Doctor Whooves: A Mare Called Missy

by tom117z

Rating: teen
Tags: Science Fiction, Adventure, Crossover, Dark
Length: 4333

The Trickster was defeated, and now the new Doctor and his companion Derpy are on a journey in time and space, but what happens when a figure from the Doctors past shows up?

The Trickster was defeated, and now the new Doctor and his companion Derpy are on a journey in time and space, but what happens when a mysterious mare shows up, wrecks a bar in Canterlot and asks a message be delivered to the Doctor.

And what if this mare has brought old 'friends' who the princesses, the element bearers and even the Doctor may not be able to stop. Can they save Equestria? Or will it burn?

(Cover art made by Chadbeats)

Published 1970-01-01 00:00:00 UTC
Last updated 2016-01-04 15:37:55 UTC

1 - Prologue

"So Miss Derpy, where to next?" Said The Doctor cheerfully, adjusting his bowtie.

Derpy and The Doctor had just come from an adventure with Starswirl the Bearded, he had helped them defeat an alien parasite that ate anything that moved into the shadows they hid in, much like the Vashta Narada from the Doctors world but a lot less powerful.

Derpy chuckled while thinking about the possibilities, "I don't know, how about the origins of Hearthswarming, I've only ever seen it in that play the element bearers did a little while back".

"Origins of Hearthswarming, its also the first time Equestria became host to Pony inhabitants as i understand it".

The Doctor walked up to the console of The TARDIS and fiddled with the controls.

"Coordinates placed in, lets go see us the origin of Christmas, or its equivalent at least," The Doctor said flicking up the lever to start the TARDIS's dematerialization.

"Any fatalities?" asked the solar guard to his colleague.

"Negative, she just threatened the staff and patrons of the bar, disintegrated a few tables with that weird device of hers and then apparently left a message for somepony"

"A message? For whom?"

"For Princess Celestia, or at least for her to apparently pass on to a fellow called 'The Doctor'"

"I'll take this message to her, I assume she will want to hear it and make a judgement on the situation herself, what was the message?"

"Well... it was a rather unusual message..."

In Canterlots throne room Princesses Celestia and Luna were conversing with Princess Twilight Sparkle and her friends about the recent disturbance in a Canterlot bar.

"A message?" asked Twilight, "What did it say?"

"I do not yet know, apparently it can't be put into letter and I have to hear it with my own ears," Celestia responded to Twilight's query.

"Seems a bit off ta me princesses, did y'all say the message was for you to give to the Doctor?" said Applejack picking up the conversation.

Celestia turned to Applejack, "Yes, but I'm afraid I do not know where he is as of the moment".

"I'm sure he will turn up, he usually does in times of crisis," Rarity chimed in.

As if on cue a wheezing sounded throughout the throne room as the TARDIS materialized, and the Doctor and Derpy stepped out.

"Welcome to the origins of Hearthswar... oh... well this was unexpected," Said The Doctor as he saw the Element bearers as well as three Princesses stare at him.

"Eh, it seems you missed, again," Said a bemused Derpy

"No, I definitely put in the right coordinates, the problem is the TARDIS sometimes takes me where I 'need' to go rather than where I want to go," Sighed The Doctor glancing back at the blue box in annoyance.

"Well then maybe it knew about the message!" Shouted Pinkie Pie

"Message? What message?" Asked The Doctor, suddenly putting on a more serious attitude.

Luna was the one to explain to the Doctor, "This morning an unidentified unicorn mare with a Blue Coat, a brown mane and tail along with an hour glass cutie mark walked into a bar down in the Canterlot market district. She pulled out an unidentified device, used it to disintegrate a few tables and then used it to threaten the staff and patrons, she asked them to deliver a message to my sister, who was then to give it to you, the guard who is set to deliver said message should be here within minutes."

The Doctor began racking his brain for any hints on who might have sent the message, "A Mare?" he muttered.

"A secret admirer perhaps?" Suggested Rarity.

"That would be one creepy admirer Rarity," Responded Rainbow Dash.

"Most secret admirers are darling."

"Well, maybe this is all one big misunderstanding" Said the barely audio-able voice of Fluttershy.

"Sadly, I very much doubt that" Said Twilight.

Just then the doors of the throne room swung open and a lone guard walked in, "Your majesties! I have brought you the message!"

"Well The Doctor is right here," Said Celestia pointing a hoof towards the Time Lord, "You can tell it directly to its intended audience.

The Doctor walked up to the guard, "Yes I am very much interested to hear this".

