Part 1a
It was a beautiful, quiet morning in the Crystal Empire. Celestia's sun was shining with barely any blockage from clouds. Only a slight, unseasonal chill could detract from the weather, but at this time of day, even having a slight chill couldn't dampen the mood.
The way the sunlight glistened off the crystal buildings was a sight to behold, with the light bouncing off the taller, more angular buildings like prisms, creating a network of rainbow in select sections of the town. This was a rare sight that could only be seen when the sun was in just the right position and only at the Crystal Empire, and anypony, or any dragon for that matter, would be awestruck at the beauty of such a sight.
Such was the case for Twilight Sparkle and Spike, who were walking down the streets of the great city on their way to the palace.
"Man, I wish Ponyville could have mornings like this!" Spike said, as he sat on Twilight's back, biting into a decent-sized sapphire.
"I know Spike. Princess Cadance and Shining Armor definitely have had great luck when it comes to beauty in their kingdom. It's a shame we can't stand and enjoy it, but with Cadance going to meet with Princess Celestia and Princess Luna to discuss specifics on how to handle the empire's reintegration into Equestrian society, Shining Armor could use a helping hoof to make sure he doesn't get bogged down on his temporary duties."
"It's paperwork, Twilight. I doubt he's going to need any help with it."
"You don't know him like I do. He may be a BBBFF, but that didn't make him very good at keeping his room straight. I figured guard training would have fixed things, but I guess they glossed over that part of the training."
Spike shrugged and tossed his remaining piece of the sapphire into the air, catching it in his mouth.
When he finally finished with it, he said, "Well with any luck it'll be a light two days. I'm looking forward to being able to relax here."
Twilight turned her head with a raised eyebrow. "Relax? Spike, we're guests here. It is only proper that we honor our hosts by doing our duties to the fullest. If there isn't much, I think we should take it upon ourselves to help get a jump start on some of the developing projects, or reorganize their library, or --"
"Um, Twilight..." Spike was getting nervous. This was beginning to sound like he'd made a mistake in choosing not to run the library.
"Just kidding Spike," she said with a wink. "Believe me, I could actually use a lighter time after the last couple adventures with the Doctor."
"Tell me about it! I don't even travel and the few experiences that you guys have in the current time wear me out. It's still weird how he flies around in that blue box of his. And how he can time travel. And how he keeps it in our basement."
"It's just a good hiding place, Spike. In any case, he's off on his own so hopefully he figures out how to have nice, relaxing trips through history while he's gone. It actually feels kind of strange not to be with him while he gallavants through time and space, but I'm sure we'll see him soon enou-"
As she was finishing her sentence, the familiar sound of the TARDIS came into her ears. A quick glance to the left, and it was clear what was coming into view.
"*sigh* Just when I was getting some time to actually miss him, here he comes following me." Twilight chuckled to herself. "Well, it must be a big deal if he's flagging me down, let's see what he's got for us to do."
"Got for you to do, you mean," Spike muttered as they approached the blue box.
It only took a few moments for the door to open and reveal the... not Doctor. Instead of the normal brown pony with the sharp blue suit, the pair were greeted by a lighter-colored brown pegasus that neither had seen before. He had deep brown, almost reddish hair for a mane, and was wearing one of the strangest outfits Twilight had ever seen. Study of past international fashions told her the plaid thing around his hip was a kilt, and he wore a white, open-collared shirt as well.
"Um... who are you?" Twilight finally asked after the two stood open-mouthed for about 10 seconds.
The new pony looked at her with a look of awe before breaking out into a deep, hearty laugh. When he finally calmed down he said. "Ay, Zoe! It looks like we're not the only ones who are ponies! An' there's wee dragons here too! Come meet the locals!"
"Hey!" Spike said to the response of no one. He and Twilight watched as the pony seemed to look at his hooves like he wasn't sure which to walk with.
As he stepped out, he revealed a female, who Twilight assumed was this 'Zoe,' and she looked distraught. She seemed like she barely had control of her ability to walk. This pony was yellow with a goofy brown manecut that looked like some of the cuts Twilight had seen in her mother's old yearbooks. Despite it looking out of place in modern times, though, Twilight had to admit it suited her somehow. As she stepped out of the TARDIS, Zoe looked at the pony and dragon in front of her before shaking her head and addressing the stallion.
