Dr Whooves: Trouble in Canterlot

by FelixTheBrony

Rating: teen
Tags: Alternate Universe, Doctor Whooves, Main 6, My Little Pony: Friendship is Magic, Comedy, Cutie Mark Crusaders, Other, Derpy Hooves, Crossover
Length: 8743

The Doctor and his companions have landed themselves in Canterlot. But things might take a turn for the worst.

The Doctor and his companions all take a trip to a past Canterlot, but, as with alot of his adventures, something is there to ruin their 'vaction' so to speak and a big mystery looms over them as well.

Rated Teen for a rough fight scene. Multiple genres, light shipping pairings, SpikeBloom, RainbowMac. (I changed the Mac pairing since I recently found out that Pinkie was possibly his cousin)

Sequeal to Dr Whoove's Beginning.

Published 2014-02-02 12:50:03 UTC
Last updated 2014-03-16 22:01:50 UTC

To The Past!

To The Past!

Golden Note sighed as she walked along the roads of Canterlot during the night, passing by the new doughnut shop, Doughnut Joe's. She had, as her name suggested, a golden coat with a blonde mane, a treble cleft made up her cutie mark.

“Where is he?” She muttered to herself as she scanned the almost empty streets. “He's never late...”

As she looked to her left, she noticed a stallion approaching her. He had a royal Canterlot armour on over his brown coat and wings, his piecing red eyes looked at her in a gentle nature as he approached her. “Iron Shield!” She exclaimed, happily.

“Sorry I'm late!” He replied, nuzzling her affectionately. “We've got a new prince and princess in the castle today, and I was held back a little longer to protect them.”

“Oh it's fine, you're here now...” She said as the two entered the shop, not noticing a slight whooshing sound as a blue box materialised in the alley way.

The door on the side opened and a brown head emerged, colliding with the wall in front of the door. “Ow!” He shook his head, before looking back at his companions sheepishly as he approached the console. “Whoops, exit's blocked by a wall!”

“Um...You do know how to park, right?” Twilight asked, raising her eyebrow. The Doctor turned a couple of dials.

“Yup! Just need to twirl it aroun...NOT THAT MUCH!!” He yelled as the whole room spun and the mass of ponies suddenly flew through the air, except him as he grabbed the level he pulled and pushed it back to it's regular position.

As the machine stopped, all the ponies crashed into several heaps. Applebloom and Sweetie Belle had landed on top of Spike, Rainbow managed to stay airborne and caught Scootaloo before she joined the 'Cutie Mark Dog-pile', Ditzy held her daughter close and landed on top of Twilight, Rarity and Fluttershy had both landed on Applejack and Pinkie had landed on Big Macintosh. “Sorry, is everyone okay?”

“Yup! It's a good thing I landed on this nice soft Macintosh!” Pinkie exclaimed, bouncing right off of the red pony, righting herself giggling. “Let's do that again!”

The others picked themselves up as well, ignoring Pinkie's outburst, with a few apologies and thanks here and there. “Alrighty, we should be able to get out now!”

“Ah don' like tha sound o' that 'should'.” Applejack muttered to herself as he opened the door to the alley way.

“Ah! Much better!” The Doctor said to himself, moving out of the way so the others can leave.

“Um...Doctor. Not that I'm ungrateful for the trip or anything...But we've been to Canterlot before.” Rarity mentioned, noticing the familiar buildings that surrounded the area.

“Yes you very well may have before, but this is Canterlot at the date of...Uh...” The brown stallion looked around confused until he spotted a yellow Pegasus stallion with a red mane and a cutie mark of a bird, trying to get down the street un-noticed.

“Ah! My good stallion, do you happen to know what the date is?” The Doctor exclaimed, causing the stallion to jump and hide in his hooves with an audible 'eep'.

“Uh...Uh...Uh...978 ABNM...” The Doctor looked a bit confused but the others all looked surprised.

“What's ABNM?” He asked the butter yellow stallion who was seen trying to step away, politely.

“Oh...um...It's After Luna Became Nightmare Moon.”

“Ah thank you, see you around!”

“Y-yes sure...” He muttered back before rushing off. The Doctor looked back at their surprised faces, not noticing that Fluttershy was looking on after the stallion with an astonished look.

“So I'm guessing by your faces that we have made it into the past?”

“Eeyup...” Big Mac replied, before Rainbow took over.

“By like thirty years!” The Doctor put on a confused look himself.

“I thought I set the TARDIS to go back three hundred years.” He muttered to himself before remembering. “Oh right, got to get use to these hooves...”

“Um...Flutters, are ya okay?” Applejack nudged her, before she looked back at them.

“That was my dad!” The others looked a bit surprised, but Rainbow clopped a hoof.

“I thought he seemed familiar! But I thought he lived in Cloudsdale?”

“He does, but he comes here once a month to check the bird's migration patterns.”

“Wow...This is when Doughnut Joe's first opened!” Spike exclaimed, looking at the building they were next to in wonder, before Applebloom knocked him in the ribs.

“Trust ya ta think about ya stomach.” And then, as if on queue, her own stomach grumbled in synch with his. The two grinned sheepishly, before turning to see if the others were ready to move.

They weren't, so the two took the initiative and slipped into Doughnut Joe's un-noticed.

“So is there anything we can do here that we couldn't already?” Ditzy asked, having never been to Canterlot before. She was a full-time mom and mailmare, thus had never had the opportunity for a vacation.

“Don't ask me. I'm as new to this area as they get.” The Doctor replied, sheepishly.

“Oh! There's a flower shop with some of the most beautiful looking lilies near the castle before they shut down. I never got the chance to actually buy any before!” Twilight said, already knowing the route by heart. Canterlot was her home city after all.

“Well guess that's our first destination then! Let's go...” Suddenly his stomach started to grumble and he blushed in embarrassment. “Ah...Well maybe after some breakfast?”

“I think you mean dinner!” Pinkie exclaimed, pointing at the clock shop on the opposite side of the street with several in the window indicating that it was half eight in the evening.

