The Pegasus Paradox

by Ianpiersonjdavis

Rating: teen
Tags: Dark, Romance, Adventure
Length: 13372

The Doctor has returned to Ponyville to prevent a paradox from occurring thanks to the actions of Discord in the past to enlist the help of Rainbow Dash and Twilight Sparkle.

The Doctor has returned to Ponyville to prevent a paradox from occurring thanks to the actions of Discord in the past to enlist the help of Rainbow Dash and Twilight Sparkle.

Meanwhile, Rainbow Dash struggles with her decisions and questions her worth as a friend as Twilight struggles with the difficulties that come with her new position of power.

(Rated for violence)

Takes place after "A New Life"

Special thanks goes to ~Optimus97 at deviantART for providing the story image and derpymuffin24 for proofreading.

Published 1970-01-01 00:00:00 UTC
Last updated 2013-05-17 21:48:40 UTC

The Doctor

The Doctor stumbled out from the TARDIS upon reaching the Ponyville library. The sun was setting as twilight cast its shadows across the town's landscape. He couldn't help, but chuckle at the irony of the thought.

Up ahead, in his blurring vision he could see a violet ball of light bouncing up and down in the air as it headed towards him as it was accompanied by a feminine voice.

"Are you alright?" she called out to him. "Do you need medical attention?"

"No." he replied weakly. "I'll be fine...I just need to speak to...Princess Twilight Sparkle."

"That's me...I guess." she replied, somewhat dismally.

Even in his weary state, the thought occurred to him that seeing an injured stallion practically fall out of Police Call Box-which didn't exist in this world, as far as he could tell-was probably very strange for the poor mare.

The jelly-like feeling in his legs made it quite difficult to stand, let alone maintain his balance, yet somehow he persevered.

Trying to gather his bearings, a strange thought had entered his head; Rainbow Dash.

He wasn't entirely sure who or what a Rainbow Dash was, but perhaps Discord had used some kind of magical perception filter on him before he left?

Or had he used it on himself again and completely forgot about it?

He shook his head. Whatever it was seemed important. After all there was no harm in asking, was there?

"My associates refer to me as 'The Doctor', I realize that you are probably very busy with your new royal duties, but it is of utmost importance that I am allowed to speak with Rainbow Dash."

He paused. Why did he say that? Did he even know a Rainbow Dash?

"Yeah...that's going to be a problem."

Twilight cantered over to his side before leaning over. "Here, let me help you." she offered as he draped a foreleg over her shoulder as she led him towards what appeared to be a large tree with windows and a red door with the image of a candle carved into it.

"Is there anyway for you to contact Rainbow Dash?" asked The Doctor, once they were inside the library.

His vision was still a little blurry. He must have lost more blood than he thought, going through those spikes. Even through his vision's haze, he could the look on the librarian's face was one of concern.

"Are you sure you don't need any help?" she asked, almost as if she were reading his mind.

"Actually, I think I've changed my mind...I'd hate to be a bother, but do you think you could try patching me up a bit?"

"I-I'll give it a try." she replied, uneasily.

It wasn't long until her horn lit up once more as a warm sensation engulfed The Doctor's entire body as the cuts sealed themselves shut, his vision returned to normal, and the strain on his muscles seemed to melt away. And for the first time, he saw the inside of the library in great detail once his eyes returned to their original focus. What was so fascinating about it was the fact that the tree itself was the library and quite a bit larger on the inside than the mass on the outside would have led one to believe.

'Almost like the TARDIS' he mused to himself.

"Why do you need Rainbow Dash?" asked Twilight.

"I don't know." he admitted. "It's like there's been a subconcious message implanted in my head, but it feels very old-something about this whole situation must have triggered it."

"Well, I'm sorry but, I'm not sure if Rainbow will help-even if I ask for it."

"Why not?" he asked. "Isn't she your friend? Your...uh, lady friend?"

"She was." Twilight replied sadly. "I'm not so sure now, though. We had a big fight earlier and she took off somewhere-probably back to her home in Cloudsdale so she could blow off some steam."

"I still don't think there's any harm in asking." he replied. "Why don't you fly up to Cloudsdale and have a talk with her?"

"All right..." she sighed. "Will you be alright alone here for a while with Spike?"

"Who?" he asked, confused.

"Spike, he's a baby dragon and my assitant-he's a pretty heavy sleeper." she explained. "But, I thought you should know on the off chance that he wakes up before I get back."

Twilight was heading towards the door before she stopped and slapped a hoof over her forehead.

"What's wrong?" asked the concered Doctor.

"I don't need to fly!" she exclaimed, excitedly. "Now that I have wings, I can transport myself to Cloudsdale without casting a Cloud-Walking spell! Isn't that great!?"

Before the Doctor could respond, her horn briefly illuminated a split-second before she teleported herself away.

Twilight reappeared at the front door of Rainbow Dash's large cloud home. 'But, is it actually a house?' She thought. 'Because since it seems like more of a mansion. But, then how could she possibly afford something like this? Perhaps it was a perk given to her for being Cloudsdale's weather manager? Or maybe her parents had given it to her as a sort of gift?'

She hated it when her thoughts wandered like this, it only happen when she was under an unbelievable amount of stress. It felt strange, trying to gather the words to make up with Rainbow Dash after they had their first real fight during their time spent as a couple a mere hour ago. The whole fight still made her feel guilty with the way she had rejected Dash's request-she really did understand her friends anger and felt that it was totally justified.

Maybe if she caved and decided to write the stupid letter, Rainbow would forgive her and she could possibly salvage their relationship. But, was it worth compromising her beliefs simply to do her marefriend a favor? And even if she sent the letter, what would happen then? Would she leave Ponyville, Scootaloo, and herself behind to tour with the Wonderbolts?

Twilight took a deep breath before knocking on Rainbow Dash's door and it wasn't long before the Pegasus herself answered the door.

"Twilight!?" she exclaimed, upon seeing her Alicorn marefriend standing there before her. "What do you want?" she asked, her voice sounding more tired than agitated.

"Rainbow Dash...I know that this is going to sound strange, but there's a stallion that showed up at the library...he looked like he was hurt pretty bad and he said that he needed to speak with you..."

"Wait, wait, wait, wait." Dash held up a hoof, stopping her. "Where is this guy now?"

"He's...still at the library."

"YOU LET A STRANGE STALLION INTO THE LIBRARY AND LEFT HIM THERE COMPLETELY UNGUARDED!?" Dash shouted.

"Spike is there..." Twilight replied, defensively.

"YOU LEFT SPIKE ALONE WITH A STALLION THAT'S A COMPLETE STRANGER WHO MIGHT BE DANGEROUS!?" she shouted, even louder this time.

"Well...he is a little strange." Twilight conceded. "But, he's not dangerous...at least, I don't think he is."

"Twi..." she sighed, massaging the area between her eyes with a hoof. "I'll go with you...but, I don't want to leave Scootaloo behind in case anything happens."

And Twilight always accused her of being the reckless one.

Dash then gestured for Twilight to follow her inside, the further they got, the more certain she became that Rainbow Dash's house actually was a mansion and briefly wondered how much a place like this had cost. But, with the artistic style of the homes design it was definitely expensive. Did being the weather manager really pay that much? That would explain how she was able to get her hooves on tickets to the Wonderbolts shows just about every month.

The home's interior actually felt quite soothing, which made sense in a way since it was literally like living in a cloud. But, it looked surprisingly like an Earth Pony or Unicorn home with carpet, walls, photos of friends and a rainbow-maned stallion with golden eyes, who Twilight could only assume was Rainbow's father. And of course, being Rainbow Dash's house there were multiple Wonderbolt posters of their leader; Spitfire, the second in command; Soarin...and while neither of them had ever seriously commented on it, Rainbow Dash had told her that she and many other fans were certain that the two had a thing. And of course, there was the less popular; Fleetfoot.

She remembered how Rainbow Dash had given her an entire lecture on how Fleetfoot was considered the underdog of the group, since she had started off doing hoof races with others as she was a late flier because her wings didn't develop properly after she was born and her smaller stature gave her less wind resistance while galloping or flying. Spectators (especially those who had bet money) on Wonderbolt races were always shocked (and slightly irritated) but, to her it had made perfect sense. For someone that so often made fun of her for being an 'egghead'-Dash had an impressive amount of insight into Pegasi anatomy and the scientific when it came to athletics.

Twilight followed her up a staircase to Scootaloo's bedroom. Inside, there were posters of Rainbow Dash and a pictures of Scootaloo with the Cutie Mark Crusaders at Sweet Apple Acres and in costume at the school talent show. There was also a photo of Rainbow Dash holding Scootaloo in a headlock, while playfully giving her a noogie as she smiled at the camera with one eye squeezed shut from the pressure of Dash's hoof in her mane.

