Doctor's Shadows

by lastsight123

Rating: teen
Tags: Sad, Adventure, Dark, Alternate Universe
Length: 9678

As darkness falls over Equestria, the Doctor must face past decisions.

Equestria is covered in darkness, and Canterlot has fallen off the grid. A formerly settled Doctor must race back into action and confront the darkest corners of himself. His intentions may be pure, but his decisions of both the past and the present may all lead to one bitter end. Can he cheat time itself? Or has he been sitting around far too long?

Author's Note: Since this is my first story on here, I'd like some feedback sometime, if anyone wants to take the time. I am always open to the opinions of others.

2nd A/N: This story is on hiatus until I can clear my head enough to properly write it.

Published 1970-01-01 00:00:00 UTC
Last updated 2012-12-13 01:54:55 UTC

Shadows of Darkness

Doctor’s Shadows

Chapter 1: Shadows of Darkness

Shadows washed over Ponyville. Throughout the darkness rang loud noises, shouts, and an occasional screech. How had things gone so wrong? Why has the sun been gone so long? Why hasn’t the moon risen with the darkened sky?

Suddenly a fire bloomed, green, in a spout. As it hit the wooden stick, suspended by a faint glow, a purple mare’s face was illuminated. Tears were streaking down her face, as the light cast by the torch fell upon the mangled body of a familiar, grey pegasus, whose yellow mane had grown damp with what one could only hope was mud. One more victim of this sudden, endless, night.

72 hours ago…

Derpy Hooves was quietly descending on Ponyville. She had been delivering a letter to Rainbow Dash, who had collided with her in the process. After a small scolding from Rainbow for interrupting her latest routine, the letter had been successfully exchanged. Dash had almost forgotten to keep her wings moving when she read it. It was a strange reaction, but Derpy had no time for questioning, today was important. In any case, Dash had quickly flown off, and there was no catching her. This marked the end of Derpy’s work day. The smile that so often graced her face widened as she thought of the day ahead.

Most of Ponyville was gathered around Sweet Apple Acres to marvel at the new renovations the Apple family had managed. Mostly it consisted of a new coat of paint, and a new patch on the roof. Things like that were community achievements in a place like Ponyville, of course. It was the epitome of close community. The friendly atmosphere and sociable people were what made Ponyville great, after all.

Derpy’s left eye lingered on the orchard as she neared the ground, part of her wanting to go have a look. Her right eye might have allowed her a relatively safe landing, had she remembered that she was supposed to do so. She could never rid her mind of that tendency for wandering. It wasn’t too bad, she thought, as she shook her head. It wasn’t like she hadn’t done it a few times before. In any case, her head was cleared now, and she had only a small walk towards her home, and the very special somepony who resided within.

He was a doctor, though in what, nopony knew. As far as they pried, he could have a Ph.D. in owning a Ph.D. Interestingly enough, his Ph.D. had never been placed on a wall, as some might do, and he never bragged about or mentioned one. Aside from curious children however, this concerned nopony. He looked quietly at the door, a calm look on his face, as it commonly was. This day was special to him. An anniversary. In honor of the occasion, his home had become an explosion of color and balloons. Pinkie Pie had insisted, of course. Strange how she hadn’t remained, but he was more than a little glad to spend a day alone with his wife. Wife…he remembered when he first encountered her…but those thoughts were of days past. He had no business in the past. Too costly.

Doctor Whooves, as he was commonly called by the townsfolk, had been preparing for this all morning. Though the decorations were all set up by Pinkie, he had been going all over town looking for things to make the day special. He had saved some cider, and was given sweets from Sugarcube Corner by Pinkie Pie. He had also borrowed a book from Twilight Sparkle to read aloud for the both of them. Not to mention the special surprise he had been going back and forth on.

As the wife walked in to encounter her husband, they both gave each other a look of unrivalled happiness.

“Hello, muffin,” he said to her, causing a small blush to cross her face, as it always did. She returned with her own name for him, only reserved for special occasions nowadays.

