.

"Howdy there, you two. No, ah was just arguing with my brother about some chores. Ah think I've seen you around, but I know ah haven't seen you before. Name's Applejack, by the way. You are?"

"Well I'm Time Turner and this is my friend, uh..."

"Smith. John Smith. Pleasure."

"John Smith? Never heard that name before. You ain't from around here, ah reckon?"

"No. Quite far away. I'm just visiting. But as my associate was going to say, we've been hearing of strange goings on around town recently, and we, or rather, Turner here was saying on the way here he had been talking with one of your friends. Fluttershy, was it?"

"Yes, she told us that you had been dealing with some uncharacteristic behaviors from your brother," Turner added.

"Yeah, she was over here a couple days ago and Big Mac an' I were goin' at it somethin' fierce. It's like he's angry at me and wants to get into a real fight over it, but he keeps avoidin' it. Ah don't know what to think. Why did Fluttershy tell you? Are you some kind of mediator? 'Cause we Apples can handle our own business."

"Not at all, but I think something may be going around and it would be beneficial to talk with him. Would you mind calling him over?" Smith said.

"Well, ah suppose if you think it'll help. BIG MAC! GET OVER HERE!"

Big Macintosh was a few trees over in the orchard and made some groaning sounds before responding. "Hrfd.. EE-YUP!"

Big Mac came into view with an upset expression on his face, but it was nothing compared to how he looked when he saw Turner. He began stampeding over to them.

"Big Mac! What do you think yer doing?!" Applejack asked as he came barreling over.

"DOCTOR!" Big Mac began to move toward Turner, but he found his left front hoof being caught. As it came down, his left hip felt another grip, and the two grips moved in a circle, sending him flipping over. When he realized what happened, he quickly shot up and glared at the Smith Doctor. He moved toward him, but before he could even realize what happened, Smith's right hoof was in his neck and he was dropping back to the ground.

"What in the hay did ya do?!" Applejack said in horror.

"Venusian Karate. He'll be down for a few minutes. Now, if I can get a good focus going, I should be able to find what I'm looking for."

"Oh no need. I can handle that!" Turner said as he moved in and waved his sonic screwdriver in his eyes. "Huh. Mind control."

Smith looked dumbfounded. "Did you just use the sonic screwdriver to read his mind?"

"Oh that's right! Yours didn't do that! Believe me it's quite helpful to have a screwdriver that has multiple purposes."

"Well then it's not a screwdriver now, is it? It's a sonic Swiss army knife!" Smith said. "Besides, why would I develop a sonic to do what I could already do with minimal effort?"

"You know, given your mode of dress you really have a surprisingly lacking sense of flair!"

"Excuse me, but why did Big Mac try to attack you? You said something about mind control?" Applejack said with concern.

"Yes, I was helping Fluttershy earlier with an attacking bear and discovered he had been a pair of changelings in disguise. I thought for sure that I'd get another one here, but it appears mind control is being incorporated as well."

"Changelings? Mind control? So the Changeling queen is at it again..." AJ said.

"So what exactly are these changelings? Some kind of shapeshifters?" Smith asked.

"Right, and it seems they are going after the holders of the Elements of Harmony, one of the main defensive weapons for the kingdom here. Fluttershy and Applejack here each held one.

"Well who else is a holder of these 'Elements?'"

Twilight, Ditzy and Jo were now deep in the Everfree Forest. They had been calling for Spike for a few minutes now and Twilight was getting frustrated.

"This is starting to concern me. He shouldn't have gone so deep that he can't hear me. We're almost at Zecora's!"

"I'm sure he's fine. There are some boulders over there, maybe you can get a view if you climb up them," Ditzy said.

"Good idea. And you can fly over the trees and see a little deeper."

Ditzy nodded and flew up and away while Jo walked with Twilight. "Will you need a boost up there?"

"No I should be able to teleport up there. With any luck when I do start teaching you that can be a spell you work up to. It's difficult but- SPIKE!"

Spike was walking over to her, but something seemed off, and Jo could tell almost immediately. So could Twilight.

"Um, Spike, what's going on? Are you OK?"

"You must come with me," Spike said in a zombie-like voice.

"Where?"

Spike then saw Jo and unleashed a massive fire breath that created a barrier between Jo and the two.

"Twilight!" Jo screamed.

"Spike?" Twilight was getting nervous as she backed into the boulder. She was too stunned to remember her magic and was focused on the very determined eyes of her dragon assistant. It was then that she noticed a metallic device she didn't recognize in his hands that he was turning on.

"You will come with me," he said again as he moved in toward a quickly-becoming-terrified Twilight.

"Spike? Spike? SPIKE!"