"Well, it's not really a spoken message," Said the guard "I'll just give you it, maybe you can make some sense of it, it is... odd."

"Ok... do it"

Play for atmosphere

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The Stallion lifted his hoof, and tapped

tap,tap,tap,tap

pause

tap,tap,tap,tap

The guard kept this rhythm up three more times, The Doctor slowly backing away in terror.

"Doctor?" Asked a concerned Twilight, "What is it".

"The drums... it can't be... no..." Said The Doctor, horror etched into his face.

"Doc? What's wrong?" Asked Derpy walking up to The Doctor.

All of the ponies in the room were beginning to get worried now, they had never seen the Doctor react like this before.

The horror the Doctor was feeling began to mix with some mild panic, "If that is who I think it is, she's followed me here and I'm so, so sorry"

Twilight thought for a second, "Hour glass cutie mark... A Time Lord?"

"Yes... and not one of the good ones..."

Celestia stepped forward, "What is her name Doctor?"

"She was a friend once, and a he," The Doctor said with a slight chuckle, but the horror and panic did not fade for a second, "Her name is..."

"Oh yes do say my name I do so love it when you do!" A female voice said, interrupting The Doctor.

All ponies in the room turned towards where the voice came from, and through the throne room doors walked a blue unicorn mare, with a brown mane and tail along with an our glass cutie mark.

"Missy," Said The Doctor

Missy rolled her eyes, "Now I may go by that alias as of late, but you know that's not what I meant, say my name, my real name, the one I chose just as you chose the name Doctor."

All eyes in the room turned towards the Doctor who only just managed to find the word, one single horrifying word that signaled what was to come next.

"Master"

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2 - The Fall Of Equestria

Missy stood in front of the group, in her cyan magical aura she held a device The Doctor knew well, she used one such device to murder an old friend after all.

"So you're the Master?" Asked a curious Twilight

"Yes but that's Missy to you dearie, you call me Master and you may have an accident" Missy said with a sinister chuckle, "And you must be the 'wittle pony pwincess' Twilight Twinkle or Sparkle or whatever that ridicules name is."

"Sparkle," Twilight deadpanned

"Yes that's nice, oh, but I have heard of a timeline where you were a really naughty girl, trying to kill sun-butt over there and all, shame the Doctor had to spoil the fun as usual," Missy shrugged.

Twilight was fairly certain she didn't like this mare, and she wasn't alone.

"Why are you here? This world could certainly do without your idea of 'fun'," The Doctor asked the insane Time Lord.

"Why am I ever anywhere Doctor, to torment you, so wherever you go... I go" Responded Missy with an innocent smile, "And I certainly see you've brought plenty of your little friends for me to play with, tell me Doctor, do you love these ponies as much as the humans I wonder, I mean this planet is technically Earth after all, just in a slightly different place that's filled with magical fairy pony things."

"You will not harm this planet in any way Master!" Proclaimed The Doctor with a stamp of his hoof.

The group of ponies began to circle Missy, the princesses ready to arrest her at a moments notice.

"Harm this planet? Moi? Oh, I wouldn't dream of it! Nope, that honor is left to some other old friends of ours Doctor," Missy said beginning to tap her hoof in a rhythm of four beats and then a pause.

"We beat your little Cybermen before, what else have you got?" The Doctor asked, thinking he may perhaps regret it in a moment.

"Oh Doctor, remember, I'm not the only one who follows you wherever you may travel... and while they might not usually be in the business

of crossing into unknown universes on a dime they will make a special case for this one, all just to get to you... Doctor," Sneered Missy. "In just a few short minutes this planet is going to get burned."

Finally Celestia stepped forward from the group and walked up to Missy, "I will not let any harm come to my little ponies or any other race on this planet."

Missy laughed at the Solar Diarch, "Very brave of you princess, but tell that to them."

For the first time The Doctor noticed Missy had been holding onto a second object in her aura, a small silver device with plenty of buttons on it, and Missy used the big red button right in the centre.

A large gust of hind blasted through the castle and a small tremor almost knocked a few of the element bearers to the ground. Through the windows the group could see the edges of what looked like a giant crack in the sky, and on the other side was open space.

"Missy? What have you done!?" Asked The Doctor in alarm.

"Oh not much just opened a rift in the very fabric of reality connecting this universe and our own, I must be going now Doctor but I would suggest finding a balcony or something to get a better look at what's on the other side of that rift"

At this the lone solar guard in the room approached Missy, "Miss you are not going anywhere"

Missy turned to look at the guard, "Say something nice," She commanded

"Pardon?" The Guard said confused

"Say... something... nice..."