“Um...Where's Applebloom?” Sweetie Belle asked, having noticed her fellow Crusader's absence.

“And Spike!” Twilight exclaimed, having finally noticed that her assistant was also gone.

“What? Ah though' Ah told 'er ta stay close!” Big Macintosh rose an eyebrow at his sister.

“Um...No ya didn'.” Applejack flushed a bit in embarrassment before stomping her hoof.

“W-well she shoul' know better than ta run off on 'er own!”

“But Spike's probably with her. So she's technically not alone.” Ditzy pointed out, confused.

“Ah...Well...Ah give up, let's jus' find tha trouble...” A slight ringing sounded and the two 'missing' group members approached with a box of doughnuts on the filly's head, Spike munching on one already.

“Ah still say ya shoulda waited before piggin' out on one.” Applebloom complained to the dragon, who shrugged as he threw the rest of the doughnut into his mouth, pointing out the small amount of sugar dust around her lips.

“Hey, you ate one too.” He countered before noticing the group in front of them. “You guys hungry?” He asked, opening the box on her back as she rubbed the offending substance off her face.

“Sweet!” Rainbow cheered, grabbing one before anyone could respond. Applejack looked at Applebloom, sternly.

“Ya shoulda told one o' us y'all were goin' off ta buy food.” Applebloom looked down, a little guilty, before Spike interrupted.

“Sorry Applejack, it was my idea. I just needed help carrying the box out of the shop and we didn't want to interrupt you.”

“Well...Ah guess Ah can let ya off this once...jus' let one o' us know nex' time ya feel like explorin'.”

“Eeyup.” Big Macintosh agreed, politely turning down the doughnut offered. “Nah thanks, Ah'm not much o' a sweet tooth Miss Pinkie.”

“Aww, c'mon Mackie...You know you want too~.” Pinkie sung, still holding the doughnut out. He stood there, looking at her before shrugging and taking the treat, stuffing it into his mouth when he got it.

After their impromptu lunch, the group made their way towards the Canterlot castle, Twilight with a bunch of purple lilies in her saddlebags, Fluttershy with a bunch of blue ones. “Ah still don' git why a florist's woul' be open at nine in tha evenin'.” Applejack stated.

“Well the regulation of businesses act was first introduced in 985 ABNM, which state specific times in which certain businesses were allowed to operate, thus during this time it was a business's choice when they should open or not.” Twilight explained.

“Fascinating...” The Doctor replied, not noticing everyone else looking very bored after that. Applebloom rose an eyebrow.

“Does tha' mean tha' Sweet Apple Acres woulda been able ta sell apples at midnigh'?”

“Well yes, I suppose you would...But I can't imagine who'd want an apple at midnight.” Twilight answered.

“You actually followed all of that?” Scootaloo asked, raising her own eyebrow at her fellow Crusader.

“It weren' THA' confusin', Scoots.” She replied, noticing a certain dragon starting to fall behind. She quickly galloped over to him and asked in concern. “Y'all okay there, Spike?”

He grumbled, grabbing his stomach and falling to his knees, the others moving forward unaware. “I think I had too many doughnuts...” Applebloom sighed, nudging him in the ribs.

“Ah told ya y'all woul' git a belly ache if'n ya ate too much.” She replied, noticing him groan as the pressure was applied to his ribs. “Can ya walk?”

“Not without falling over again...” Applebloom sighed, noticing that they were falling way behind the group. She did not want to be in trouble just because Spike was greedy.

“'ere, hop on an' Ah'll carry ya.” She said, crouching in front of him.

“Are you...urg okay...” He replied, sprawling himself over her back, adjusting himself to a more comfortable position.

Applebloom stood up, and easily started to make her way back to the bigger group. “Y'all need ta burn off some o' tha' fat, Spike.” She commented, teasingly. He chuckled lightly before it settled down and she heard a light snore in it's wake.

Applebloom sighed and smiled wistfully, a faint red tint to her cheeks. “He's jus' plain adorable sometimes...”

The group ahead were just looking around, taking in the sights until they noticed something peculiar.

Ahead of them they noticed a young mare with a green coat ducking into an alley, presumably trying to get somewhere in a hurry, but she was being tailed by two brown stallions as well. “Um...Do ya think we shoul' intervene?” Applejack asked, having noticed a slight smirk upon one of the stallion's muzzles.

“Well I don't know...We don't know what their intentions are as of yet, dear...” Then they head a scream from the alleys that sent a chill up most their bones, however the braver souls immediately jumped to help.

Rainbow, Big Mac and Applejack entered the alleyway to notice that the green mare was now surrounded by four stallions, two white and two brown. “Hey!” The four offenders blink and turned, surprised to see three newcomers. “You better not be going to do what I think you're going to do!” Rainbow continued, flying up ready.

“Cause, unless ya jus' walk away, bad thin's are gonna happen...” Applejack continued.

“Eeyup!” Big Macintosh finished, crouching down into a more ready, combat stance. The four sneered at them, before smirking.

“Well...I assure you we weren't going to violate this mare...” The first one said, before his eyes turned into a pure black sphere. After that, the others following his lead, they began to morph into something else.

In place of the four ponies stood four bat like, bipedal creatures, their two front arms had claws that extended a couple of inches and their maws widened to about the size of a normal ponies head, their skin a strange pinkish colour.

“We were just going to consume her!” Another hissed, before they rushed forward to meet the two siblings and Rainbow.

Rainbow took straight to the air, causing one to break from the group to chase after her. Applejack nodded to Big Mac and she bucked a loose brick towards the remaining three, who ducked out of the way, so Mac could rush through and stand in front of the mare, who was now cowering on her haunches, regretting ever coming into the alleys.

Two of the creatures saw this and moved back to engage the red work horse.

Rainbow flew back to the group who were just about to get their bearings straight. “Guys!” She called, suddenly jutting left as the creature tried to tackle her in mid air. “Little help!”