***End Part 1***

Author's Note

Thus ends the first part of the story! The story shall continue and more of the pieces shall be revealed in Part 2. The rest of the Mane Six will make their first appearance in Part 2, which will most likely be spread across multiple parts as well so updates don't take as long. We'll also see the Doctors and the companions start to work with each other a little more. Also I figured out how to put in videos, so enjoy the old-school closing credits sequence. Thanks for reading!

P.S. One final point. Yes, this is the Roger Delgado incarnation of the Master.

Part 2a

***Theme song. "Time Lords in Equestria"/"Written by SeanNetFiction"/"Part 2"***

Spike began moving in toward Twilight, who was too surprised by this turn of events to think clearly. She was cornered, of course, but she still had her magic at her disposal. Unfortunately, focus was not something that immediately available with her best friend staring her down with a maniacal look on his face.

"Spike, why are you doing this?" Twilight said in a very emotional state. It seemed like Spike was about to make his move when...

OOF!

Ditzy had picked up Jo and dropped her onto Spike. She had meant to bring her in close to buck him, but she was in a hurry and didn't get a firm enough grip when preparing to fly over the fire.

"Sorry about that," she said before turning to Spike. "Now what do you think you're doing? Twilight is your friend and she's been worried about you. Now what's this all about?"

Rather than answer, Spike kicked Jo off of his body and began shooting fireballs.

"Sorry. The Doctor already knows I can't carry ponies for very long."

"It's fine. At least we slowed him down."

Twilight, finally breaking out of her shock, began dodging the fireballs and tried to figure out what was going on.

"SPIKE! What do you think you're doing? Why are you doing this?!"

Spike was no longer responding, only blowing fire at Twilight fighting off Ditzy and Jo as they tried to subdue him.

"I know this can't be you, Spike, so who are you? What do you want?" Twilight used her magic to teleport over and tackle him, but Spike used her forward momentum to push her off balance. This allowed him to slip out from under Twilight and run off while she face-planted into the dirt.

"Twilight! Are you okay?" Ditzy asked, helping her out of the dirt.

"That can't be Spike. It has to be an impost- of course! It's a changeling! Come on, you two. We need to figure out where the real Spike is."

"What is a changeling?" Jo asked as the two tried to keep up with the now-determined and angry Twilight Sparkle.

"It's like this bug creature that can change its shape to look like anypony. We were dealing with one earlier today that looked like a bear," Ditzy replied.

"And they can breathe fire?"

Ditzy paused before speaking to think about that. "Actually, I don't know if they can. That may actually be Spike. Twilight!" Ditzy called out, but Twilight was combining her gallop with her teleportation and was now quite far ahead.

"Get over here, you imposter!" Twilight was pursuing Spike with one of the most focused looks of her life. She'd had Spike near her since she was a filly, and she was not about to give up on one of her oldest friends.

Spike dived behind a bunch of bushes. Seeing this, Twilight stopped in front of the bushes and began to walk through them, looking for movement. However, she didn't notice until too late that there was a trap to be sprung. Before Twilight knew what hit her, an electromagnetic field had shot up around and above her. She was caged.

Twilight tried to teleport, but to no avail. "Hey! What is this?! How is my magic being suppressed by this?" Twilight called out as Spike popped up.

Spike merely hit a button on the bottom, and the cage began to leave the ground. It then shot off toward the middle of the forest.

Spike looked on for a few moments before beginning to head in the same direction. But as he took a few steps, he was suddenly tackled by an incoming Pegasus.

She held him down tightly, telling him, “Don’t even try to kick me off, mister. I’ll just catch you again. Now I can’t catch Twilight, but I can make you tell me where that… thing… is taking her. Why would you do it, Spike? She’s one of your best friends.”

Spike tried to unleash a fireball, but Ditzy was able to dodge. So he tried a lower trajectory. That forced her off, but allowed him to roll away.

“Oh no you don’t!” Ditzy said as she tackled him. This time his back was to her. They struggled for a few moments until Jo ran over, panting.

“Okay… I need… to work on… that magic teleporting…” she eked out. After catching her breath, she asked, “So did he tell you anything?”

“No, he just keeps struggling against me.” Ditzy was getting frustrated.

“Let me see him,” Jo said, moving toward the dragon. He fired at her, but she was far enough to dodge. She immediately held his mouth shut while she looked him over. She quickly found what she feared.

“He’s been hypnotized.”

“He is? Who could do something like that? I don’t know of many skilled evil hypnotists in Equestria.”

Jo cringed. “I know someone we see a lot who could do this, but I’d like to root against it being him. In any case, I can fix this. Spike, I want you to follow my fi-“ Jo realized she had no hands.

“What’s wrong?” Ditzy said.

“I can’t snap with hooves.”

“Wow, you and the Doctor are really bad at using your pony bodies. Hold Spike, I’ll do it.”

After a momentary struggle, they had Spike back under control. Jo then talked to him while Ditzy held her hoof up.