The heartwarming nature of the photo had helped relieve some of the stress Twilight was feeling. As tough as Dash seemed on the outside, she still always cared about her friends. Besides, she was the Element of Loyalty and seemed more than willing to help out with...whatever was going on.

Scootaloo's bed was identical to Rainbow Dash's albeit, slightly smaller. The blanket was a sky blue with an image resembling her idol's Cutie Mark; a cloud emitting a lightning bolt made up entirely of primary colors. Beneath it, the filly was sleeping peacefully.

Rainbow Dash gently shook her awake with a hoof before she wearily opened her eyes and sat up, rubbing some grit out of her eye.

"Mmh...Rainbow Dash, what's going on?" she asked. "It's still night time."

"We're going on a litte trip, okay Squirt?" she asked rhetorically as she picked the filly up as she wrapped her arms around Rainbow Dash's neck for support.

"I can take all of us back to the library with a teleportation spell." Twilight explained. "I think that will be easier than flying all of the way down to Ponyville with a passenger in tow."

"Yeah," Dash agreed. "And if this guy really is some kind of lunatic and tries something...we'll want to be at the top of our game."

"Okay...everypony ready?" she asked, the tip of her horn lighting up. Rainbow Dash nodded. While, Scootaloo seemed to have fallen back to sleep.

A split-second later they were standing in the center of the library, where The Doctor appeared to be sitting in the exact same spot Twilight had left him.

"She can have my bed, upstairs."

"Thanks, Twi."

Twilight followed Rainbow Dash up the staircase, when they reached Spike and Twilight's room. The baby dragon was sleeping in a basket at the foot of Twilight's bed, snoring loudly. Rainbow Dash put Scootaloo down to rest before pulling the celestial patterned sheets over the young filly.

"I'm not sure about this guy." Dash whispered to Twilight. "But, it wouldn't feel right to leave Scoot home alone..."

Twilight nodded in understanding as the two mares headed back downstairs to speak with the mysterious stallion.

"I'm sorry that took so long, Doctor." apologized Twilight.

"Oh, that's quite alright." he replied, brushing it off. "And I see you've brought Rainbow Dash with you as well...good."

"So are you gonna tell us what's going on?" Dash challenged, hovering in the air with her arms crossed.

"In time." he replied "But, first we need to reach Princess Celestia in Canterlot and I promise to explain everything there."

"Alright." Twilight conceded. "Just give us a second to let Spike and Scootaloo know what's going on, so they don't panic if we're not back by morning."

"Oh, I doubt that will be a problem." the stallion replied confidently.

"What's that supposed to mean?" Dash demanded.

"Follow me," he instructed as head stood up and headed towards the library door.

The mares behind him exchanged glances before reluctantly complying with his request.

"I don't like this." Dash whispered to her marefriend. "We know nothing about this guy and he's already telling us what to do...he might be leading us into some kind of trap."

"That's definitely a possibility." agreed Twilight. "But, we don't know that yet for sure...besides, aren't you the least bit curious who he is or where he came from?"

"Yeah." She admitted. "But, I'd rather not take any chances..."

Their conversation was cut short as The Doctor came to an abrupt halt before what appeared to be a wooden blue box. Despite the shroud of darkness that had enveloped them in the starless night, they could still make out the words; 'POLICE PUBLIC CALL BOX'. Rainbow Dash gave Twilight a look that was a non-verbal way of asking what in Tartarus that was. The Alicorn could only shrug in response.

The Doctor pulled out a silver key with his mouth before inserting it into the lock and turning it (with some difficulty) and pushing the door open slightly with his head.

"Sorry," he apologized. "I'm just not used to this new form, quite yet."

Twilight was about to ask what he meant by that before the thought was cut short by Rainbow Dash.

"So this is what you wanted to show us?" she demanded, irritation growing. "A blue outhouse with random words painted on it?"

Instead of responding with anger like Twilight expected, he merely chuckled and gestured for the couple to follow him inside. Rainbow Dash became even more skeptical of an odd stallion luring two mares into a secluded area, alone, in the middle of the night. While, Twilight was more focused on trying to figure out how three grown ponies would fit into a wooden box of moderate proportions.

Once stepping inside, Rainbow Dash was immediately reminded of the device Flim and Flam had used to make their cider with a large glass tube in the center of a large room with turqouise energy coursing through it.

Twilight, on the other hand. Was amazed by how large and complex the interior was in stark contrast to it's simplistic outward appearance. Even with all of her intelligence and nights of endless study, she still found the dimensions of this...thing difficult to comprehend.

"It's bigger in here..." She commented dumbly.

Around the glass cylindrical tube was what appeared to be a control panel filled with various buttons, levers, knobs, and switches. The room around theme seemed to be built from some kind of chrome decorated in a bronze color and the ceiling appeared to be far taller than the maximum height of the blue box they had entered through. It also felt like they were standing on some kind of steel grate.

"Doctor..." Twilight began, finally getting her bearings. "What exactly is this?"

The TARDIS

"This is the TARDIS." The Doctor explained. "T-A-R-D-I-S. That's Time And Relative Dimensions In Space-it's how I get around."

"But, what is it?" Twilight pressed, still confused.

"It's my ship...and when convenient, time machine, library, medical bay-" but, Twilight's ears perked up at the word 'library' and tuned everything else out.

"Did you say library?" she asked, excitedly.

"Yes, but I'm afraid the tour will have to wait..." he replied, trotting over to the control panel where he pulled a few levers.

"What did you mean by 'ship'?" asked Rainbow Dash, suspiciously while thinking of the bizarre science fiction novels that Twilight was always trying to get her to read.

"And what did you mean by 'this form'?" Twilight added, remembering his comment from earlier.

The Doctor stopped fiddling with the control panel before sighing.

"All right, this may come as a shock to you...but, despite my outward appearance-I am not a pony."

"Then what are you?" Dash challenged, raising an eyebrow skeptically.

"I am an alien...a Time Lord to be more precise, from the planet Gallifrey." he explained.

Rainbow Dash and Twilight could only stare at him in awe. If this whole thing was an elaborate prank, Rainbow had to give him props for keeping a straight face for this long. Twilight on the other hand, seemed completely fascinated by the 'Doctor's' claims.

"Anything else you'd like to share?" Dash pressed, fearing what the answer might be.

"Ah...yes, I've been around for centuries, I have two hearts, and I hate pears."

'Yeah, he's flipped.' Dash thought to herself, while giving Twilight a look to convey this message to her.

"So this isn't your real form?" Twilight asked, her studious nature getting the better of her.

"Well...yes and no." he replied, thoughtfully. "You see...my physical body used to represent a race of sentient beings entirely, after my regeneration however, I found that my body had regenerated into that of an equine."

Rainbow Dash rolled her eyes, she could hardly believe Twi was buying this.

"How does that work?" she interjected.

"Well, the simplest way I can think to put it is like a snake shedding it's skin." he replied.

"When a Time Lord regenerates, we usually only do so if we've been mortally wounded and it's how are bodies compensate with such injuries." he explained. "I'm still me-with all of my memories and experiences intact, but my skill sets are randomized. For example; I may have previously been gifted in sports and athletics in a previous form, but the next form may forfeit those abilities in favor of more artistic attributes."

"Yeah..." Rainbow Dash began nervously while backing away slowly. "Why do you need us again?"

"Oh, yes...I was getting distracted." he muttered to himself before returning to the control panel. "Next stop; Canterlot!" he exclaimed.

Once again, Dash glanced over nervously at Twilight who smiled back at her. She wasn't sure what she was feeling so upset about, she was the fastest (and strongest) flier in Equestria. And with her newfound Alicorn powers, Twilight was now practically a demi-god so they could more than handle one crazed stallion, right?

"HOLD ON!!" The Doctor shouted.

The machine seemed to begin shaking as a strange noise filled the room and the turqouise lighted tube began flashing, as smaller cylindrical objects inside of it began pistoning up and down.

Even the powerful Alicorn had difficulty keeping her balance as this went on, Rainbow Dash was flung backwards and almost slammed her back against the wall before being caught at the last second with Twilight's magic.

She whispered a "Thanks" before everything stopped.

"What happened?" she asked, looking around.

"We've arrived." The Doctor replied with a smirk.

Twilight gazed back at the doorway with uncertainty.

"Go ahead." he encouraged her. "It's quite safe, I assure you."

She took a deep breath as she pushed the door open and placed a hoof down outside.