"Jamie, this is serious. We've been a lot of places, but we've never had our bodies changed when we traveled!"
"Just stay calm, Zo. The Doctor will sort things out. Just relax a minute and enjoy the ride!"
"ENJOY THE RIDE?! I was raised on The Wheel with a sense of reason, and turning into a horse does not qualify as 'reasonable.' DOCTOR! GET OUT HERE!"
At this point, Twilight wanted answers from the Doctor as well. Unfortunately, as he came out, there were even more questions raised, as the pony who emerged was not the Doctor she knew. This Doctor had a grey coat with a black mane that looked like a dust mop. His eyes had circles underneath, but he was still fairly young. He was a little wider and slightly shorter than before, his cutie mark had changed so that more time in the hourglass was in the top than the bottom, and his suit had changed to a simple black blazer and a blue dress shirt. He looked like a stowaway on a train more than the Doctor.
"Now, just come down Zoe. Jamie has the right idea. I think exploring would be quite nice right now if I do say - oh hello, there! Nice to meet you! I'm the Doctor..." he said as he shook the hoof of a dumbstruck, speechless Twilight.
***1967 theme music - Following title crawl: 'The Yeti of Equestria', then 'Written by SeanNetFiction', finally 'Part 1'***
"... and you are?"
Twilight stood there gasping at the air trying to find the right words for this incomprehensible sequence of events. Thankfully, Spike was not so stunned silent.
"You... are not the Doctor."
This earned a look from the Doctor like the dragon had gone barking. "What? Yes I am."
"No, you aren't. I've met the Doctor and he looks nothing like you."
"He's right. Who exactly are you? And what have you done with the Doctor?!" Twilight said, finding her speech again.
The Doctor leaned in with a slight eyebrow raise. "Have we met before? I feel like I would have remembered coming to a planet of ponies and lizards, but then again, maybe you never were a pony and a lizard."
"WHAT?!" the two said at once.
"Well, maybe you were a different species last we met, like I am now, and I don't recognize you because you've advanced into a new stage of your life cycle, though species that turn into earth-esque equines and lizards just sounds silly. Maybe you all have been changed and just haven't realized it ye-"
"Dragon."
"What's that?"
"I. Am. A. Dragon." Spike said, a little flustered at this imposter-Doctor.
"Are you really? Oh that's just fascinating! The humans used to be so fixated on the existence of dragons, so maybe you're the species that inspired them. Though you are a bit small. You must be younger."
"Hold on a minute! Focus here, fake Doctor! You pop in here with the TARDIS at random when I've never seen you befo-"
"Now I have to stop you. How do you know of my TARDIS?"
"Yeah, I'd startin' ta' think you all have forced us here. Get behind me, Zoe. I don't want you gettin' into danger if we all come to blows," the one called Jamie said.
"Oh, honestly. I can handle myself Jamie!" Zoe said.
"Calm down you two. There's no need to make any rash assumptions. These two seem to have seen my TARDIS and have met me before, but I have no recollection of this event, so the answer is quite obvious!"
"IT IS?" everyone besides the Doctor said.
"Of course." And with that, the Doctor pulled out a recorder and began trying to play it, stumbling over himself as he tried to get the notes right with his hooves.
After a few tries and a few steps, he pulled the recorder out of his mouth and said aloud to himself, "This was much easier with fingers. Now I'll have to practice all over again to accommodate these bloody hooves."
As he returned to playing and exploring the area around the TARDIS, Jamie and Zoe began whispering and speculating on what went wrong with the last trip and how they ended up as ponies. No other planet had ever altered their species, and they wondered how peaceful the planet was.
Twilight and Spike, however, were beside themselves. This pony claiming to be the Doctor answered no questions and had just walked away like nothing was happening. At this point, Twilight's best guess was that the trio were nothing more than a random group of escaped wackjobs who had somehow managed to get inside an open TARDIS and set the thing into motion.
I'd better tell him to lock his box better when I track him down.