“Hello, doctor”. He smiled, his mind drifting once again to the past, before it was called back again in remembrance of his plans for the rest of the day. He moved towards the cabinets, grabbing two of the nicest cups from inside, and pushing a small barrel of cider out from the kitchen. He looked over to Derpy with a smile, pouring cider in a cup, and handing it to her.

“Drink up. I’ve got a nice little date planned out. Hate to miss a minute.”

“I can’t wait,” she replied as she took the cup in her hoof.

The day wore on towards the afternoon, and the cider had been steadily drained to its end, and cupcakes and muffins eaten alongside it. The two had been enjoying the Daring Do book, exchanging small stories of their own as they went along. The day seemed perfect. Nothing was left out of place.

Across town, everything had gone wrong. Rainbow Dash saw it before anypony else could. She had received a letter from Twilight telling her that the next few days were going to be some of the worst since the days before Equestria was found, and that a meeting was in order. She trusted her friend enough to know it was worth pushing back her nap for a while. All the same, she wondered what could possibly be so bad. Were dragons invading? No, that would be more obvious. Did every crop in Equestria dry up and die? Nope. Sweet Apple Acres had a big harvest coming up. Did Canterlot explode? Just as the last thought crossed her mind, her view of Canterlot in the distance was suddenly gone. She stopped. Her wings forgot to flap. She began to fall, so shocked that nothing registered with her brain anymore. She saw the ground coming and suddenly everything was dark. She was certain she was dreaming now, knocked out by the fall. Something was tingling around her. It was glowing. Weird dream. Actually, she didn’t think she had been close enough to the ground to be hit by it. Suddenly, the tingling stopped and she did feel the impact.

“Rainbow Dash!”

Dash looked around rapidly, unable to see anything. She could hear panic begin to spread, started by a loud scream from the direction of Sugarcube Corner. The normal instigator of panic in Ponyville it seemed. Green flames lit up a few streetlights, and Spike and Twilight Sparkle ran forward, meeting their now grounded friend.

“Twilight, what happened?” Her voice carried a small level of what could almost be panic, if she would ever let anyone believe it.

“I got a letter from Princess Celestia. She said that Canterlot had been attacked. She didn’t seem to have much time in writing the letter. She only said that the sun and moon were in danger.” Twilight took a breath here, looking towards where Canterlot usually would be. “It looks like we’re too late…”

Sudden screams of panic could be heard outside as the sunlight that was once filling the home vanished as quickly as Derpy could blink. The small candle that had been lit for a ‘more romantic mood’ flickered softly in the darkness. A cry was heard above, and the soft thud of somepony falling could be heard. The shout sent Derpy moving quickly up the stairs, eventually fumbling in the darkness of their second floor.

With Derpy moving upwards, her husband was moving into his own course of action. He peered out the window, as instinct would have it, to see…nothing. A small gathering of streetlights were lit quite a distance away, but he couldn’t make out the gathering beneath them. Pulling his head back in, he could see his wife and daughter making their way down the stairs.

“This shouldn’t have happened,” he mumbled quietly to himself.

“What is it?” he heard Derpy say behind him.

“There isn’t anything in the sky. Sun, moon, all gone. That shouldn’t happen.”

His family stood silent. He could feel them looking at him. A small fire inside him began to burn. Something was going wrong. Something bigger than the other ponies. It had been a while since he felt that fire. Other ponies seemed to take care of any emergencies these days. But the disappearance of the sun and moon? This wasn’t something to ignore. I wonder if Fluttershy is home…

End Ch. 1

Shadows of Fear

Doctor’s Shadows

Ch. 2: Shadows of Fear

The cottage lay just on the outside of the Everfree Forest. Animal carcasses were strewn about, still fresh. A pool of blood lay around the chest of the yellow-furred pony who had tried protecting them. The body was taking shallow breaths and looking back into her home, where a group of ponies were looting the stores of food. She couldn’t figure out how something like this could happen. Tears streaked down her face, and her breathing ceased.