Looking around, she realized that it was just as The Doctor had said earlier. They were in Canterlot in the middle of the night, she glanced up at the clock tower to see that it was literally only minutes ago that they had been back in the library. It was almost as if the trip had been instantaneous.

Rainbow Dash came up behind her, as similar thoughts ran through her head. But, just because this 'Doctor' had been telling the truth about one thing didn't necessarily mean he could be trusted. Why did he want to come here to Canterlot before telling them what was really going on? And if what he needed them for was really so important, wouldn't Celestia have told them about it herself?

"Come along, now." The Doctor's voice could be heard from behind them. "We've wasted far too much time already."

"But, Doctor...you never told us where we're supposed to be going." Twilight reminded him.

"Oh, didn't I? Well...we need to get inside the castle to speak with Princess Celestia and I will explain everything there, I promise you." he replied before galloping on ahead.

Twilight, ignoring her wings-cantered along the streets at a steady pace despite the apparent 'urgency' of The Doctor's task-whatever that might be. She also noticed Rainbow Dash was deep in thought about something. Normally she'd poke fun at it, but this seemed serious.

"Something wrong, Rainbow?" she asked, softly.

"Yeah," she crossed her arms. "This guy's an Earth Pony, so how can use magic to travel through time and teleport places with that weird box thing?"

"It's not magic." Twilight explained patiently. "It's science and technology...very impressive actually, I've never seen anything like it."

"And do you really believe that he's an alien?" Dash challenged.

"Well...I'm not really sure." Twilight admitted. "I mean, I was skeptical at first, but there's no other technology like that in the entire world. Wouldn't it make sense that he's not from around here?"

"Fair enough." The pegasus grumbled.

"But, what about sneaking into Canterlot in the middle of the night with two of the Elements of Harmony-and one is the personal student of Princess Celestia?" she pressed.

"What's so suspicious about that?" Twilight wondered aloud.

"Exactly!" Rainbow practically shouted. "It's the perfect way to avoid suspicion and then...when we least expect it, he'll probably turn out to be a spy or something to try and assassinate the princesses or take over Canterlot!"

The young Alicorn was about to brush the sentiment off as being ridiculous, but it made a certain kind of sense, after all nobody but her suspected Cadence, once Chrysalis had taken her place.

"All right." Twilight conceded.

"We'll keep on eye on him, if he doesn't do anything suspicious then he's been telling the truth."

"But, if he does?" Dash pressed.

"Then we interrogate him, find out what he knows, what he's been hiding from us and what he's really planning." she replied darkly.

Much like her marefriend, Twilight's loyalty to the princesses was unquestionable and if anyone dared to insult or try to harm them, that was when she lost her temper.

Even under the cloudy night sky, the city seemed to shimmer with regality often causing her to wonder as a young unicorn if there was a special material or enchantement used to build the royal city.

Or maybe it was just a part of its natural allure?

She made a mental note to herself to look it up once she was back in the library.

They stopped before the castle gates, which were guarded by a white pegasus and black unicorn stallion.

"Halt." commanded the pegasus as The Doctor approached them. "State your name and business."

"Ah, yes..." he replied, pulling out what had appeared to be a wallet with his teeth and showed it to the guards with a muffled response. "I'm dah Doctah, I fink you'll find everyfin' you need right here."

The Pegasus examined it for a moment before responding.

"Everything appears to be in order. Sorry for the inconveniance, sir."

He then put the wallet away as the guard let him inside.

"Hold on." The unicorn guard stopped them. "There's two more coming."

As they saw the figures come more into focus the two guards straightened up and offered a salute.

"Princess Twilight!" They exclaimed in unison.

"I hate it when they call me that." Twilight muttered under her breath.

"A-apologies, but we weren't told to expect you here tonight." The unicorn explained.

"That's alright, I'm kind of here on short notice..."

Both guard's eyes darted to the rainbow maned pegasus hovering beside her.

"Who's this?" The pegasus guard asked.

"This is Rainbow Dash." Twilight introduced her. "She's my 'plus one'."

Dash shot her an annoyed look, which she could only shrug at and smile sheepishly.

They gestured for them to go inside.

""Plus one?'" Dash repeated. "I help save Equestria four times and those jerks don't even recognize me?"

She crossed her arms as she continued to gripe.

"That's gratitude, for ya."

As they followed The Doctor towards the throne room, Princess Celestia could be seen with a quill and roll of parchment levitating before her.

"Shouldn't you be resting, princess?" asked Twilight. "You look exhausted."

It was true, her normally regal appearance was somewhat diminished as dark circles could be seen forming under her eyes.

"Yes, Twilight." she replied, calmly. "However, recent events have caused much stress and tonight I suspect something terrible as happened, as is customary when you show up Doctor-no offense."

"None take." he replied, waving a hoof dismissively.

"Wait, you mean you know this guy?" Dash asked, taken off-guard.

"Yes, but I'm afraid it's a long and complicated story." The sun princess replied before turning back to The Doctor. "Now, Doctor-if you would be so kind as to fill us in."

The stallion stepped forward, clearing his throat.

"Princess Celestia...once Discord was released from his stone prison the first time, what do you remember after sending Twilight and her friends to retrieve the Elements of Harmony?"

"I...I can't remember a thing!" she exclaimed. "It's all a dark void..."

"Which means your memories are being rewritten..." he mumbled.

"And what's that supposed to mean?" Dash demanded.

"Once Discord successfully pitted you and your friends against each other, he was confident that he had secured his victory." he explained. "So much so in fact, that he transported Celestia through time-this time."

"So?" Dash pressed. "That's good, right?"

"No."

"What?"

"A being like Discord, probably didn't contemplate the consequences of his actions-normally two of the same beings can co-exist without a problem." he elaborated. "But, when that being is as powerful as Celestia-time and reality can become distorted to the point where the fabric of this world begins to rip apart."

"But, that hasn't happened yet?" Twilight suggested, hopefully.

"No, but the longer two Princess Celestias inhabit this time period-the greater the possibility will become."

A Royal Apology

"So do we why don't we go get her then?" asked Dash.

"Because we don't know where she is." The Doctor replied, rubbing his face with a hoof. "Wait...that's it!"

"What's it?" asked Twilight.

"A Locating spell!" he exclaimed excitedly.

"I'm not sure I follow..." began a very confused Twilight. "Wouldn't it just lead us back here to our Princess Celestia?"

"If it was cast by anyone else, then that would be the case." he turned around to face the princess. "I know you're feeling weak, but if you could just try casting a spell to locate your past self..."

"I'll try..." she replied, before closing her eyes and with some noticeable effort her horn began to glow with its golden aura.

Almost as quickly as it had been cast, the spell faded as Celestia collapsed back onto her throne.

"PRINCESS CELESTIA!!" The two mares shouted in unison, rushing to her side.

"I...I'm fine." she insisted. "I just need to rest and I'll be alright..."

"Do you know where she is?" asked The Doctor.

"Yes...in the caves beneath Canterlot." she replied. "Doctor...Rainbow Dash...I would like to speak to Twilight in private for a few moments."

The two exchanged glances.

"All right, we'll be outside if you need us." Rainbow Dash assured her before they went outside.

Once the door closed Celestia returned her gaze to her faithful student.

"Twilight, I...I'm so sorry."

The younger Alicorn's ears perked up.

"What?"

"Not long after I took you under my wing as my student, I began to see you as something more...like a daughter." she explained, choosing her words carefully. "When you gained this newfound power...I was afraid it would corrupt you."

"Like Princess Luna?" she finished. "But, I don't have any anger or jealousy in my heart..."

"Neither did my sister, at first." Celestia replied, sadly. "It took centuries, but those feelings festered and boiled within her heart-to the point where I couldn't save her and had no choice-but, to exile my own blood to the moon for the safety of Equestria."

"Why are you telling me this?"

"Because I want you to understand that the only reason I was being so selfish was because I had convinced myself that the only way to avoid more heartache was to control you...I knew that your royal duties would pull you away from your friends and in time you would begin to resent me for saddling you with this burden."

Twilight remained silent as her teacher spoke.

"For many centuries it has been believed that our destinies are assigned to us at birth and they are only revealed to us once we've earned our Cutie Marks..."

"But?" prompted Twilight.

"But, now because of you-my faithful student-after what you said to me that night, I am beginning to believe that they merely guide us to the right path...why else would thieves, murderers, and tyrants exist in ponykind?"

The younger Alicorn could only stare blankly at her.

"I have come to the conclusion that despite whatever a pony's Cutie Mark is telling them, they still retain their free will as I've yet to see a natural one representing such atrocities." she explained.

"Despite all of my years, I am far from infallible as you have seen for yourself...and even if you can't find it in you heart to forgive me-I hope that at the very least you'll understand."