“What, pray tell, is that thing?!” Rarity asked, pointing out the bat like monster. The Doctor gritted his teeth as he recognised them.

“Krillitanes!” He vented as he looked around himself for something to use. “Don't get to close, Rainbow! If it catches you, it'll eat you!”

“Gee, thanks for the vote of confidence!” She called back, spiralling to try and shake the creature off of her, disappearing through the clouds.

“The other one must have been a Krillitane too, c'mon Big Macintosh and Applejack will need our help!” The Doctor exclaimed, turning to Ditzy and Fluttershy. “Do you think you can fly up and help Rainbow?”

“Of course!” Fluttershy responded, unable to just let her oldest friend from flight camp to be fighting that thing alone and soon, her and Ditzy zoomed upwards.

“Sweetie Belle, you stay here with Scootaloo, Dinky, Applebloom and Spike, you hear me?” Rarity asked, to which Sweetie nodded, slightly put off they can't be 'Cutie Mark Crusader Monster Hunters'.

Applejack and the one she was facing circled each other, daring the other to make the first move. A game of patience passing between the two, knowing that, unless you land a good hit, those who fought first were more than likely to be at a disadvantage.

After a few more seconds, the Krillitane lost and charged forward, crying out when Applejack swivelled round and bucked the creature in the gut...

...But the hit wasn't high enough for the creature to lose it's balance and it grabbed onto Applejack's legs before she could react, swinging her into the wall.

As she impacted, her stetson fell off of her head and onto the ground, her groaning from pain. She struggled back up, before she was kicked to the ground again.

A sudden lesson from her father rang through her ears. “In a fight, Applejack, make sure never to fall to the ground...For if you fall down, you lose...”

“Ah kinda wish ya weren't so wise pa...” She wheezed before she was lifted off the ground and pinned to the wall.

Big Macintosh stood firm in front of the mare, staring down the two bat-like things in front of him. “Ma'am...When Ah start fightin', run for tha exit...” He whispered to the scared mare, before turning to the creatures.

One charged forward, emitting a war cry until it got a hoof to the face for it's efforts, the second tried to take him on while he was distracted, but Mac just side stepped and the Krillitane face planted into the wall, before he lashed out his hind leg and crushed the creature further.

The mare, seeing an opportunity, was going to run, before she paused, swivelled round and kissed Mac on the cheek. “Thank you!” She cried, before she ran straight out of the alley, her tail tucked between her legs in fear.

Mac was caught off-guard by the sudden kiss, so didn't notice when the Krillitane he punch had gotten up and pounced on him.

Rainbow bobbed and weaved her way through the clouds, the Krillitane close on her hooves. “Damn! How can he be keeping up with me?! I'm the fastest flyer there is!” She thought to herself, before she noticed the creature pop out of the cloud in front of of her, so she made a split second decision and dived down to evade it...

...however she didn't react soon enough and the creature had managed to clip her left wing with it's claws, causing it to flail helplessly, as she plummeted. “AHHH!”

Fluttershy and Ditzy found the Rainbow from the scream and gasped as they found her falling, the Krillitane pursuing. Fluttershy glared at the bat like creature. “Ditzy, catch her!” Fluttershy ordered, charging to face the beast.

Ditzy saluted and dived down to intercept the rainbow maned Pegasus as she broke through the cloud line, now dangerously close to ground.

“Oh...Not how I thought I'd die...But at least it's a pretty awesome way to go...” Rainbow thought to herself as she heard a few gasps and an all too familiar voice scream.

“NOO!” Scootaloo cried, seeing her mentor, idol and 'sister' plummeting to her demise. Even someone as awesome as Rainbow couldn't survive a fall like that.

Just as Rainbow said her last goodbye in her head, Ditzy flew round and tackled the cyan mare twisting round and landing on the ground in front of the four fillies and the dragon.

Rainbow shook for a little bit before realising that her impact was a lot softer tan she thought it was going to be and opened her eyes to see a pair of happy gold eyes looking back at her.

“Yay! You're okay!” Ditzy cheered, lifting herself and Rainbow onto their hooves. “Now to help Flutter...” Just as she was about to finish her sentence, the Krillitane from before could be seen colliding with the floor, a very angry looking yellow Pegasus following and diving onto the poor creature.

She then glared at the cowering creature, before she lifted her hoof and sent it crashing into the beast's face. “Nopony! Hurts! My! Friends!!” She punctuated each of her words with a hoof to it's face before she was sure it wasn't going to stand back up.

She let out a breath and turned to see six astonished faces looking over to her, causing her to hide behind her mane in embarrassment. “Oh...um...sorry...Was I too brutal?” She asked, shyly.

“Uh no! Not at all!” Rainbow suddenly said, laughing. “That was awesome!”

Applejack cracked her eyes open to look the creature in the face as it held it's hands around her throat. “Look death in tha face an' don' be afraid...” She remembered, quoting her fathers words in her head.

She glanced to the side and saw Mac bucking to try and removed the Krillitane he was dealing with off of his own back. “Y'all take good care o' AB an' Pinkie when she ponies up an' tells ya...” She thought to herself, catching Big Mac's eye, who's own started to widen as he realised what was going on.

“Git off me ya VARMIN!” He roared, charging sideways against the wall, crushing the Krillitane as it found out the literal meaning of being caught between a rock and a hard place.

However Mac had used far too much energy and collapsed to the ground in a heap. “No! You git ya no good legs! We've been through much more than tha'!”

However true that might be, he had spent five years trapped in one room and there was only so much exercise you could do in that small room before you break something. He teared up as he looked at his sister helplessly, the others only just entering the alley.

Suddenly, a sphere like device landed on the ground beside the Krillitane, causing it to look at the thing in curiosity, before it dropped Applejack, who had started gasping for breath.

The Krillitane held it's hands over it's ears, crying out in anguish.

Applejack locked eyes with the creature one more time, before she charged the remainder of her adrenaline and sent one good buck right into the bat-like creature's face, sending it crashing into the wall opposite and caving it's skull in.