64 hours earlier…

Doctor Whooves was galloping at his top speed in the direction of the Everfree Forest. It had been an hour in preparation, and he knew time was of the essence. If he hadn’t had to talk his family into staying, he may have been quicker. He quickly recalled the discussion in his mind.

“You need to stay here. Lock the doors, don’t let anyone in.”

“But where are you going to go?”

“There’s something I have to do…Just stay.”

He hadn’t given her the time for a response. He had bolted out the door, and slammed it shut, not waiting to hear the click of a lock. His only goal was to find Fluttershy. She was undoubtedly scared out of her mind, and he needed her. Not too long now. I just hope she hasn’t let anyone inside. He powered through his incoming exhaustion, and made a turn for the last leg of his trip.

Derpy stared at the door, lost for words. Her daughter tugged at her, but to no avail. Derpy stood for ten minutes with that blank stare before she finally locked it. She looked down at her daughter, thinking about what they were to do. What were they to do? They had no defense, and no way out other than the front door. The windows had been boarded shut after a while due to Dinky falling out a few too many times. She frowned.

Dinky looked up at her mother with worry. She hardly ever stopped smiling. Dinky looked out through the peephole, and leaped back in surprise.

“Are you ok?” her mother asked as she looked into the hole, also jumping backwards. She quickly opened the door, welcoming back her husband. He looked worn down. “You finished already?”

He gave her a blank look, shaking his head after a moment. “We have to go. Pack up.”

Both Derpy and Dinky gave him an inquiring look, but he shooed them off. He took a rest against the wall, checking through the door. I can’t let it happen, he thought quietly, she doesn’t deserve what she gets.

His family returned, and he looked outside again. No sign of trouble. He signaled quietly for their motion. Bringing again the weird looks of his family, who was now seeing he looked much worse than worn down. He looked like he was breaking. His mane was wild, and he was speckled with blood. Even his eyes had lost all of their shine. They stepped outside, and he opened the door of a nearby shed.

Fluttershy peered out her windows, having lit at least 50 candles, including ones cut in half to make extras, to keep her home lit. Rarity had been visiting, and was in the process of lighting even more candles. “Fluttershy, you must get away from there. Staring out into the dark will only worry you more!”

She looked back at Rarity, who now noticed the tears building up in her eyes. “I-I can’t…Angel was out there. He could be lost or scared or hurt or alone…or what if he isn’t alone! There are so many mean creatures out there…”

Rarity sighed, but only to herself. She didn’t want to sound angry with her friend. “Maybe we should get you some tea. To calm your nerves.” She pulled the pegasus away from the window and sat her upon her couch. “Stay here while I go make it.”

Fluttershy watched as she walked into the other room, and could faintly hear the water begin to boil. She knew Angel was a fighter, but that didn’t help. She needed him just as much as she felt he needed her. “Oh Angel, please stay out of trouble.”

A round of knocking rattled the door. A small scream issued from Fluttershy’s mouth. It was Rarity who walked into the room and checked the door. An odd sight greeted her.

“Did you call the doctor for a visit?”

“Oh, um…Doctor…?”

“Doctor Whooves.”

Fluttershy shook her head, and her friend opened the door cautiously, leaving space to speak, but to shut the door fast if need be.

“Hello, Rarity, is Fluttershy home?”

Rarity peered back into the house for a second, and then gave a slow nod. “She wasn’t expecting anyone to call…”

“It’s important. Can I come in?” he peeked over his shoulder, and a small rabbit hopped on top of his head from his back. Angel Bunny.

Rarity opened the door wider and stood aside for him to come in. “How rude of me, I must have forgotten my manners.”

Fluttershy didn’t move as the doctor-in-nothing approached. He waited a moment before speaking, “I need to get into my shed.”

Panic struck at the shy mare. “Bu-but you said bad things come from it! You said it was dangerous to open!” She was surprised at her shouting, but maintained her new stance.