"I do understand, Princess." replied Twilight. "And I do forgive you...I'm sorry too for the way I yelled at you-but at the time I felt it was totally justified."

Celestia nodded in understanding.

"I am glad that we had this talk, Twilight...but, time is running out for all of us...you should return to The Doctor and Rainbow Dash to see if they have any other leads."

“What about you?”

“Now that my fears have been alleviated, I will rest.”

“You’re not coming with us?” Twilight asked, slightly disappointed.

“Nothing would make me happier.” Celestia replied, smiling warmly. “But, I’m afraid the spell I cast earlier drained most of my remaining strength and I require rest…besides, if my doppelganger saw me-or if were even in the same proximity to one another the results could be even more disastrous than the effects of Discord’s magic on its own.”

She then draped a wing around Twilight.

“When you completed Starswirl the Bearded’s unfinished spell, I told you how proud of you I was…and I still am.”

Celestia then looked down at Twilight still smiling, but with a hint of sadness in her eyes.

“After taking you on as my student, you’ve become like a daughter to me-and I’ve grown to love you as such.”

“Now,” she continued releasing Twilight. “Go. I have the utmost faith in you and The Doctor to set this right.”

“Thank you, Princess.” She replied before heading back outside to meet up with Rainbow Dash and The Doctor.

Shining Armor

"So what was that thing you showed the guard earlier?" asked Dash.

"Psychic Paper-it shows someone whatever message or form of identification I want-makes it easy for getting in and out of high-security buildings like this one, quickly." The Doctor explained.

"Then why didn't you just tell them that you knew the Princess?" She challenged, cocking an eyebrow.

"Because it saves time!" he exclaimed. "It's like I didn't just finish explaining it you!"

Rainbow Dash looked back at the large doors to the entrance of the structure behind them with the two ponies who had been standing guard, once again resuming their posts.

"If time is really that valuable, then why are we just standing around here while they're inside talking?" she wondered aloud. "What could be so important?"

"I don't know." The Doctor admitted. "But, whatever it is...Celestia must think it's very important if she's willing to put something as risky as this on hold."

Dash then shuddered as she felt a cold chill run down her spine before wrapping her arms around herself to keep warm.

"Why's it so cold out?" she asked.

"Because it's night." he replied. "Isn't that typically what happens when the sun goes down-even on this world?"

"Well...yeah, but in the middle of summer?" she pressed.

"I don't know...aren't you supposed to be the weather pony?" he retorted.

"And that still doesn't explain all of the missing ponies...even when it's this late I was always told the city was very loud and busy, but instead..."

"It's like a ghost town." he finished as a realization dawned on him.

"What is it? What's wrong? You know what's going on?" she asked, once she saw the look of horror on his face.

"I have a few ideas..." he answered, composing himself. "And none of them good."

A distant sound came to their ears, galloping and it was getting louder by the second. The two guards also seemed to have hear it as they prepared their spears for a possible assault from the invader. The moon seemed to decide to come out from its cloud cover as it's light shone on some of the material the approaching figure was wearing.

"It looks kinda like armor..." Rainbow Dash commented, squinting in the distance.

"A returning patrol, maybe?" suggested The Doctor.

"All patrols have already checked in." grunted the Pegasus guard.

"Who goes there?" The Unicorn demanded.

The figure then came skidding to a halt.

"It's okay guys!" Shining Armor called out. "I just came to speak with the Princess."

"Prince Shining Armor!" Both guards exclaimed in unison before lowering their weapons and saluting him.

"It's okay guys...relax." he then noticed a certain Pegasus waiting outside.

"Rainbow Dash!" he exclaimed, trotting over to her. "How's Twily?"

"She's inside, speaking with Celestia."

It was at this point he noticed the stallion beside her with the image of an hourglass on his flank.

"Who's your friend?"

"I'm The Doctor." he introduced himself.

Shining Armor frowned.

"Doctor Who?"

"Just The Doctor." he replied, smiling cheerfully.

"Is he your boyfriend?" Shining Armor asked Rainbow Dash who began scratching the back of her mane with a hoof.

"Um, no...Actually about that..."

"SHINING ARMOR!"

They trio turned to see Twilight galloping towards them before throwing her arms around her brother, nearly tackling him to the ground.

"Ooph, Twily!" he managed to choke out.

"What are you doing here?" Twilight asked, releasing him the bone-crushing hug.

"Well, every month we usually send a status report to Princess Celestia, but Cadance thinks I've been working to hard so she asked me...well, ordered me to deliver the message in person before seeing you." he explained, scratching the back of his mane nervously.

Before Twilight could respond The Doctor cut in.

"Sorry to interrupt, but we've got kind of an emergency on our hands-we'll walk and talk...Allons-y!" he exclaimed before galloping back towards the TARDIS.

"What!?" shouted Rainbow Dash, flying behind him.

"Its French-it means 'Let's Go!'" he shouted back.

"Then why didn't you just say that?" retorted the annoyed Pegasus.

The two siblings were behind them, Rainbow Dash wondered if Twilight neglected to use her wings because she forgot about them or if she wanted to stay at the same pace as her brother.

"So Cadance had to order you to leave the Crystal Empire!?" asked the shocked Alicorn.

"Yeah...but, not because I didn't want to see you!" he added defensively. "By leaving Cadance behind to look after the Empire herself I felt like I'd be..."

"Abandoning her and shirking your royal duties?" she offered.

"Yeah...despite what we thought as kids being royalty is no picnic, y'know?"

"Boy, do I..." she muttered.

"Whoa!" Shining Armor skidded to a halt before the TARDIS as The Doctor produced a silver key, which he once again used to unlock the door.

Reluctantly, he followed the trio into the small wooden box after seeing that they weren't all crammed inside.

Once inside the strange box, Shining Armor's confusion only grew as he looked around the impossibly large room which actually seemed to be part of a larger machine.

"What is this thing?"

Secrets

While Twilight got her brother up to speed on everything that had happened to them, The Doctor began fiddling with the round control panel which encircled the large glowing green tube jutting out from the center of the room.

"But, why are we using this thing to get underground?" asked Dash. "Aren't we already in Canterlot?"

"Yes." The Doctor replied. "But, after the Changeling invasion last year-Princess Luna had personally sealed off all of the tunnels and secret passages had been installed in the castle in the hopes avoiding a future crisis from the creatures."

He then looked sternly at the other three.

"I hope none of you are claustrophobic.” He commented before pulling a lever.

Once again, there was that odd noise as the TARDIS began shaking.

“What’s going on?” asked a slightly panicked Shining Armor.

“Relax, this is all completely normal.” The Doctor assured him.

After a few moments the TARDIS seemed to have settled itself.

“I’ll go outside first.” The Doctor announced before pulling out what appeared to be a small metallic instrument with a blue node at the tip.

“What’s that?” inquired Rainbow Dash.

“Sonic Screwdriver.” He replied, nonchalantly before trotting outside.

Shining Armor was about to follow suit before he was stopped by his little sister’s hoof blocking his path.

“Sorry, BBBFF…but, there’s still one more thing we need to tell you…”

“There is?” asked a confused Rainbow Dash.

“Yes…Shining Armor we’re….Rainbow Dash is my special somepony…” she admitted, fearing the worst.

Ever since her fillyhood, keeping secrets from Shining Armor was something that she had never done and while she trusted him, all too often had she heard stories about mares revealing their sexuality and relationships with their marefriends before being shunned by their previously loving families.

The two siblings were always very close and she feared that if he didn’t accept her, then neither would their parents.

Her brother’s expression was unreadable and the silence that accompanied it did nothing to alleviate her fears.

He glanced over at Rainbow Dash, who was grinning sheepishly as a few small droplets of sweat fell from her forehead.

Finally, he spoke.

“Well, that was definitely a surprise…”

Twilight’s face fell as Rainbow Dash’s ears flattened.

“But, I am glad that you’ve found a special somepony that cares about you.” He continued.

In a way this was a relief, he was always protective of his sister and most of the other stallions he knew in Canterlot were the exact type of ponies he secretly hoped she stayed away from, which didn’t seem like it would be a problem at the time considering her disinterest in social interaction and focus on studies.

Of course, the more he thought about it-the more sense it made.

For just about all of recorded history, Equstria’s gender ratio had been ten to one with mares largely outnumbering the stallions.

The Doctor’s head popped back through the doorway.

“Something wrong?” he asked.

“No,” replied Shining Armor. “My sister and I were just talking.”

“Well, you talk while we explore the cavern-we’ve got a world to save!” he exclaimed.

“Allons-y!”

The trio followed him out of the TARDIS, where there was indeed a large, dark cavern.