"Uh... this was a well constructed plan, on paper at least?" The Guard still looked confused but shook it off, "Not that it matters your still under arrest."

Missy lifted her first device up and disintegrated the guard where he stood.

"Murderer!" Shouted Luna charging a spell

Luna launched the spell full force at Missy, but by the time it hit Missy had already gone, blowing the Doctor a kiss as she used her second device to teleport away.

The Doctor tried to process everything that had just happened, the Master had just returned, murdered somepony and opened a rift back to his universe, what had she, what had HE unleashed upon this world.

"Doctor?" Derpy asked placing a hoof on The Doctors shoulder.

"I'm fine," He lied

"She was certainly an unpleasant... thing..." Muttered an appalled Rarity

"So whatta we do now Doctor?" Asked Applejack

"I..." The Doctor muttered, his thought process having completely broken down.

The five element bearers and Derpy gathered round The Doctor hoping he would provide answers, he gave none. The three princesses hung back looking on, concern etched into their faces, it was Celestia who spoke first.

"Firstly I think we should take her advice on one matter, we find a good view of this rift and see what we are up against," She advised

"Good idea," Twilight said to her fellow princess and mentor.

Slowly the group emerged from their daze and agreed with the princesses, the group of ten heading for the nearest balcony.

The Doctor already knew what he was going to see when he looked through the rift, it was this reason he was acting so distant. What could one up the Cybermen? What followed him wherever he went?

The group walked down a hallway being led by Celestia, at the end was a door that led directly onto a large balcony overseeing much of the city.

"I'm so sorry," He said to the group at last.

"I'm sorry sugarcube?" Applejack asked her gaze moving towards the Doctor

"I'm sorry."

"What are you sorry for?" Asked Twilight

"I know what's on the other side of that rift..."

Twilight looked surprised at The Doctors sudden insight, "You do? What?"

They reached the far door, using her magic Celestia swung it open to reveal a full un-obstructed view of the rift. In Canterlot they could see hundreds, if not thousands of ponies were all looking up at the same thing, not the rift itself, but what was in the rift.

Just beyond the rift sitting in the vast emptiness of space where hundreds of starships, saucer shaped starships that made The Doctor sick to the stomach to see again after all this time.

"Daleks," He proclaimed in renewed horror

Play for atmosphere

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"Daleks?" Celestia asked

"The most ruthless and deadly killing machines my universe has ever, and will ever know, it was they who my kind fought during the Time War, it was they who brought reality itself to near destruction, and it is they Missy intends to use to burn Equestiria, and all of Equus to ash,"

The Doctor said, his horror turning into anger.

"But then why are they just sitting there?" Asked Rainbow Dash

"Hold on, Doctor? Didn't your 'friend' say something about burning us to get to you?" Luna questioned The Doctor, feeling more than a little alarmed.

"Yes," He simply stated, "A portal to a whole new universe has opened, they don't know anything about it they don't know whats here! But right now they will be actively scanning the planet, and they are going to find one lifeform who stands out, a Time Lord, and not just any time lord, the one who is the only being in the galaxy who the Daleks fear".

The group had turned to listen to the Doctor, watching intently as he spoke.

"Me."

All of a sudden there was a blur of activity in the Dalek fleet and the ships began to make haste towards Equus, the voice that still haunted the Doctors nightmares blared out for everypony to hear.

"EMERGANCY EMERGANCY, THE DOCTOR IS DETECTED, EXTERMINATE THE DOCTOR!"

"EXTERMINATE"

"EXTERMINATE"

"EXTERMINATE"

"Tia what do we do?" Asked a now extremely alarmed Luna

Celestia turned to her fellow princesses, "Luna you coordinate the Lunar Guard and get civilians to safety, Twilight you and I will organise the Solar guard and..."

The Doctor cut in, "No! They won't be any use we have minutes at best I'm sorry we have to leave!"

Celestia glared at the Time Lord "We need to get my little ponies to safety before their ground forces land."

The Doctor sighed, "Oh Celestia, they aren't going to use any 'ground troops' until after the planet is already dust!"

Sure enough the ships began to file into formation in the planets upper atmosphere, readying for an orbital bombardment.

The mane 5 all shared the same expression, sheer terror, The princesses all glanced between each other.

"There must be something we can do! We can't just leave them!" Shouted Twilight to nopony in particular.