“It’s an emergency, and I know how to handle it. Please show me where you’ve placed it.” He offered a small smile to reassure the poor pegasus. Angel hopped up and looked at her expectantly. After a moment, she nodded and stood up.

“I think I’ll…stand back when you open it.”

The group walked outside, taking one of the candles to light the way. The shed had been stripped of paint by the weather, but it remained structurally solid, as if protected by an invisible force. Doctor Whooves stepped forward, taking the key from Fluttershy. “I have to warn you…you won’t see it anymore once I’ve gotten in.”

Fluttershy thought best to not ask questions. That and her mouth was sealed shut in fear. Rarity, however, stepped forward.

“Fluttershy, dear, I think I’ll join him.”

“No, neither of you can.”

“Too bad, I’m going.”

“No.”

“Try and stop me.” At this, Rarity knew she had won, as he simply opened it up, and stood aside for her to enter. The insides were dark, but Rarity walked in with little hesitation. It was just as dark outside, and far dirtier by her estimation.

Fluttershy backed away. “I’ll just stay…my animals need me…”

Doctor Whooves gave a small nod, still mildly upset from Rarity’s insistence upon entering. “Stay safe.” He walked inside and the door was shut.

Fluttershy watched it disappear, sighing with a small sort of relief. Suddenly, something was materializing around her, and she began screaming relentlessly. The shed formed around her and disappeared once more.

After Rarity had stumbled around long enough in the dark, the lights suddenly flickered on. The sight astounded her. No shed looked like this. Doctor Whooves ignored her surprised questions and remarks, and went straight to the console. He fiddled around with it as if it were his favorite hobby. A whirring noise started up, and the machinery began working.

Only then did he turn to face Rarity. “It’s sort of a gateway to another part of the universe. Time doesn’t go here either. The shed is much smaller than the inside. Anything else?” She gave him a gaping stare, speechless. He looked at her a moment longer, before turning away, sighing to himself. He was back in the saddle, so to speak. So why was he feeling so…off? His worst fears began to creep into his head. Can this be fixed? Is it something that needs fixing? Am I still the man I used to be? What if I just make things worse for everypony? I shouldn’t have left my family…

The streetlight illuminating the two mares was slowly but surely losing strength. The riotous screams were beginning to die down though, allowing a moment of easy breathing for Rainbow and Twilight. They took a moment to assess the situation.

Twilight spoke first. “We should try and find our friends. If we’re all together, we’ll be better able to fix this.”

“But what are we fixing?” Dash’s question struck a dark chord in Twilight’s heart, causing her to fall flat in her planning. RD instantly felt for her friend and tried consoling her. “We’ll just have to find out if our friends know. Let’s get to looking, alright?” She waited for an acknowledgement she did not receive. She then urged Twilight onward, into the darkness.

As Twilight moved on, she couldn’t push the questions from her head, extrapolating fears inside her. Is everypony still ok? How could this be happening? What exactly is happening?

End Ch. 2

Shadows of the Past: Part One

Doctor’s Shadows

Chapter 3: Shadows of the Past

Part one

Luna awoke. The world view was blurry, and a throbbing sensation rocked her head continuously. She tried to move a hoof to her head to check the damage, but found herself bound in chain, with limited movement. What is going on? She began to look around for her sister, who was standing by her at last memory. She saw another shape moving in the dark room. She tried to illuminate the room, finding herself incapable. “Sister? Can you hear me?” Silence. What could have brought this upon them?

At an undetermined time…

Doctor Whooves looked back to the console, noticing a small metal device with a blue light at the tip sitting in plain sight. He smiled, picking it up. It was old. Probably too old by now. There was more than one occasion where he had pushed it past its standard uses. But he had to focus on the matter at hand. He picked the screwdriver up and put it in his saddlebag. He hadn’t thought much of where he was going when he originally entered commands into the console. Now curious as to where they were going to land, he slapped down a handle on one of the smaller panels, and they came to a halt that sounded much like the wheezing of a very old dragon. “Rarity, would you open the door for me?”