“How’re we going to find Princess Celestia, if we can’t even see our own hooves in front of our faces?” complained Rainbow Dash.

The Doctor was about to once again reach for his Sonic Screwdriver when, almost as if on cue-the walls began to glow a dull green which seemed to be emanating from veins embedded within the rock.

The tunnel they were in also seemed to have a path carved leading to a larger area that seemed to be glowing a very bright shade of green, in stark contrast to their current location.

“Well, that’s certainly peculiar.” He commented.

“Its magical energy,” observed Twilight, “…And not the good kind.”

“What do you mean by that, Twily?” asked a concerned Shining Armor.

“I’ve only seen this particular type of magical energy used by one species.” She explained.

“Who?” pressed Dash.

“…Changelings.”

Lies

Moments after Twilight’s realization, almost as if on cue-the underground came to life with the seemingly endless stream of chitinous life bursting forth from the walls of this makeshift hive-surrounding the group.

“What are we going to do, Doctor?” asked Twilight.

“We fight,” replied Rainbow Dash.

“I could cast a Shielding spell…” suggested Shining Armor.

“No,” whispered The Doctor. “We surrender.”

“WHAT!?” exclaimed the trio in unison.

“But, Doctor!” protested Twilight.

“Listen,” he whispered. “This is the best way for us to find Celestia, they obviously have her captive, but we need to find out where.”

He leaned in close to her ear and whispered a set of instructions as the army of Changelings advanced on the group.

As they got closer, the group stumbled into unconsciousness.

They were in a circular room built from stone with glowing green veins, presumably filled with magical energy coursing through them.

The Doctor awoke first, standing there before him was a large equine form which appeared to be a mix between an Alicorn and some form of insect with a tail and mane that seemed to be made of gossamer with two large viper-like fangs and green eyes with a crown resting atop her jagged, black horn.

The majority of the room’s illumination appeared to be emanating from a different source however, as he looked up to see a large green chrysalis hanging from the ceiling with the same eerie glow.

Squinting up at it, The Doctor could see that inside of it seemed to reside an unconscious Princess Celestia.

Directly across from him and behind Queen Chrysalis was Rainbow Dash, to her left and right were Twilight and Shining Armor respectively, all bound to the wall with an odd mucus-like substance he had never seen before.

“So…where are we?” asked The Doctor casually, as if he were talking to someone off the street about the weather.

“In a hive?” he pressed, observing their surroundings. “Colony?”

“…Conglomeration?” he added, noting the holes in the walls that the Changelings had emerged from earlier.

“You are in my domain-and that’s all that matters.” She replied proudly before turning to face Twilight.

“And oh, look! If it isn’t my old nemesis; Twilight Sparkle!”

This earned her a glower from the young Alicorn.

“I’m sorry…Princess Twilight Sparkle.” She corrected herself, lifting her chin up to meet her.

“Not that it really matters-even your beloved teacher was no match for me as I proved during our siege on Canterlot.”

“You mean with the energy that you stole?” Twilight retorted.

“Yeah!” Rainbow Dash cut in. “You only won because you cheated-it wasn’t a fair fight!”

“All’s fair in love and war.” She replied coolly, not taking her eyes off Twilight. “Nobody knows that better than the Changelings.”

“By hiding and stealing emotions for others?” Shining Armor retorted, “Sounds pretty cowardly if you ask me…but I guess that’s to be expected from a group of parasites.”

“Shining Armor…” she replied as a sly grin spread across her face and her eyes moved to meet his.

“I’m curious-have you told your beloved bride of that magical night we spent together before our wedding day?” she asked.

The stallion felt his blood run cold as the questioning stares of his little sister and her marefriend turned to meet him.

“I…I…” he stammered, searching for the right words to convey his feelings and reasons for not telling her-but, being put on the spot like this with his darkest secret revealed and the horrified expression of his sister gave him a newfound sense of hatred for the changeling queen.

Satisfied the distrust she had planted between the two siblings she then turned to Rainbow Dash.

“And then there’s you…you look familiar, but I can’t seem to recall your name-not that it matters anyway-as I recall; you were one of Twilight’s friends and that’s all the justification I need to drain you until your nothing but an emotionless husk.”

Before an alarmed Twilight could vocalize her objection there was a lapping sound coming from the opposite end of the room causing Chrysalis to turn around, facing The Doctor.

“What are you doing?” she demanded.

A trail of the glowing green slime from the binding connected to the tip of his tongue.

“Analyzing the substance so I can identify its makeup.” He replied matter-of-factly.

The frown that spread across the Queen’s face signified that she was not amused by The Doctor’s antics.

“Which reminds me…”

Her jagged black horn began to glow with the same eerie green aura as she levitated the Sonic Screwdriver before him.

“What…is this?” she asked, eyeing it suspiciously as if she were afraid that it was some sort of explosive device.

“Some kind of flashlight?” she guessed, noting the blue node at the end.

“Oh, tatsh mah Shonic Scroodahver.” He replied through a mouthful of the substance.

“Don’t eat it!” exclaimed Rainbow Dash.

“Yeah, you have no idea where it’s been or where it came from!” Twilight agreed in protest.

“It’s actually really good,” he replied, swallowing it. “A lot like green gelatin.”

“STOP EATING YOUR PRISON!” demanded the Changeling Queen, stomping her hoof for emphasis.

“Oh, sorry…” he apologized. “As I was saying; that’s me Sonic Screwdriver-careful with it-you’ll poke your eye out.”

“What does it do?” she asked, examining the object with a frown.

“Oh, all sorts of things…for example it’s fantastic as a power amplification device.” He replied cheerfully.

“Power Amplification Device?” she repeated quizzically.

“Yeah, I show you…just point the blue end at your horn and press the button on the side.”

She did as instructed, but instead of a vast power surge, green spark burst from her horn as a searing pain surged down it and into her skull, cutting off her magic as the Screwdriver was dropped to the ground and all of her prisoners were simultaneously released.

“NOW!” The Doctor shouted as Celestia fell from the ceiling, Rainbow Dash and Shining Armor stood guard around Twilight as she helped her teacher back to her hooves.

“Twilight…what’s going on?” asked a dazed a Celestia.

“There’s no time to explain, princess-but, you need to come with us right now!” her student replied frantically.

The quartet then began heading through the tunnel from earlier in an attempt to reach the TARDIS as Changelings began filing in behind them.

Shining Armor who was bringing up the rear cast and shield spell to prevent the changelings following from behind, but there were others dropping from the ceiling and holes in the walls ahead of them.

Twilight began zapping the Changeling ahead of them with magical blasts from her horn and Rainbow Dash was covered in the ones that dropped from the ceiling in mid-flight, she slammed against one of the cave walls to scrape them off.

Soon, a familiar blue box came into view.

“Everyone inside!” shouted Twilight as she levitated the key that The Doctor gave her into to the lock.

With the other three were behind her Rainbow Dash continued fighting to keep the creatures away from the Princess as Shining Armor worked on generating a force field.

The tip of his horn gave off a few sparks before the magical energy faded from it, he had wasted too much power on the shield from earlier and unfortunately, the Changelings trapped behind it earlier were beginning to realize that they could use the various tunnels to get around the shield instead of trying to force their way through it.

Celestia wanted to help, but all of the energy the creatures had leeched from her earlier still left her weary and on the verge of collapsing.

The key to the TARDIS which Twilight had levitated to its home was shaking slightly as the chaos surrounding the group made it extremely difficult to concentrate and focus her magic on manipulating the small object.

The lack of proper lighting in the gave also made it difficult to see things in detail and the magical aura around the objects Unicorns and Alicorns manipulated only gave off minute amounts of light.

Click.

Finally, the fruits of her labor seemed to have paid off as the TARDIS door swung open.

“Everyone inside, now!” she shouted.

Shining Armor, Celestia, and Rainbow Dash all filed in before the latter slammed the door shut before pressing her back against it in an attempt to keep the creatures out.

“You don’t need to do that, Rainbow,” spoke Twilight. “I think the door only opened for us because we had the key-they can’t get in.”

“What about that Doctor guy?” she asked, sliding to the ground, with the door still at her back.

“How does he get back in?”

“I…I don’t know…” admitted Twilight. “But, I think he has some kind of special connection to this machine, so it might let him in even if he doesn’t have the key…that’s probably why he gave it to me.”

“What about the Changelings still outside?” pressed Shining Armor. “How is he supposed to get past them without letting any of them in?”

“I’ve known The Doctor for a long time,” Celestia cut in, breaking her silence for the first time since she had been released from her prison.

“He’ll find a way.”

Allons-y!