“Okay, Spike, just follow the hoof. See how it moves. And…”

*snap*

Spike dropped to his knees. “How did you make that sound? Nothing happened.” Jo asked in confusion.

“I just snapped,” Ditzy shrugged. “Spike, how are you feeling?”

Spike sat up, feeling a little woozy. “Whoa, what happened? Huh? Who are you? I’m pretty sure I’ve seen you before, but I know I’d have seen that hairdo before.”

“What’s wrong with my hair?!” Jo asked, feeling a tad insulted.

“Nothing, it’s just… wait, I’m not in the prison anymore! How’d I get out here?”

The two looked at each other, unsure of how to approach telling him.

Ditzy began. “You see, Spike, you were kind of hypnotized to trap Twilight in a cage and send her to this prison you mentioned and…”

“WHAT?! I didn’t. Where is she?!” Spike began to panic.

“Don’t worry. We’ll find her,” she tried to reassure him.

“No, you don’t understand, they’re trying to get the Elements of Harmony!”

“Who are?”

“The Queen of the Changelings and… and… her changelings! She must be working with them for power!”

The stutter was not lost on Jo. “He’s been commanded to forget the queen’s partner. I have no doubt who is responsible. I’ll have to talk to my Doctor, and your Doctor too, about this. What are these Elements of Harmony, by the way?”

“Super-powerful magical jewels. Spike, would you be able to give our friends some more information? Something tells me they’ll need it,” Ditzy asked.

“If it gets Twilight back and protects my friends, absolutely. Where to?”

“They said they were going to Sweet Apple Acres, so let’s go!”

The trio began to make their push toward the farm.

Back at Sweet Apple Acres, Big Mac was just waking up. He was in a complete daze. As his vision started to clear up he realized he was tied to a chair. He turned his focus toward the pony responsible only to be met with a brown hoof that made a snapping noise, clearing his mind significantly.

"I honestly have no idea how you are able to snap with a hoof," Smith told Turner.

"I really don't either, but Derpy did it and I eventually figured it out."

"Do y'all always ramble on 'bout nothin'?" Applejack asked, a little frustrated at hearing the random conversations over the last few minutes. She turned her attention to her brother. "Now Big Mac, what in the hay happened?"

Big Mac had no memory of the last few minutes and was completely lost. "Uh..."

"Do you remember anything of what just happened, Mister, er, Mac?" Turner asked.

"Ee-nope."

"Do you remember being disruptive and angry over the last few days?" Smith added.

Mac raised an eyebrow. "Ee-nope."

"Whoever these changelings are, they must be incredible at hypnosis."

Mac's eyes finally widened with realization. Applejack immediately picked up on this.

"So ya do remember the changelings? Alright, Mac, who were they pretendin' to be?"

Suddenly, Big Mac's cheeks became flushed with a look of embarrassment. He also stopped looking directly at AJ.

AJ's voice went deadpan. "It was Cheerilee, wasn't it?"

"Ee-yup."

"Met her in town?"

"Ee-yup."

"Led you into a trap?"

"Ee-yup."

"Turned out to be a changeling in disguise?"

"Ee-yup."

"Did some shenanigans and now ya can't remember anything from the past few days?"

"Ee-yup."

"Alright, y'all can untie him," she said, addressing the Doctors, who stood surprised but somewhat impressed.

"Er, yes, I suppose we can do that. Turner, if you could help."

"Of course. Uh, thank you, Miss Applejack. How did you pick up on that so quickly?"

"Ah know my brother. It was pretty easy, actually."

"Well, now we know who is a changeling and we can visit this... Cheerilee," Smith said.

"Ee-nope."

"What do you mean, no?"

Mac's now-free hoof pointed out in the direction of the school, then to the sun in the sky.

"Ah think ah get it. School should've been happening when ya saw Cheerilee and the fake made some excuse. So the real Cheerilee is still there," AJ explained.

"Ee-yup."

"Blast! A dead end, then," Smith said.

"Well, I don't think we can get anything else from here. Let's go to see how Derpy and Jo are doing with Jo's magical unicorn training. EEEEE!" Turner had already set his mind to the new task and was anxious to see how unicorns trained to learn their magic.

"So unfocused. Oh, very well. Thank you for your assistance, Miss Applejack," Smith said.

"Not a problem! If y'all need any help with those changelings, ah got plenty experience dealin' with 'em."

"I shall keep that in mind, though I don't think it will be necessary. Come along, now, Turner."

The two took their leave of Sweet Apple Acres and began the walk to Twilight's library.

Author's Note

So first part is down. The opening scene of this had been done for a while, but I wanted to get Smith and Turner's scene written. I'm thinking of switching to releasing these as soon as a scene is complete, but then I don't want these to be too short. As it is, part 2 will probably be divided into three parts, possibly four. If I go by scene, the updates may be frequent, but they could be very short. Thoughts?