After that, Applejack had passed out from exhaustion, Big Macintosh falling quickly behind.

The Doctor scanned the two with his sonic, checking for injuries, before letting out a relieved sigh. “They're alright, just tired...”

“Oh cool, what's this!” Pinkie exclaimed, knowing that her friends are okay, pointing to the ball like thing.

Everyone had gathered in the alley, Rainbow leaning against Ditzy's side for support, before the Doctor scanned the ball.

“Wow, a supersonic sound-wave emitter...” Noticing their confused looks, he chuckled. “It's a ball like thing that lets off a sound that can be set to any pitch, very good for distracting enemies...”

“Uh...Supersonic means a speed greater than that of sound.” Sweetie Belle mentioned, quoting her dictionary again.

“Oh I know, but it sounds cooler than pitch adjustable sound-wave emitter...” He replied before his eyes went wide with surprise... “Um...Applebloom was with you three, right?”

“Um yeah...Why?” Scootaloo asked, raising her eyebrow.

“Um...cause of this...” He replied, pointing to the little scripture on the ball stating 'with love, Applebloom'.

Author's Note

Hey guys, well here's the start of my sequeal and I hope you guys enjoyed the start. Thank you for reading, see ya. :)

Royal Pains

Royal Pains

Applejack stirred in her sleep as she heard machinery powering around her. Cracking her left eye open, she spotted her brother lying in front of her, looking incredibly worried with Applebloom at his side.

Both smiled widely when they saw her eye open and both hugged her immediately. “Y'all need ta stop getting' yaself inta trouble, big sis!” Applebloom scolded, trying to look like the big sister.

“Eeyup!” Big Mac agreed, before turning. “She's awake!”

About a second after that, Pinkie popped up next to him, smiling widely. “Yay! You're okay!” The three jumped a bit at her sudden appearance as she threw some pink confetti into the air and bounced excitedly.

“How in tarnation did ya git over here so fast?” Pinkie grinned at Mac, making a 'zip' motion across her lips.

“Sorry, trade secret.”

Just as she said this, Rainbow zoomed in with the others not too far behind. “Damn! How does she do it?”

“It's Pinkie, just grin and bear it.” Twilight replied, approaching Applejack. “You okay?”

“Ah'm fine.” Applejack replied, getting onto her hooves, stifling a yawn. “How long was Ah out?”

“About two hours.” Ditzy said, waving a hoof to the door. “We're back on the TARDIS, the Doctor wanted to look at the supersonic sound wave emitter.”

“Uh...Tha what?” She asked, tilting her head to the side.

“The ball that Applebloom threw to save your life.” Applebloom gave Scootaloo an annoyed look.

“Ah didn' throw nothin'! Ah was wit' ya arguing whether tomatoes were fruits or vegetables!” She paused for a bit, before adding. “An' they're fruits!”

“I think I got it!” They heard someone exclaim before they heard a crash and a small yelp.

They all rushed towards the control room and saw the Doctor covered in multi-coloured wires, a light bulb in his mouth, his fez hanging off his tail. He grinned a bit at their confused looks and sat the light bulb out. “I'm okay!” He said, shaking the wires off his body before rushing back to the console to stare at the ball that had saved Applejack's life.

“So what have you got?” Twilight asked, looking curious.

“I think I've found a little DNA on the ball.” He explained, proudly, to their even more confused faces. Well, Twilight looked like she understood, but the others.

“What's DNA?” Rainbow asked, facing Fluttershy, who shrugged.

“I'm pretty sure it's a hoofball team.” Spike mentioned, to which the Doctor looked stunned.

“Um...no. It's an abbreviation of Deoxyribonucleic acid, a genetic fingerprint if you will...Um genetic hoofprint?” He asked, looking at his hoof, noticing that there was, in fact, a strange little set of patterns on the bottom of his.

“Yes, a genetic hoofprint, like one, DNA is always singular. No-one, except an identical twin, will ever share your DNA. So it will be able to tell us who made this!” He noticed that his audience, except Twilight and, to some extent, Applebloom and Spike, looked very bored and muddled.

“Uh...Okay.” Applejack shrugged, muttering a “Fancy scientifics' under her breath. He grinned, before taking a pair of scissors and, quickly, snipping some of Applebloom's mane off, much to her annoyance.

“Hey!” She yelled, jumping back as he took a small bit of her red mane to the control console.

“Sorry, but I need a sample to compare to the DNA sample I found. Otherwise I can't prove or disprove anything.” He explained, before putting her mane sample into a funnel on the control console, before winding a crank on the other side.

“Alright, this should prove that this Applebloom and the Applebloom that saved Applejack are not one and the same.” He explained to them as he heard a ping on the screen and the results were shown on there.

“See they are...” He stopped half way when he read the results. The others gathered around and were just as surprised as he was.

The screen showed one double helix spiral with several lines connecting the spiralling lines together per interval with the title 'unknown' over it, and on the other side of the screen, the same image but with Applebloom's name on the top, the word 'MATCH' shown on the screen.

“...the same pony.”

“But wouldn't that make her fourty two years old?” Ditzy asked, curiously.

“Older, dear. She'd have to have the experience to build this, especially without magic.” Rarity explained, looking at Applebloom surprised and another thing. “...How do get yourself to look so young?”

“What?! No way! Ah am not that old!” Applebloom argued, stomping her hoof on the ground to try and emphasise her point. “Maybe it's a twin!”

“Ah was there when Applebloom was born, maybe it's a glitch?” Big Macintosh agreed, remembering when his littlest sister was brought into Equestria.

“Hm...Maybe the TARDIS's change is affecting her circuitry.” The TARDIS rumbled slightly, much to the other ponies shock, before the Doctor patted the console. “I know you don't usually make mistakes but it's the only logical explanation.” He consoled before jumping out the TARDIS. “Now c'mon, we have to stop whatever the Krillitanes have planned!”