Chrysalis was still writhing in pain as The Doctor spotted the Sonic Screwdriver on the ground a few feet across from him.

He was actually quite surprised, before winding up in Equestria he had thoroughly believed that magic was all just superstition or advanced science that most societies were too primitive and ignorant to even try and understand, but after a while he came to accept that this world worked far differently than any of the others he had ever been to.

The Screwdriver usually only worked like that on other machinery and pieces of technology, rather than organic mass and he actually had no idea if that bit of trickery would work actually work on the Queen or any other magical source for that matter, he had just made the plan up at the last minute, so as not to worry Twilight.

But, for once it actually seemed like everything was going the right way as he slowly crouched down to try and avoid detection from injured Queen’s peripheral vision-which seemed unlikely-as her eyes were screwed shut and she was still flailing around, shrieking obscenities, that he had no idea even existed in Equestria.

In his experience, it was always better to be safe than sorry, but given the state of his current adversary-it seemed like he could risk it.

Breaking into a full gallop, he lowered his mouth to the ground before picking up the Screwdriver, once more lamenting the fact that he no longer had fingers to grip things with and that he would have to once more wipe his saliva from the device once he got back to the TARDIS.

Chrysalis opened her eyes at the sound of the object being picked up, glaring daggers at The Doctor.

“That…give it to me!” she hissed.

He was about to reply before remembering the Screwdriver still in his mouth and put it down before offering his rebuttal.

“Why don’t you wave your magic horn and take it from me?”

This earned a snarl from the irate Changeling Queen.

“Oh, that’s right-you can’t-because it’s broken!” he laughed.

She was about to call for her guards before remembering that she had sent them after those other cretins before a cruel smile spread across her lips.

“I may not be able to harm you,” she realized. “But, my loyal subjects have cornered your friends in that blue box of yours-their fates have been sealed-it’s only a matter of time.”

“Hardly,” he replied, unfazed. “It doesn’t matter how strong they are or even how many of them there are-they’ll never get inside.”

“But, they’re trapped!” she insisted.

“Well, for now…” he conceded. “But, what if I do this?”

He picked up the Sonic Screwdriver once more and pressed a button on the side with his teeth, causing the blue node at the end to light up with a whir.

The cave began shaking as chunks of rock fell from the ceiling.

“WHAT DID YOU DO?” she shrieked.

“That wasn’t me, this is the reason we need to return Celestia to her proper time-a being as powerful as her cannot co-exist in the same timeline without pulling the fabric of the universe apart-there will be more violent tremors like that one if we’re not allowed to leave right now.”

There was an odd sound as a blue object began to materialize behind him, Chrysalis’ eye darted between the appearing object and the stallion trying figure out if the was some trick to cheat them out of their meal or if he was actually telling the truth.

Taking note of the uncertainty in her eyes, The Doctor kept going in an attempt to appeal to her better nature-or instinct for self-preservation if she didn’t have one.

“Right now things like these are happening all over Equestria; Earthquakes, Hurricanes, Tornadoes, Volcanoes-they aren’t natural disasters-they’re the universe ripping itself apart-and everything, everyone will be erased, unless we stop it.”

“NO!” she shrieked before green electrical magical energy fluctuated from different parts of her fractured horn, before shooting a jagged beam at The Doctor before her.

The Doctor picked up the Screwdriver once more before diving towards the door of the now fully materialized TARDIS, which Twilight had flung open.

Catching sight of the emerald green blast at the last moment, without thinking Twilight magically slammed the door shut, she wasn’t sure how powerful The Doctor’s machine was, but given what was at stake-she didn’t want to take any chances.

Once the blast made contact with the box it completely dissipated into a shower of green sparks before the TARDIS began disappearing in the same manner which it had arrived.

Chrysalis tried to charge up a second shot, but only sparks were emitted as she screamed in a mixture of pain the strain persisting to use powerful magic in spite, of the damage done to her horn, and frustration from being outwitted so easily, by an Earth Pony of all things.

That device he carried…and that box…what was that magic?

“Doctor, how did the TARDIS transport like that?” inquired Twilight. “None of us pressed anything!”

“That’s because I made a few modifications to my Sonic Screwdriver before heading off a while ago, losing the TARDIS or having it confiscated has been a bit of a problem in the past, I used the Screwdriver as a point for it to home in on so it could materialize near my location.” He explained.

“But, what if someone else gets that thing?” pressed Shining Armor.

“Well, unless they have a key to the TARDIS or they’re also a Time Lord-it wouldn’t really matter, would it?” he replied, setting the coordinates.

“Where are we going now?” asked Twilight.

“We’re going back to Ponyville, two years in the past.”

He turned to Celestia.

“When we arrive, teleport yourself back to Canterlot and do what you originally planned-the rest of the timeline should straighten itself out.”

“I understand, Doctor.”

“Well then,” he pulled a lever of the TARDIS.

“Allons-y!”

A Choice

As soon as the TARDIS landed, Celestia followed The Doctor’s instructions, magically teleporting herself back to the throne room in Canterlot with a flash of golden-yellow light.

The Doctor then began heading outside before being stopped by Twilight.

“Doctor, where are you going?”

He slowly turned around.

“To speak with Discord, in less than an hour you and your friends will arrive to return him to his stone prison.”

“But, if we’re here now doesn’t that mean you failed to talk him down?”

“Time is more complicated that that besides, I have to try. You and Rainbow Dash remain here in the TARDIS until I return, we narrowly avoided one paradox and we don’t need to risk causing another.”

“What about me?” asked Shining Armor.

“You can stay or go with me-it doesn’t really matter-you were still Captain of the Royal Guard up in Canterlot if I remember correctly, so there’s no risk of you running into yourself.”

He glanced back at Twilight and Rainbow Dash.

“I’ll go with you.” He replied, before following The Doctor out of the TARDIS.

The only time he’d ever seen Discord was as a statue in the castle courtyard outside of the hedge maze and now seemed to be as good a time to satisfy his curiosity as any.

Once the two stallions were gone and she was sure they were out of earshot, Rainbow Dash turned to Twilight.

“Hey, Twi…I uh…” she rubbed arm nervously in the same manner she had the night before.

“I just wanted to say that, I’m sorry about snapping at you…I’ve been doing a lot of thinking and I realized, that it was really selfish of me to ask you a favor like that when you were dealing with your whole ‘becoming an Alicorn princess thing’.”

“I forgive you and I’m sorry, too-you were right that I didn’t want to send that recommendation…but, not because I think I’m better than you!” she quickly added, defensively when Dash gave her a questioning look.

“It’s just that…I know about that old saying about how power can corrupt someone and…I need my friends to keep me grounded an remind me of who I really am, but most of all; I need you-Rainbow Dash-and I was afraid that if you did get accepted into the Wonderbolts you wouldn’t be able to help me through all this.”

The Pegasus placed her hooves on the Alicorn’s shoulders.

“Twi, you know how much being a Wonderbolt means to me…but, I’m not going anywhere as long as you guys need me.”

The Doctor and Shining Armor stood before the draconequus, still sitting in his throne on high, enjoying the world of madness he’d created around him.

“DISCORD!” The Doctor shouted, grabbing his attention.

“Oh, it’s you again…” he grimaced. “Still alive and in one piece I see…a pity.”

“Celestia is back where she belongs and the Elements are on their way…I’m giving you this last chance to see reason and put a stop to this madness.” He continued, ignoring the remark.

“Do you really think I’m stupid enough to fall for such an obvious bluff?” Discord chuckled.

“Doctor…are you sure about this?” asked Shining Armor.

“I have to give him a choice.”

“Ha!” laughed Discord, “And just what kind of choice would that be, hm?”

“The kind that may very well save you from yourself…all you need to do is change all of this back and you won’t have to go back into stone.”

“Surely, you jest.” He replied, draping his serpent-like body of the side of his throne so he was look at Shining Armor and The Doctor upside-down.

“I have no intention of going back to being a glorified lawn ornament, nor do I have any inclination of changing this beautiful work of art…” he gestured, waving a claw to the area around them.

“Well this ‘work of art’ is dangerous! It’s a miracle nobody’s gotten hurt or killed yet!” Shining Armor growled, noting the soapy roads.

“I’m sorry and…who are you again?”

“Shining Armor, former Captain of her majesty’s Royal Guard and prince of the Crystal Empire.” He stated, with a hint of pride in his tone.

“Ah…”

The Doctor stepped forward.

“I’m not sure if you don’t realize the trouble you’re causing for these people or if you just don’t care-but, I will not stand idly by watch innocents be tormented in this manner.”

Discord merely rolled his eyes at this statement.

“I suggest that you take this more seriously as this is your last warning; leave this people alone or what happens next will be your own doing.”