The Doctor looked positively crestfallen "I'm so sorry, but we can't save them, any of them, on the whole planet! The only way we have a chance is to get to the TARDIS and sit this out, when its over we gather the survivors and come up with a plan, I know this is hard and if there was any other way... I am so sorry..." The Doctor fell to the floor, this was all his fault, he should have left Equestria long ago.

"Trust him!" Shouted a tearful Derpy, "Its horrible I know but he's fought them, he knows what he's talking about and we should trust him!"

Celestia sighed, her regal mask faltering as she let a single tear slide down her cheek. She simply nodded in confirmation.

The Doctor got to his hooves, nodded and then turned to the door, running with the group back to the TARDIS as fast as their legs could carry them. As they ran Luna bellowed out a order to evacuate the city in her royal canterlot voice, projecting it all across the city in the hopes at least some would make it out in time, The Doctor however knew any survivors from Canterlot would be unlikely, the Daleks would have pinpointed his presence here and Canterlot would almost certainly get the worst of it.

On reaching the familiar blue box they burst through the doors and The Doctor set the TARDIS to take them to the open fields between Ponyville and Canterlot three days from now. Outside they all heard several loud explosions and screaming following shortly after, however these noises faded as the TARDIS' engines started and they dematerialized, entering the depths of the time vortex.

Throughout the trip nopony said a word, not one.

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The TARDIS materialized in the middle of a field just next to a rather tall hill, all those aboard held their breaths as they exited the TARDIS. They were met with fire. The days sky was red from all the flames and destruction, the fields around them were all burnt to a crisp and they couldn't see any life anywhere. The Dalek ships still sat in orbit.

"Canterlot... its gone," Rarity near shouted in horror pointing a hoof in the direction Canterlot once stood. The mountain it sat on wasn't even there anymore, all that would exist there was a massive crater and the dying echoes of thousands.

The mane six didn't take the realisation of just how devastated the planet was well. Fluttershy began to sob, Applejack held her Stetson to her chest, Rarity fainted, Pinkie Pie's hair deflated as she began to climb the hill, Rainbow Dash was trying to keep a tough face but was failing miserably, while Princess Twilight Sparkle simply stared into the distance keeping to her own thoughts.

The Princesses of day and night sat apart from the rest, they simply stood staring at what was once Canterlot with no visible emotion on their faces.

The Doctor walked up behind his companion who had completely broken down at her surroundings.

"Derpy? I'm so sorry, this is my fault I...."

Derpy pounced on The Doctor and pinned him to the floor, "No! Don't you ever say that! It was the fault of that crazy mare and not you! Never, ever blame yourself for this!"

"So Twilight..." Rainbow Dash said slowly, "What do we do now?"

Twilight immediately snapped out of her trance and looked Dash straight in the eyes, "What do we do? We save as many as possible and then we kick those things off, our, planet!"

"We couldn't agree more!" Exclaimed Princess Luna as she and Celestia walked up to the group

"First things first," Said Celestia, her calm regal demeanor somehow returning despite everything, "We need to locate any place that may yet hold survivors, ideas?"

"How about that!" Shouted Pinkie Pie from on top the hill, her hoof pointing at something beyond the hill, whatever she saw caused her mane to re-inflate slightly.

The group climbed or flew up the hill in haste, when they got to the top they all saw what Pinkie was pointing at.

"Ponyville!" Exclaimed Twilight in surprise

In the distance they could see Ponyville, despite looking a bit damaged it seemed like it fared better than most places, but what really caught their eye was the rather familiar giant pink magical field protecting it.

"A field like that will almost certainly be keeping out the Daleks!" The Doctor shouted excitedly.

"But who's doing that?" Asked Rarity pointing at the protected town.

The three princesses looked between them, all saying at once...

"Cadance."

3 - Cadance

Cadance didn't like paperwork, no she hated paperwork. And this paperwork wasn't even hers!

But alas she had promised to cover for Twilight while she was in Canterlot and so she would do so.

'Why do my visits to Ponyville never go to plan?'

Shining Armor sat to her right, face planted into a plate of pancakes. Like sister like brother she supposed.

Smiling in amusement at her special sompony's situation she continued going through paper after paper, just reaching something about planning permission for a new shop around Ponyville market.

And that was when she heard it.

Fantastic and terrifying explosions rocketed the castle, shards of crystal fell onto the cutie map as the whole structure shook violently.

"Huh- what?" Shining awoke with a start.

"Your highness!" One of Cadance's personal crystal guards burst into throne room, panic written all over his face.

"Private, what is it?" Shining barked removing the remnants of pancake from his fur.