The others followed, but they were all stopped at the by several royal guards outside, pointing spears directly at them. “Halt Doctor!” The one at the front, a grey Pegasus at the front ordered. “You are to be taken to Princess Celestia under the name of the A.C.U.”

“Um...What's the A.C.U.?” The brown stallion answered, ushering the TARDIS to close the others inside. The TARDIS obeyed and her doors shut everyone inside.

“The Alien Containment Unit. Surely you should know that. This isn't the first time we've met. We have recorded data of you.” The Doctor looked confused, before remembering.

“Oh right...I guess I must have been in their past, in my future.” He muttered to himself when he noticed a golden coated Unicorn stand in front of the door.

“We wish for your companions to join us as well. As recorded a Miss Ditzy Doo and Dinky Doo!” The Pegasus ordered. “She's been with you everytime!”

“Really!” He thought to himself in shock. “But...Most people I travel with last only a few months before they want to go back to family and/or die...”

Inside the TARDIS, the group looked at each other in slight worry. “Um...What do we do?”

“We can't ignore an order from the Royal Equestrian Guard, Fluttershy. We'll just have to go.” Twilight answered, going to open the door, before Ditzy stopped her.

“Hang on, Twilight, you of all ponies shouldn't!” She argued, pushing her away from the door, gently. “They only asked for me and Dinky, so we're the only ones who need to go.”

“Why do you think it's so important for us to stay?” The purple Unicorn asked. Ditzy just waved her daughter over before answering.

“Because you know Princess Celestia and have met her in the future, if she knows of you now it could cause a paradox and the Doctor said those are dangerous. That's why he was going to go back three hundred years, so there's less chance of us changing the future.” She explained, before she and her daughter stepped outside.

“Ah there they are!” The Doctor said, feigning a look of relief. “Yes there are my only two companions on the whole TARDIS!”

“Hiya!” Dinky said, cheerfully. The guards nodded and surrounded the three.

“We'll escort you to Princess Celestia. She has requested an audience with you three.” The front most guard said, walking forward with the rest of them.

What they didn't notice was a cloaked figure from on top of Doughnut Joe's tailing behind them.

“I'm bored!” Scootaloo whined, staring at the ceiling of the TARDIS. Rainbow nodded.

“Join the club, Squirt.” She replied, looking over to what the others were doing.

“How can you be losing THIS badly Spike!” Twilight asked, astonished that Spike only had two of his checkers left while Applebloom had all of her's, three of them having been kinged.

“I don't know!” Spike responded, moving his piece forward, only for his last two pieces to be taken by said farm filly.

“Yay!” She cheered, turning to check her flank for a cutie mark, then lowering them in disappointment when she came up blank. “Aw...”

“Ah told ya it'll come in time, AB...Besides Spike sucks at every board game.” Applejack told her sister, much to Spike's annoyance.

“I don't suck at every board game!” He argued.

“Yeah you do! Remember when we played snakes and ladders?” Sweetie Belle asked, noticing Spike wince a little.

“I don't know how I kept rolling ones!” The dragon folded his arms before turning to Applebloom. “Chess?”

“Y'all on!”

“Ooh!” Dinky said, looking at the stain glass windows and statues lining the corridor leading to the throne room.

“I'll say!” The Doctor replied, staring intently at the one that depicts the Elements of Harmony. “What's the story behind that one?”

“The Elements of Harmony? They're an ancient weapon used to dispel all negative energy out of a being.” The front most guard, Iron Shield, began, walking to stand next to the Doctor. “There are six elements that make up harmony. Honesty, Kindness, Laughter, Generosity, Loyalty and Magic...”

The Doctor then remembered Pinkie and Twilight mentioning that they were the Elements of Harmony to him. “To think that these Ponies can build a weapon specifically to destroy darkness. It's magnificent.” He thought to himself, smiling. “If only half the races I ran into tried doing stuff like this.”

“Doctor...” A powerful voice asked from behind him. He turned to be face-to-face with a larger white mare with a horn and a pair of wings standing before him, a crown adorning her head along with a multi-coloured wavy mane.

“Ah! You must be the Princess.” The Doctor said, bowing slightly after the guards and his companions. The Princess smiled and waved a hoof.

“Oh stop with the formalities. Just call me Celestia.” She replied, as they all rose to their hooves. “We've met plenty of times before.”

“Ah yes, of course.” The Doctor grinned. “But for me this is a first...You know what it's like. Wibbly wobbly, timey wimey.”

“Ah of course. This is your first time meeting me even though I have met you before.” She replied, nodding. “But that is neither here nor there. There are far more urgent matters I need you to investigate. Such as those bat like things I'm sure you've seen.”

“You mean the Krillitanes? So you've seen them?” The Doctor asked.

“No...I just got some descriptions from eye-witnesses. Most of which appear to occur from the Sunset Gardens. I would like to request that you help in the investigation with the A.C.U. and a certain individual...”

“Hold up. What individual?” Celestia pointed her hoof behind him Ditzy and Dinky.

“Her...” They looked and saw a yellow Earth Pony filly with a red mane, wearing a white robe that went down to just below her flank, her tail pointing out the end of the robe which lifted it up enough to see a cutie mark of a hammer across an apple.

She grinned at them, the pink bow in her mane giving away her identity immediately. “Howdy Doctor, Ditzy an' Dinky.” She said, casually pulling a ball like device that was very similar to the previous used. “In case ya don't recognise me. Tha name's Applebloom...”

In the Sewers

In the Sewers

“Hold up!” The lead stallion called, holding up his hoof. The others heeded his warning and stuck behind him. He as well as two more men were sent ahead of Applebloom, The Doctor and Ditzy since they were going to get 'reinforcements' in their words.

“What is it?” Another soldier asked, moving up closer. The first one, Flash Point, peered round the corner of the hedge and saw two Earth Ponies standing on either side of a manhole cover.

“It's just a couple of civilians sir.” Flash replied to his superior, Fracture. Fracture nodded and led his two men towards the Earth Ponies.