Once again Discord had his eyes rolled as his talon magically transformed into a crude sock puppet of The Doctor which he moved in way that kept it flapping its gums.

When The Doctor finished, the puppet reverted back to his talon before sitting back upright in his throne.

“You know you’re so sanctimonious and preachy you remind me of Celestia…worse than that actually, you’re more look ten of her…so boring.”

This earned a snarl from Shining Armor as he prepared to charge at him before The Doctor held up a hoof signaling him to stop.

“He’s trying to provoke us-don’t give him the satisfaction. Besides, he’ll get what’s coming to him.”

Turning around he began to leave with Shining Armor glaring at the draconequus with a growl before the being simply waved the digits of his lion’s paw at him in a playful, condescending manner before reluctantly following The Doctor back to the TARDIS.

A Storm of Chaos

“So how’d it go?” asked Rainbow Dash as the stallions returned to the TARDIS.

The Doctor shook his head.

“He wouldn’t listen.”

“I’m not surprised.” Dash had crossed her arms and was now hovering in place.

“At least Discord’s reformed in the present…” Twilight offered, hopefully.

“I’m afraid the jury’s still out on that.” He replied, glumly.

“So…what’s the plan?” asked Shining Armor.

“We return to Ponyville in the present; Twilight and Rainbow Dash need to rest and check in on their pets and loved ones, in the morning I’ll take you back to the Crystal Empire with the TARDIS.”

“You mean you’re just going to leave us?” Dash demanded.

“I have a feeling that this is far more than a single time paradox and I’m going to need both you and Twilight to get to the bottom of it, but you won’t be much help if you’re worn out and worried about how things are going at home.”

“But, you know so much more about time travel than us-how could we possibly help solve something like this?” pressed Twilight.

“Yeah,” Dash added. “And I’m not exactly an egghead, either.”

“You two really shouldn’t sell yourselves short-Twilight, your brain is filled with encyclopedic knowledge of dates and historical facts about Equestria which I still know next to nothing about.”

He turned to face the Pegasus.

“And Rainbow Dash, you’re more important than your realize; your fast, strong, and loyal...I can’t think of anyone else more suited to travel with me.”

“But…what about the Elements of Harmony?” protested Twilight. “If Discord begins acting up again…or some other disaster befalls Equestria while we’re gone?”

“I’m sure Fluttershy can handle him,” The Doctor replied confidently. “Celestia can handle just about anything thrown at her and even if they can’t…we have a time machine, remember?”

“And why do think any of what’s happened has anything to do with Rainbow Dash?” demanded Shining Armor as the trio exchanged glances.

“Because I’m a Time Lord, I can feel these things in my bones. I’m not saying that she’s the cause but, she’s definitely connected in some way.”

“Now,” he placed a hoof on a lever of the TARDIS. “As I said earlier, we need to go back to Ponyville and rest up for are next adventure.”

“But, first…” he pulled the lever hurling the machine through time and space.

“Where are we now?” asked Twilight.

“Cloudsdale,” he replied. “Eighty years into the future.”

“Rainbow Dash, come with me.” He ordered.

“But, Doctor!” protested Twilight. “If Rainbow Dash sees or learns anything about her future self, couldn’t it interfere with the timeline?”

“Yes,” he acknowledged. “But, this is a very special case and I know she won’t believe me until she sees this for herself.”

“And what do we do while your gone?” asked Shining Armor, impatiently.

“You stay right here in the TARDIS where it’s safe, until we get back.”

Rainbow Dash reluctantly looked back at Twilight before following The Doctor outside, she was surprised to see blinding fluorescent lights the second she stepped out of the TARDIS.

“Where are we?” she asked, raising her hoof to shield her eyes from the drastic change of light intensity.

“Cloudsdale Medical Center.”

“What!? Why?” she demanded. “And if we’re really in Cloudsdale, then how come you haven’t fallen through the floor?”

“Because in the future they found a way to solidify the floors of emergency service centers like police stations, fire departments, and hospitals after a few unicorns who cast the Cloud-Walking spells on themselves had a few accidents and at the worst possible time they wore off.” He explained.

“But, why are we here?” she pressed impatiently.

“Ah! Here we are!” he burst out, ignoring the question.

He burst into a room at the end of the fourth floor, where Rainbow Dash was getting fed up with being strung along, until the sight of the patient in the hospital bed stopped her.

“What!?”

The old mare seemed to be in pretty bad shape, her wrinkled body was covered in ugly bruises, there were dark circles under her eyes, and her formerly luscious rainbow mane had degenerated into thin graying strands, she was wearing an oxygen mask and various tube stuck into her arm.

“Is…is that…ME!?” exclaimed a shocked and horrified Rainbow Dash.

“Yes, but I didn’t just bring you here to show you yourself on your deathbed.”

“DEATHBED!?” she shrieked.

“Calm down,” he whispered before moving towards future Dash’s bedside, who had awakened at her past self’s outburst with her eyes following the stallion as he moved, taking off her mask.

“Doctor…what took you so long?”

“I’m sorry, but I can fix everything-I promise-I just need you to tell us what happened…and how did you get like this?”

“She’s like a hundred years old!” Rainbow Dash shouted, throwing her arms up.

“No,” The Doctor replied, “At this time period, medical technology has advanced to the point where in an equine’s lifespan, one hundred and twenty years old is considered middle-aged.”

“It was a just a few years after Twilight’s coronation after Nightmare Moon, Discord, Chrysalis, that one from the Crystal Empire…and a few others; enough time passed that it seemed like the world no longer needed the Elements of Harmony.” She explained.

“Twilight moved to Canterlot to take up her role as the ruler of Equestria once Celestia passed away in one thousand and four, Rarity moved there as well to open up a new dress shop, and I finally got accepted into the Wonderbolts-it took me a decade of working my flank off to earn the rank of Captain, because Spitfire’s successor was a total b-”

“Rainbow Dash!” The Doctor shouted, “The Elements!”

“All right,” she sighed. “Not too long afterwards, there was some kind of emergency, Rarity was easy to get a hold of since she and Twi both lived in the city; AJ, Pinkie Pie, and Fluttershy all stayed in Ponyville, so it was easy to get the word out to them.”

“And what about you?” asked The Doctor.

“I was on the other side of the world, touring with the Wonderbolts, by the time I heard anything about it-I was too late.”

“Too late for what?” asked the Rainbow Dash from the present.

“Look out the window,” instructed The Doctor.

The sky was covered in a dark cloud layer with thunder strikes of what appeared to be rays of twilight cracking overhead.

“THUNDERSTORMS!?” exclaimed Dash. “How is that even possible? We are in Cloudsdale!”

“It’s just as I suspected…” The Doctor muttered.

“What?”

“You and your friends drifted apart and you can’t really seem to recall the precise reasons why, correct?” he asked, turning back to the elder Rainbow Dash.

“Yes,”

“What about our relationship with Twi?” Younger Rainbow Dash cut in.

“We broke up shortly after she moved to Canterlot, once Celestia passed away she buried herself in her work-she felt like she’d be letting her down otherwise.”

“I though Celestia was supposed to be immortal,” The Doctor commented.

“She was, until the sky ripped open, wreaking chaos and disharmony down onto the world, and…as ashamed as I am to admit it, I feel that this is very important for you to know, Doctor-Rarity, Twilight, and I-we…didn’t want to come back or use the Elements of Harmony.”

“But, I thought you said that by the time we heard about all this, it was already too late?” pointed out Rainbow Dash.

“Yes,” her future self sighed, “But, afterward the thought had occurred to either Pinkie of Fluttershy…I can’t quite seem to remember, maybe it was both? Even though we still have no idea who or what is behind this, they pointed out that we could still use the Elements to restore the damage that had been caused and then investigate it’s source.”

“But?” pried The Doctor.

“But, while the three of us had achieved our lifelong dreams, we were by no means happy, but somehow content with how things were and perhaps on some subconscious level we feared that we’d be forced to talk to each other again, to look each other in the eyes and confess what we’d done.”

She looked her past self in the eyes and spoke softly.

“I’m not sure how things are working out in your timeline, but in this one we used to each other to achieve our life’s goals and not too long after that began to get irritated by each other, seeing the others as dead weights, holding us back from our full potential-we no longer had time for friends.”

Rainbow Dash’s heart was caught in her throat at what she was hearing.

Could it really have been true?

Would the accomplishments everything they’d worked for in there lives really drive them apart and cause them to hate each other?

To no longer have time for each other?

The fear that had gripped her seemed to have tightened around her lungs, making it even more difficult to breathe once another thought occurred to her, but she had to know.