Rarity nodded, still unable to find words. Her horn lit up and the door opened up, revealing a busy cityscape. “That’s certainly…not Ponyville. Where are we?”

A quick peek outside revealed even more things about the area. By the Doctor’s estimation, and the fact that the sun was shining, they were in Manehattan, somewhere around…40 years ago. He had been there before. Well, not me. The area was safe enough. Why here though? He always seemed to end up where he needed to be when he was haphazardly travelling. He was certain this would be no different. “Well, Rarity, welcome to Manehattan, 40 years ago. Don’t speak to any cream-colored mares, or anything like that, and we should be fine.”

Rarity gave him an odd look then finally found her words. “You mean to say, we are actually in the past? In another place? During one of the most interesting fashion revolutions of all time, and you don’t want me speaking to somepony who might match one of my dresses perfectly?!”

All she received in answer was a blank stare, followed by a nod. “I’m sure you would want more of an off-white color than a cream color anyways. Let’s go take a look around.”

40 years later…

Rainbow Dash could see Sugarcube Corner ahead of them. It was lit up like a late night club, and was giving out the sounds to match. Honestly, what else could be expected of the party pony? The loud music indicated that she was not the only occupant of the building. Twilight’s head perked up as she heard it. At least she knew Pinkie was still safe, if there was as much going on as that, she had to be.

The door swung open as they reached the steps, revealing the one and only Pinkie Pie, with one of the biggest grins ever seen. She quickly pulled them inside, locking the door, and peeking out the windows. She said something, but could not be heard over the now louder-than-ever sound system. Twilight sat against the wall in mild relief, but Rainbow could not settle herself with all the noise. Spreading her wings, she flew over to the pony behind the wall of speakers, and signaled for the music to stop. The strikingly blue-maned mare frowned a little, but complied.

Pinkie practically flew over to Dash screaming “What have you done!? They could be coming any moment now!” She leapt back over to the window, peering out at the silent streets.

Twilight poked her head back up. “What are you talking about, Pinkie?”

Pinkie Pie stared madly between the new arrivals, and they began to shift uneasily. She dropped down to the ground, acting as if she saw someone. “The sun and moon are gone! They’ll come for us next! They have to.”

Rainbow, Twilight, and even Vinyl looked at the pink pony as if she were speaking nonsense, which, really, was exactly what they were thinking. She had snapped. It wasn’t easy to watch when Pinkie’s optimism and happiness faltered.

Vinyl spoke up first, shouting over the silence. “Maybe she’ll feel better with the music back on. She seemed ok before, y’know?” She received a nod from the others, and put the music back on, at a fraction of the original volume. She knew the others had shown up for something important. They needed to talk.

“Hey, Pinkie Pie,” Rainbow gently approached her friend, “We’re trying to find everypony and get them all together, do you know where they are?”

Pinkie froze in place, and then began bouncing around in usual style. “Rarity was with Fluttershy for the day, and Applejack was selling apples in the market!” A loud gasp issued from Pinkie. “That’s where most of the screaming came from!”

Rainbow was already out the window whenever she heard about Applejack. Her friend was perfectly capable of defending herself, right? Still, she bolted out into the direction of the market, leaving Twilight with the other two.

Twilight stood up and flung the door open with her magic. Pinkie bounced out of the room, and Vinyl began packing up her equipment.

“Good luck, girls, I’m taking my bass cannon back to my place.” She carted her cannon out the door, waving as she disappeared into the night.

“Let’s go”. Twilight rushed out the door, followed by Pinkie Pie.

As they stepped into the streets, Rarity took a look back at the mysterious shed, which now looked to have a fresh coat of blue paint. What a poor color scheme. Then out came the Doctor, joining her in her gaze.

“Beautiful, right? She’s called the TARDIS.” He smiled, noting that it had recovered from the time it had spent alone. It just needed me back.