“Excuse me you two. But the gardens are a restricted right now, we're going to have to ask you to clear off the premises.” The two turned to each other, feigning disappointment.

“Are, but we were just about to have lunch.” Flash Point rose an eyebrow, not noticing a bipedal creature approaching from behind.

“Um...Well you'll just have to eat somewhere else.”

“Oh then you'll have to come with us...” One said, his eyes turning pure black, causing the three to point their spears in shock.

“...because you're on the menu!” The other hissed, fully transforming. The two struck at Flash Point and the unnamed pony as the one creeping from behind struck at the Captain, their cries of terror dying in their throats.

“So how can you be sure that Applebloom won't recognise...you...herself?” The Doctor asked, slightly confused about the situation. Applebloom grinned, lifting her hood over her head, causing her normally yellow fur to turn pitch black.

“Perception filter. Now ta tha unsuspectin' pony eye, Ah'm a black Earth Pony.” She explained as they got to the doors of the TARDIS. “Oh, an' refer ta me as Ambrosia in front o' them. Ah don' wanna draw attention ta maself.”

“Gotcha!” Ditzy replied, winking. The Doctor grinned, rolling his eyes before opening the doors.

“Oh come on!” They heard Spike groan, followed by a filly cheering that she won battleships. “What even is a battleship?”

“Oh hey, look who's back!” Rainbow called, pointing towards the four. “...and they brought a friend?”

“Oh yes...This is Ambrosia. Princess Celestia sent her with us to help against the Krillitanes.” The Doctor replied.

“A pleasure to make your acquaintance.” 'Ambrosia' said in an impeccable Canterlot accent. “I apologise for the disguise, but my face has to remain hidden. For security reasons.”

“Oh wow dear, where did you get that outfit?!” Rarity said, looking over the detailed embroidery on the trimming of the robes. “It's such a lovely and simple design.”

“I'm afraid it's a uniform, dear, I'm afraid I'm not allowed to tell you.” Rarity pouted a little, but simply accepted the answer. She looked over and saw Spike with his arms crossed and Applebloom grinning with a large pile of board game boxes piled up next to them.

“Ah...Good times...” 'Ambrosia' reminisced, grinning a bit. “Ya never did get better wit' tha games Spike...”

“Now that the introduction is out of the way, we need to get to the Canterlot Gardens!” The Doctor declared, jumping up to the control console.

“Um...You might want to hold on to something.” Ambrosia said, clipping a safety harness on the railings. The others all ran to grab something something, not at all trusting The Doctor's driving.

“Here we go!” He exclaimed, pulling down a lever and the trademark whooshing sound accompanied the rumbling.

“He comes! Sir he comes!” Another bat-like creature said to the first Krillitane who appeared to have black skin rather than pink.

“Who comes?”

“The Oncoming Storm! He comes!”

“There is little he can do now!” The black Krillitane smirked, deviously. “We have finally evolved enough and now the night is ours!” The black one said, lifting his palm. Suddenly a black aura surrounded it. “We have their magic!”

The quiet garden's tranquillity was spoiled when a whooshing filled the entire garden as the TARDIS materialised in the centre. Then out came the group of ponies, some holding their hooves over their mouths.

“Where did you learn to drive?!” Twilight asked, heaving a little. The Doctor grinned sheepishly.

“Sorry, I lost the manual in a fire...” He stated, before looking around. “I thought the Princess was sending some of the A.C.U.?”

“What's the A.C.U.?” Pinkie asked. Ambrosia looked at a device in her hoof, shrugging her shoulders.

“The Alien Containment Unit. You don't think The Doctor is the only alien to come to Equestria, do you darling?” She replied, before looking at the manhole cover, leading to the sewers. “Who thought it was a good idea to have a manhole cover right in the middle of the garden?”

“I know, it's so terribly drab!” Rarity agreed. Rainbow rolled her eyes.

“They had to put it somewhere?!” She groaned, not really wanting to get into the whole 'fashion of the garden' thing.

“Well, unfortunately, it looks like this is where we'll find the bats.” Ambrosia said, pointing at the device. “Strong alien reading that isn't The Doctor.”

“Wow! A device that let's you find aliens! That's so cool!” The Doctor said, looking at the box. Ambrosia shrugged, handing it to him.

“Ah you can have it. I make plenty of them. Standard issue for the A.C.U.” Ambrosia replied, opening the manhole cover. Rarity shook a little.

“Ah come on, Rares, Ah'm sure tha Krillitanes won't be tha' bad!” Applejack reassured, the white Unicorn with a one armed hug.

“It's not that dear...Just think of all the dirt and grime and...faeces down there!” She cried, cringing at the thought. Ambrosia rolled her eyes and immediately jumped into the hole.

“Well...guess we follow the leader.” The Doctor grinned. “Allons-y!” He cheered before jumping down. Ditzy giggled before going after him. Rainbow shrugged and went down after her.

Pinkie hopped down, Applejack going next. Big Mac and Twilight followed after. Spike shrugged and followed Twilight, just glad he was taken along on a journey for once.

“Well girls, you know what to do?!” Dinky cheered, before they all grinned together.

“CUTIE MARK CRUSADER ALIEN HUNTERS! YAY!!” They cheered before jumping down after them. Rarity gasped and jumped down after the four children.

“Alright looks like we've reached a dead-end.” The Doctor said, leaning against the wall. There was a four way division in the dank sewer system. “This doesn't make any sense! Why would they come down here?” He muttered to himself.

“Maybe they like the dark?” Ditzy offered, shrugging. “They do look like bats.”

“That doesn't necessarily mean they're nocturnal.” The Doctor muttered again. “Looks like we'll need to split up.”

“Are you sure that's a good idea?” Twilight asked.

“Ooh! Ooh! Bugsy Team Leader!” Pinkie cheered. The Doctor laughed.

“I'll be second leader then. Twilight and Ambrosia can be the third and fourth.” Twilight rolled her eyes.