But then that made no sense. These ponies seemed to think they weren't ponies. Are they aliens? Who are these people? And why does this 'Doctor' continue to poorly play that incessant recorder?! That was all Twilight could take and she suddenly began galloping to the grey pony. It was all Spike could do to keep from falling off.
She used her magic to confiscate the recorder, and when he turned, he was looking right into her glare.
"Who are you and what is going on?"
"How are you doing that?"
"Doing what?"
"Holding my recorder in mid air like that."
"It's a spell I used the magic in my horn to-- STOP THAT! Start answering my questions before I lose my mind!"
"Magic, you say? You mean magic is a real manipulator of elements here? Incredible! Now, what were your questions again?"
Twilight was about ready to punch this pony. "Who. Are. You?"
"I. Am. The. Doctor."
"How can you be the Doctor? The Doctor I know is brown, younger and looks nothing like you."
The Doctor frowned slightly. "Oh, so I'm brown in this time? What a shame, I'd have loved to have a unique, pastel look like you have."
Twilight's eye was twitching and Spike was beginning to massage her shoulders in an attempt to keep her from going off on him.
"Well, to answer your question, miss, um..."
"Twilight Sparkle. And I'm Spike," Spike answered for her.
"Twilight Sparkle, eh? Well that's a... unique name," the Doctor said as he raised his hoof to his mane. "Well, to answer your question, Miss Sparkle, the simple answer is that the Doctor you've met is the Doctor I will be in the future."
At last, Twilight had an answer. And it only raised another. "What?"
"Has your Doctor said anything about regeneration?"
"Yes, he has. He said that he did it before coming here. When he's about to expire his body heals itself and... changes shape! So that's what he meant! But you look REALLY different. I didn't think the change was that drastic."
"Oh you'd be surprised with what you get with regenerations. I was an old fuddy-duddy before I regenerated into this much more fun-loving form! But seeing as I know all of my past regenerations, I can only assume the one you know is from the future ones."
"But then, why don't you remember me?"
"Ah, an excellent question! I can see why I hang around you. You see, recently I was held on trial by the Time Lord High Council for stealing a TARDIS and..."
"Wait, wait, wait. You mean to tell me that I've been flying around in a STOLEN vehicle?!"
"Not stolen. Commandeered. I got tired of simply being an observer of time on Gallifrey and decided I needed to explore the universe. But the Time Lords eventually caught up with me and found me guilty. They adjusted the memories of my friends over there and sentenced me to exile.
"My true sentencing will begin soon, but before they did so they asked me to do a few missions on their behalf. The most recent one proved quite difficult, so I requested Jamie and Zoe's memories of me be restored temporarily to help me. We succeeded, but for some reason, the TARDIS malfunctioned on re-entry back to Gallifrey and that's how we wound up here."
At this point, Twilight and Spike were seated trying to keep this whole situation straight.
"As for why I don't remember you in my current regeneration, my memories of these extra missions will most likely be adjusted as well before I am regenerated and sent to Earth for my exile, so I may well not remember this little excursion for very long myself."
"So your people have the power to just adjust people's minds?" Spike asked.
"Only with special machinery and it needs to be agreed upon by the Court."
"DOCTOR! IS EVERYTHING OK OVER THERE?" Zoe yelled from the TARDIS about 50 feet away.
"JUST FINE. COULD YOU TWO COME HERE?"
Twilight felt like she needed to ask the next question, and to her, there was only one that needed to be asked next.
"So let's say I just accept everything you just said. The question still remains why you're here at all."
"Well, assuming that our trip wasn't completely accidental, which I assume it's not because the Time Lords would have probably been able to pick us out by now had we been thrown off by a glitch, then I would assume it's because something serious has happened that needs our intervention. So now you can answer me a question: Has anything around here been unusual and troublesome lately?"
By this point Jamie and Zoe had come over. Twilight began to think of the news around the kingdom for anything out of the ordinary. "Not really. The last threat to any area was beaten a few weeks ago. At this point, the most off thing right now is the weather in this city."
"Really? How's so?"
"It's unseasonably cold right now, but the pegasi haven't done anything to cool things down, so it's happening naturally. I just assumed its the last remnants from the last invasion of King Sombra."