“What about Pinkie, Fluttershy, and AJ?” she asked, barely above a whisper.

“They stayed behind in Ponyville and still seemed quite happy there when I last saw them…but, that was about seventy-five years ago…”

For a minute her heart stopped.

Seventy-five years.

It had been seventy-five years since her future self had any contact with her friends…

“A-and Squirt?” she asked timidly, although she feared she already knew the answer.

“Scootaloo…” the older mare sighed. “When I got accepted into the Wonderbolts, she was happy for me-at first. But, when she realized that meant we would no longer be able to spend time together, with the tours, pres releases, the Gala, and trying to train and pick out new recruits from the academy, I just had to cut all personal attachments out of my life.”

“You what?” Rainbow Dash growled, uncharacteristically silently, her tone filled with underlying rage.

“Listen to me,” she continued, keeping the same tone.

“Our friends…our family…is way more important than we are…even becoming a Wonderbolt is secondary to them and their needs, I don’t know who you are-but, you are not me.”

With that, she curtly turned around.

“Let’s go, I’m sick of this place.” She spat, before heading back to the TARDIS with The Doctor reluctantly following behind and leaving her older self in a state of shock at how absolutely disgusted her past self seemed to be at her for doing what they’d always wanted.

Plans for the Future

Down the hall, Rainbow Dash stopped short of the entrance of the TARDIS leaning against the wall.

“Are you alright?” The Doctor asked, it was a stupid question, but the only one that seemed right to ask given the circumstances.

“I can’t believe we turn into such selfish jerks in the future…” she grumbled.

“Not necessarily.”

She glanced up at him with a questioning look.

“Time can be rewritten,” he explained. “This isn’t what the future is supposed to be like, someone or something is rewriting history…and not for the better.”

“But, who or what is doing this and why?”

“I don’t know,” he admitted, “But, I intend to find out.”

He was about to enter the TARDIS before she stopped him.

“Doctor, I wanna stop whatever’s doing this…but, I have to know; if I become a Wonderbolt, Rarity gets her dress shop or whatever up in Canterlot, and Twilight does take over for Celestia and we do find and stop whatever’s doing this-will we still turn into jerks?”

He stared into her eyes, which betrayed her tough exterior he could see that she was afraid of betraying Equestria for her own desires.

“No,” he replied, “What happens to you is a fixed point in time that must always happen, no matter what.

Her ears drooped a little as a look of confusion spread across her face.

“Even though you all have these new responsibilities in the future-you still remain a very tight-knit group of friends, always there for each other to keep on saving the world and once or twice if recall, even the entire univ-” he cut himself off.

“Ahem, sorry I can’t say anymore-spoilers and all that.”

“But, you just said that I become a Wonderbolt!” Dash exclaimed, with stars in her eyes.

“Yes, because at this point nothing in your timeline could possibly prevent that from happening.”

“What about what I said…I mean, the older me?” she pressed.

“I think Spitfire, Soarin and the other Wonderbolts would understand the need for the Elements of Harmony to remain in constant contact with each other.” He replied with a knowing grin.

A huge sense of relief could visibly be seen washing over her face as The Doctor moved to open the TARDIS with the key between his teeth.

CLICK

The door unlocked as Twilight and Shining Armor could be seen, leaning against one of the railings and catching up with all of the events that had transpired since her coronation ceremony.

“So what’s the plan?” asked Shining Armor.

“Well, first I’m going to need to speak with Twilight in private.”

Shining Armor and Dash both exchanged glances before heading down a flight of stairs to explore the TARDIS some more.

“What is it, Doctor?”

There was a hint of anxiety in her tone, as she wondered whether or not she did something wrong and completely messed up the timeline.

“So…becoming an Alicorn and princess at nearly the same time, that’s a pretty big adjustment-especially for someone so young-it must be pretty scary for you.”

“Yes,” she replied softly, averting her gaze.

“Hey,” he leaned in a little closer so she was looking right at him.

“That’s nothing to be ashamed of, while change isn’t always necessarily a bad thing-it can be scary-and nobody knows that better than I do.”

“What?”

“You don’t think I’ve always looked like this, do you?”

She merely stood there with a look of confusion plastered onto her expression.

“But yes, I have always been this handsome.” He continued, brushing a hoof through his mane confidently, causing her chuckle a bit, but then suddenly stopped.

“That’s not the biggest thing that worries me…”

“Oh?”

“It’s what Princess Celestia said about Alicorns being immortal and outliving all of their friends and family…” she sighed.

“Oh…”

He placed a hoof on her shoulder.

“Twilight, I don’t think she knows if you’re actually immortal or not, but she cares about you so much, that she wanted to prepare you for that possibility…since an ascension from Unicorn to Alicorn has never happened before in recorded history, it’s a completely unpredictable process.”

‘Much like my regeneration’ he thought.

“She just expressed it in the wrong way.” He explained.

“You’re a time traveler, so don’t you know for sure?” she asked, timidly.

He regarded her for a second with what she thought might have been disapproval before he burst out laughing.

“I wouldn’t worry about it.”

He could see a cyan ear pressed up against one of the grates in the floor.

“Yes, you two can come back now Rainbow Dash!” he called out, shocking both the prince and the Pegasus.

The two emerged from their hiding spot.

“Twily…” Shining Armor began.

“Why didn’t you tell us?” Dash burst out.

“I…I didn’t want to worry you guys…I’m sorry…” her ears were flattened and she was holding her foreleg shamefully.

Rainbow Dash looked furious, but then her expression dropped as she flew to the young Alicorn’s side before putting her in a headlock and ruffling her mane.

“You egghead!”

“We care about you,” Shining Armor added throwing his arms around his sister. “It’s our job to worry about you!”

The Doctor threw a switch as the TARDIS began to hum, causing the trio turn in his direction.

“Doctor, what are you doing?” asked Twilight.

“We are heading back to the library, so we can get some rest, in the morning I have an errand to run and at noon I’ll return Shining Armor to the Crystal Empire.”

“But, what about-” Dash began before he held up a hoof to silence her.

“I’ll return in a few days to pick you up…and Twilight too if she wishes to join us, but until then I think it would be best for both of you to try and relax.”

“You’re leaving!?” the couple exclaimed in unison.

“Just for a short while, I do these kinds of things all the time and I’m feeling a bit worn out-I can scarcely imagine how you two must feel.”

“So…I’m going back to the Crystal Empire?” asked Shining Armor.

“Tomorrow,” he whispered. “I need time to think, to ascertain whether or not these anomalies are the result of meddling with their timelines or the cause.”

“I don’t follow…”

“I think that whatever is causing all of these problems through time may have it out for your sister and her friends.”

“Couldn’t it be Discord?” Shining Armor protested, “I mean, in our time the Princess released him so he could be ‘reformed’ and as much faith as I have in her…I still can’t find it within myself to believe that he’s truly changed.”

“Neither can I,” agreed The Doctor. “But, for now we have to give him the benefit of the doubt-Discord causes chaos for more of his own amusement-these changes seem more malicious, like whatever is causing them wants people to suffer.”

“So who does that leave?”

“I don’t know…” he admitted, “But it might be someone we haven’t even met, yet.”

“What?”

“From what we’ve seen so far, the only events that have been affected are in the future-so it’s quite possible that whatever-or whoever is out to get your sister and her friends hasn’t met them yet; Nightmare Moon was purified by the Elements of Harmony, the events I’ve encountered aren’t Discord’s style, plus I doubt even he has that kind of power-is there anyone else you can think of?”

“Well…” Shining thought carefully, “There was Queen Chrysalis, but she feeds on love for power-so unless she found a never-ending supply of it, she couldn’t even take on the Princess-let alone affect time in the way you’re saying.”

“Anyone else?” The Doctor pried, “Anyone at all?”

“When Cadance and I moved to the Crystal Empire after our wedding ceremony, there was an old tyrannical unicorn that resurfaced along with the Crystal Ponies-King Sombra-he was so evil that it was said that his heart was as black as night and so powerful that it took the combined power of both Royal Sisters to seal him away for a thousand years.”

“Could it be him?”

Shining Armor shook his head.

“No, Sombra was killed the moment the Crystal Heart was returned to its rightful place, the love and hope of the Empire’s inhabitants wiped out the fear and hatred that had oppressed them for so long.”

“No, no…” The Doctor sighed, “If it isn’t any of them, then who else could possibly possess that kind of power.”

“Aside from an Alicorn?” Shining Asked. “No.”

“Then we’re still missing something…but, we’ll figure it out tomorrow-it’s been a long day for all of us.”

TO BE CONTINUED…

The Doctor will return in; “GHOST OF THE CRYSTAL EMPIRE