“Fine then. I pick Rainbow.” Rainbow whooped and stood next to her.

“Alright my turn...I pick Ditzy!” The Doctor said, feeling strangely compelled to pick her. Ditzy let out a happy gasp and a yay.

“Yay! I never get picked this early!” She said, standing next to him.

“My turn! My turn! I choose...Applejack!” Pinkie replied, trying not to be too obvious. Applejack rose an eyebrow and joined her.

“Ah coulda sworn ya woulda picked ma brother.” She whispered, to which Pinkie replied.

“I'll explain later.”

“Okay. I pick Applebloom.” The group was surprised by Ambrosia's pick, but Applebloom still stood by her.

“Um alright. I'll take Big Mac.” Twilight said. Mac shrugged and stood between the cyan and lavender mares.

“I'll pick Dinky.” The Doctor said. Dinky cheered and hopped on her mother's back.

“Oh come on!” Rarity muttered, frustrated.

“Don't worry Rarity, you'll get picked.” Pinkie replied. Rarity looked up a little hopefully, before Pinkie said. “Sweetie Belle.”

“I'll take Spike.” Ambrosia replied. “I work better in a small group.” Applebloom tilted her head, before shrugging as Spike came to join them.

“Scootaloo.” Twilight said as the orange Pegasus cheered and stood next to Rainbow Dash, the rainbow maned Pegasus grinning back.

“See Rarity. Now I pick you.” The Doctor said, Rarity just huffed in response.

“No, you don't pick me. You're stuck with me.” She replied.

“Okay everypony! Pick a tunnel and we'll meet up where we need to be.” Ambrosia said, handing each team leader a walkie talkie. “Simple but effective.” She winked before she took Applebloom and Spike down the first tunnel on the far left. The others just shrugged and each went down their own tunnel.

“So Pinks, explain.” Applejack asked, Sweetie Belle was talking to Scootaloo through the walkie talkie and was, thus, oblivious to the other two.

Pinkie sighed, taking a scroll out of her mane and handing it to her. “This should explain it.” Applejack rose an eyebrow before opening the scroll.

“It's a family...tree...” Applejack said before she read it further. She saw that, somewhere down the line, the Apple family and the Pie family were actually connected.

“I was messing around on the TARDIS console earlier and thought, maybe I could find some past relatives to party with when it's my turn to pick some place to go...” Pinkie's hair drooped down to be flat. “And it spat out that family tree for me. I found the partiers alright...But it told me that we're actually cousins Applejack.”

“Oh wow! This is cool!” Applejack grinned before it hit her.

“Yeah...I'm the weirdo with a crush on her cousin...” She answer Applejack's unspoken question. The orange mare saw Pinkie's sad look and gave her a one armed hug in response.

“Hey, don't y'all worry 'bout tha'. Y'all didn't know we were cousins when ya started liking Mac an' it's lucky ya found out before ya, a dunno, married an' had foals wit' 'im.” She replied, supportively. “An' now ya know, ya don't still like 'im like tha', do ya?”

“Well...Not really...” Pinkie said, her mane starting to poof up again as she giggled. “It's actually kind of funny now that I think about it...” She continued, laughing as her mane and tail, once again poofed out again.

“There ya go. Don't y'all worry 'bout it, Sugarcube.” Applejack finished before laughing herself. Sweetie Belle turned to them, confused.

“What? I don't get the joke.”

“So why did she wan' us ta go wit' her?” Applebloom whispered to Spike as Ambrosia led them down their pathway, holding another device in front of her.

“Cause she knew we would be able to kick flank?” Spike suggested, shrugging. It had been bugging him as well, but he and Applebloom were good friends since she came to the library every so often for books about arts and crafts and cutie marks. She even borrowed a construction book to help rebuild the CMC clubhouse.

“Sure...But as good as Big Mac?” She pointed out, emphasising the name with a kick. “Ah've seen 'im knock full grown trees down...by accident!”

“If you two are trying to talk without me hearing, it's not working.” Ambrosia interrupted in a teasing manner.

“Seriously, the deaf would be able to hear you two...As well as the Krillitane that's been following us for about three minutes!” She exclaimed, pulling another device from under the robe and firing a green energy bolt out of it over the two kids heads, and right into the chest of the pink creature behind them.

It yelped in pain as it fell to the ground, dead. Ambrosia smirked and blew the smoke trail that was emitting from the barrel of the, more visible, hoof gun like device. Applebloom and Spike looked back and forth from the creature, to her again.

“That's bin followin' us this whole time an' y'all only decided ta tell us now?” Applebloom asked, incredulously.

“Trust me, Dear, we wanted to be out of the area we were in first...” She said, turning to continue forward...

...and turned in time for three large claw marks to be scratched right through her throat, tearing her hood off in the process.

Ambrosia clutched at the wound as her blood pooled around it, staring into the eyes of her murderer, the pink, fleshy bat thing in front of her as she fell forward and landed on the ground, her blood pooling around her.

“AHH!!” Applebloom screamed, crouching and hiding behind her hooves. Spike didn't respond, but was struck silent.

The creature, not hungry right now, advanced past the dead pony, moving forward to take out it's next victims.

Spike noticed this, and stepped in front of the yellow filly, ready to protect her if necessary. The Krillitane smirked, claws extended. It screeched and tackled Spike, striking it's claws at his cheek...

...however the claws literally just bounced right off of his dragonic scales as if they were striking titanium.

The Purple dragon noticed this and decided to give the monster a taste of it's own medicine. He pulled his arm back and slashed his claws against the Krillitane's chest.

The beast cried out in pain and jutted back, Spike quickly getting to his feet. As the Krillitane held his chest, it felt something solid connect to the back of it's head with a mighty thunk.

It staggered forward and glanced back, noticing the previously cowering filly holding a metal pipe, that was previously loose on the wall, in her hooves, ready to take another swing.

Just as the creature was going to pounce on her, a green bolt of energy connected to it's temple and it fell to the ground, lifeless.