The Doctor had begun walking around, now having a more serious expression on his face, like he was deep in thought. "I'm not sure what happened with this Sombra character, but if its the most odd occurrence then that's what we'll have to start with."
"It does look like summer here, and I certainly don't remember feeling like I needed more clothes in the summers we traveled to on Earth, so you may be right," Zoe added.
"So where should we go then?" Jamie asked.
"I'd say the best option would be to ask Princess Cadance, who is the leader of this area, but since she's on royal business, we'll have to ask my brother, Shining Armor. He's Captain of the Equestrian Royal Guard and Cadance's husband."
"Oh, I didn't realize we were addressing royalty then! Pleasure to make yer acquaintance, m'lady."
Twilight actually had to blush at this. Though she was technically royal be married blood now, it hadn't even crossed her mind until that moment. "That's ok, really. I don't think of myself that way. I'm Twilight Sparkle, by the way, and this is Spike."
"Jamie McCrimmon at yer service!"
"I'm Zoe Heriot. Nice to meet you."
"Well, now that introductions are out of the way, how about we meet your brother?" The Doctor said.
"Ok then. I'm late as it is. Follow me, everypony!"
And with that, the four ponies and one dragon walked the last half-mile to the Crystal Palace.
Deep underground, directly beneath the Crystal Empire, sat an elaborate room that was as impressive to the scientific mind as it was terrifying to most minds. It was an area isolated from the rest of the world. Where any noise made would simply echo and never make it to the surface. The walls were gray and damp, and made from brick covered in a metal no pony had probably ever seen. It reflected minimal light and was very apt at keeping any heat out.
Throughout the room were dozens of large machines that shamed all but the top of Equestria's scientific research divisions. Most were confined to the room, but some had pipes that carried through to neighboring chambers. And some led to rooms that the scientist residing here hoped he'd never have to enter.
The enclosed chamber had very little light, as it was powered entirely by candle flame. It was the only heat available for the professor. Prof. Micro Scope had not spent all his years studying biology of the rarest species across Equestria in order to get such an uncomfortable location, but when the prospect of money and power are involved, you make compromises.
Scope had a small rodent in a glass cage with an opening at the top for air now closed. Covering the rodent and beginning to fill the rest of the space in the box was a mysterious substance that appeared to be a liquid. It had only filled a small box the size of a child's building block initially, but like all other experiments, it had absorbed all the space in the cage very shortly.
"How go the experiments?" Commodore Charcoal asked.
"Same as always, the liquid absorbs everything in its path. These specially enchanted boxes remain the only thing that can hold it," Prof. Scope said.
"And of the subject in the cage?"
"You mean before it gets overrun? Same as with all test subjects, ponies and other creatures alike. Upon contact with the liquid, the animal becomes aggressive and enraged. Are you sure about this plan? It seems far too risky?"
"First of all, you know as well as I do that it is not my plan, but yes I do support it. For far too long I have sat around taking orders from Celestia when I could be in control and giving them. This Crystal Empire is a perfect testing ground for when we go after Canterlot and the rest of Equestria.
"And why wouldn't you want to be part of this? Think about it. Once our boss seizes control, we will have full obedience from all creatures. You will be able to study the world without interference. You will have total ability to manipulate the world to your will. Well, all but me and our boss."
Scope nodded along. "I suppose you're right. For too long, the alicorns' control has granted them the advantage. I would like to see the look on Celestia's face when she realizes her defeat."
"And we will both see that soon. This Crystal Empire was a great, large location for all of our equipment to be hidden, and the recent cold spell from Sombra has left them thinking it's residual magic. Have our unicorn subjects been keeping up with their spells?"
"Yes, the air is being masked so no one notices the cold is coming from under the ground."
Charcoal smiled. "Excellent. It's almost time to move forward with the plan."
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Allow me to give you your first comment post, woooo. I am interested to see where this goes, I have watched the second Doctor so I know of Jamie, Zoey and the Intelligence. I like you see a lack of 2 and 3 and 5-9, most of the time when they are included they get 2 to 3 sentences and that is it. It will be amusing to see how Two and Twilight get along, if memory serves Two can get frustrating to others. I look forward to see what happens next.