"It's... it's... you should really see for yourself," Then guard all but whimpered.

Now the prince and princess were really concerned, and faster than they have ever moved in their lives they bolted to the balcony right at the front of the castle.

As they approached they began to hear the screams, wails of despair as the citizens of Ponyville witnessed whatever horror awaited. Bursting through the doors they first took in the orange glow that dominated the days sky, secondly there was the ponies of Ponyville all pointing towards two things.

Some of the hooves pointed towards the sky, where circular metal objects lay in wait, however most hooves pointed towards Canterlot, or what was left of it. Dozens of those cylindrical objects hovered high above the city, firing down green bolts of energy at a astonishing rate.

Cadance let out a scream of despair as she saw Canterlot's state, the city was burning. No, it wasn't just burning, it was all but gone And the mountain wasn't faring much better.

And Cadance knew that her aunt's and sister lay within that devastation.

Shining just stood there, gazing into the destruction, the same thoughts going through his mind.

"Cadance," He finally said, "Shield, now."

"Huh?" Cadance sniffed, tears staining her fur.

"They had no time to defend themselves, but we do, come on Cadance they won't stop at Canterlot. The others... wouldn't want us to share their fate."

Cadance nodded slowly in understanding, her horn lighting up with a cyan energy, before a magnificent beam shot up into the sky, and surrounded the town.

Across the horizon way up north, Cadance's home lay defenseless. The Crystal Empire would not survive what was to come, and she knew it.

Everything had happened so quickly, the devastation would rock the globe.

A very tired Cadance and what few guards she had sat in the throne room sat at the cutie map, which displayed a devastated Equestria. Mount Canter was gone, Manehatten and all the other cities were burning. Most smaller towns had been destroyed by the Daleks themselves, not wasting their ships ammunition on 'insignificant targets'.

Daleks.

It was on the second day she discovered their foes name.

First they had blasted the shield from orbit, but the magical energies proved to be a match for whatever type of weapon their ships were outfitted with, so they stopped.

And then one of those creature somehow got through.

The metal creature approached the infuriated princess, who was flanked at both side by what few guards she had and her husband.

The group stood in the centre of towm, a large crowd surrounding them, fear in their eyes.

"How did you get through the shield?" Cadance demanded to know.

"YOU ARE WEAK, YOU SHALL BE EXTERMINATED!"

"But why? What reason had you to come through the rift? To destroy Canterlot and beyond?"

"Who cares?! They killed Twilight! And the princesses! Turn it into a smoldering crator already!" Sompony shouted.

Mumurs of agreement spread throughout thr crowd, the creature just stood there however, it's glowing blue eye staring.

"YOU ARE ENEMIES OF THE DALEKS, YOU PROVIDED SHELTER TO THE TIME LORD KNOWN AS THE DOCTOR, YOU WILL BE DESTROYED."

"All this? Just to get to one individual? Where is he now?"

"HE WAS IN THE SETTLEMENT DESIGNATED CANTERLOT, HE IS NO MORE!"

"Then why continue? Leave this place, or I will kill you."

The Dalek remained motionless for a few moments, then-

"EXTERMINATE"

A bolt of blue energy thrust forwars towards the pink princess, with one of the guards jumping to intercept the shot.

The brave and unfortunate stallions skeletan glowed through his flesh momentarily as the bolt struck him, shouting in extreme pain before falling to the ground, dead.

Retaliating Cadance's horn filled with dangerous sparking magic, which she launched at the Dalek before her, the creature exploding into a massive fireball on cantact with the masses of magical energies.

After that day Shining had quickly set up a militia to watch for any more incursions, of which there were none. And now after three days they had yet to depart, and Cadance had a terrible feeling they wouldn't until every being on the planet was 'exterminated'.

"Your highness," One of the guards reported in, giving a salute.

"Go ahead."

"One of our forward sentries has reported a group of ponies in the field outside of Ponyville!"

"Understood, I will go down and-"

"No ma'am, you don't understand. The sentry said that all three other princesses were among the group!"

All eyes shot towards the guard as a shocked silence.

"They're alive."

"Of course they're alive, honestly give them some credit!" A new voice remarked emerging from a... blue box? How long had that been there?"

Out of the blue box the stallion was followed by Derpy Hooves, the element bearers and of course, Princesses Celestia, Luna and Twilight.

"I... what?"

"Cadance, good to finally meet you!" The Doctor said, straightening his bowtie, "In this timeline anyway. Now, I'm The Doctor... and I'm going to save your lives and the lives of everypony on the planet around us, got a problem with that?"