In shock, the two turned to Ambrosia, who was sitting up in the blood puddle, the three claw marks sealing back up on their own...except the hood of her robe was gone, so the perception filter was no more.

“Wow AB, she looks just like you!” Spike pointing out, noticing the same red mane, yellow fur but most notably, the bright pink bow.

“Spike...Ah think she is me!” Ambrosia, now aware that the hood was gone, grinned sheepishly.

“Ah ha ha...Um...Guilty.” She replied, in her own voice.

“Fascinating...So Princess Celestia raises the Sun and Princess Luna raises the moon? That's incredible!” The Doctor said, enticed by Ditzy and Rarity's explanation of the World of Equestria. “In my dimension they don't rise so much as the Earth orbits around the Sun and the moon around it.”

“If it were that way, I imagine the Princesses would get a lot more free time.” Rarity replied, equally interested in the Doctor's universe...especially since it's apparently law for them to wear clothes. Being obligated to wear her magnificent dresses might be a world she could get used to.

“Yes they would...Maybe we should suggest it! She and her sister must get really tired raising those heavy things everyday.” Dinky said, thinking it as a great idea.

“I'm sure the Princesses are used to it by now, muffin. Besides, too much free time can get boring. Imagine a life where you have nothing to do, sooner or later you would have done everything and you would get really bored, trust me.” Ditzy told her daughter. “Remember when I was unemployed, muffin? I couldn't be motivated to do anything cause I'd already done it or it just wasn't for me. My job gives me a purpose, a sense of being and I'm sure the Princesses feel that way about raising the Sun and Moon.”

The Doctor took the words of the Pegasus in and smiled. “A purpose...A sense of being...But then, what's my purpose? I know I try to protect the worlds I visit...But sometimes I can't. I live as the fear in my foes, The Oncoming Storm. Is that my purpose...” The Doctor contemplated, frowning. “To be feared...”

“Why are you sad Mr. Doctor?” The doctor was shook out of his thoughts when he looked down at Dinky Doo. The little purple Unicorn smiled up at him, sweetly. “Can I help you smile again?”

“That's my purpose! I'm the fear of my foes, but the hope of my friends!” The Doctor reassured himself, smiling brightly at Dinky. “You already have, Dinky. You already have.”

“Ah closed ma eyes fer a second when Ah sneezed an' suddenly Ah was in tha' room.” Big Mac said to the three ponies, who were all listening intently. Twilight had asked what had happened for him to be transported into the Time Room.

“Ouch...Sorry it took us so long, Big Macintosh.” Twilight replied, looking almost ashamed. “If we had maybe taken what the Doctor was saying a bit more seriously at first, we might have been in time to save you...”

“Yeah...We kinda screwed up there and you spent five years in that room.” Rainbow also said, cursing herself under her breath. She had the potential to be out there, staring at the statue in seconds and yet she took her time like an idiot.

Big Mac smiled at them, reassuringly. “Now hey there, Ah don't blame y'all none...Sure Ah was a bit hostile when Ah came outta tha room, but Ah thought y'all abandoned me...Ah didn't know it had only been two hours until Pinkie told me, an' even then Ah didn't believe her until Ah saw tha paper tha next day...” He said, now glancing at Rainbow Dash a little apologetic.

“Sorry Ah snapped at ya in tha house Miss Dash, Ah know Ah did look a bit like a hobo when Ah walked out. It wouldn't 'ave killed those Weepers ta give me a new razor now, would it.” He told her.

“Oh no Mac, no need to apologise...And don't call me Miss Dash, it makes me sound like an old mare. Just Rainbow or Dash, please.” She responded, looking vaguely embarressed.

“Just so you know, you don't need to call me Miss Sparkle either, Mac. We're all friends here. You can just call me Twilight.” The purple Unicorn put in. Mac smiled.

“Alright, if'n it makes y'all two more comfortable...” He paused before looking at Scootaloo who was talking to Sweetie Belle on the walkie talkie.

“I'm sure you don't have to call her Miss Scootaloo, Mac.” Rainbow said, rolling her eyes.

Mac grinned before glancing up...

...and seeing a pink claw reaching towards Rainbow Dash.

“LOOK OUT!” He cried, tackling her to the side as the Krillitane jumped down onto nothing. Twilight used her magic to pull Scootaloo back.

Rainbow looked up at Mac and suddenly noticed their close proximity to each other. “Y'all okay?”

“Better than ever...” She let out, breathlessly as things she hadn't noticed before started to stand out, like his freckles and his calm green gaze.

He nodded and kicked out one of his powerful hind legs, catching one of the Krillitane's legs as well, resulting in a sickening snap to resound through the area.

The Krillitane cried out as it fell and clutched his leg. Mac stood up and looked down at the monster. “Twilight, turn Scootaloo around for a second.”

Scootaloo obeyed on her own, while Twilight rose an eyebrow. “Okay...What are you...”

Mac suddenly picked the creature up by the back of it's head and slammed it back to the ground again. The Krillitane screamed in pain as Mac picked it up again. “Which way ta y'all secret base, or Ah snap tha other leg!” He hissed in the creature's ear. “Ah don't much appreciate ma friends bein' put in danger!”

The Krillitane, terrified, pointed towards the area they're heading in. “Thank ya.” He replied, before slamming it's head on the ground one more time, knocking it unconsciously. Mac laid his ear next to it's mouth and grunted. “It's still alive...Fer now.”

He then remembered something very strange. “Wait a minute...Where's Fluttershy?” The other three, shocked, only now just realised that their shy friend had never gone into the sewers in the first place.

“Um...Hopefully still in the TARDIS.”

On the TARDIS, Fluttershy poked her head round the corner, a towel wrapped round her head. “I'm back from the shower.” She called, ever so quietly.

That's when she realised how empty the TARDIS was.

“Oh...Are we playing hide and seek?” She asked softly, seemingly to the thin air. “Okay...Ready or not, here I come!” She giggled before wandering off through the TARDIS.