“I suppose if that’s your definition of beauty, it could be…I’ll have to come back to that. Why are we here when our friends are in danger?”

He smiled. “I’d like you to notice something. See that city, off in the distance? Canterlot, right?” She nodded, and he continued. “That means Canterlot still exists. Which means we can fix this. So rather than worry about the danger it poses in the future, let’s see what sort of danger could have been posed to it here.”

Rarity took a moment of processing. It was now dawning on her what was actually happening. They were in the past. They had a shot at saving Equestria. Great! But how?

Doctor Whooves suddenly turned and began walking. Quickly. Rarity ran to keep up. He seemed like he’d seen a ghost. He turned around suddenly and pulled out his screwdriver, aiming it at the TARDIS door, which swung shut. He then knocked Rarity off the sidewalk into the back of a carriage, surprising her with the strength of the movement. As she was carried off, he ducked into an alleyway. Rarity looked around to see what could have caused all of that, and she saw the mare he mentioned earlier. A cream-colored unicorn. Her cutie-mark…it looked very similar to his…

Separating from Rarity was…necessary. He couldn’t explain his actions and hide away at the same time. He didn’t want to interfere with the flow of time too much here. It could influence his past and his mission could become skewed. That pony he saw…he wasn’t himself when she was around. Or he was exactly who he should have been. It didn’t matter anymore. He’d never had to deal with his past so directly before. But he remembered what he was doing in Manehattan all those years ago, and he could tell he would be seeing a lot of that mare. As for Rarity…he’d figure it out. He stopped for a breather.

“Could I have missed something last time I was here?” He felt a clutching at the pit of his stomach. The idea that the enemies of his past could be haunting him was too much. And now he was alone again.

The carriage was bumbling down the road at a fair pace. Looking out the window, Rarity could tell the stallions leading it were entirely unaware of her presence. She assumed they may be en route to something important, and to her, this was the perfect place to be. The height of fashion at the time, anywhere in Manehattan was the best of all of Equestria.

The sudden halt of the floor beneath her shocked the mare off of her balance. She fell to the floor, and, seeing the door begin to open, took a deep breath and, in what she thought was the bravest of actions with the worthiest of causes, rolled under the seat towards the back of the carriage. She felt the dust lightly tickling her muzzle, but held her ground. She could not be found if she wanted to find the destination.

“Thank you, kind sirs. Daffodil’s, if you will.”

Daffodil’s? As in the Daffodil’s School for Fashionable Fillies? It was closed down 10 years before I was school-aged. To see it in full operation? What an opportunity! I’m sure I can just…take some time before finding out how to save my friends…they’ll understand.

The ponies above her shifted. “Well, auntie, it certainly was a nice trip. The concierge at the hotel seemed to have quite an eye for you.”

“Oh, hush. You know we have no time for that sort of thing. We have so much to do. It’s been months since we were first asked to come here alone. Not mentioning everything else we’ve yet to do.”

“We have plenty of time. You can’t simply forget that.”

“You know what I mean. Nothing ever lasts…” The speaker fell silent, having trailed off the end. Rarity could hear the two shifting around again, one of them moving to the seat in the front of the cabin, to better face the other.

“Well, we shouldn’t ever forget to enjoy what we can, while we can. Nothing has to last if it’s worth it, you know.”

A sigh issued from above. “Of course, Cadance. Of course. Though you are still much too young to be talking of such, by my standards.”

Rarity almost hit her head on the seat, barely containing herself. She was sitting in a royal transport. She had barely any time to adjust to her excitement before the carriage halted again, and she heard the two preparing to leave. She would have to get out too.

“Well, I suppose we had better get inside. They’ll want you to address them, yes?”

“They always do.”

I guess I’ll have to wait for the cart to start moving and sort of…jump out. I see no other way…

As the two alicorns stepped out, they were swarmed by their subjects. The carriage door swung closed and Rarity gladly rolled out from under the seat, dusting herself off. She waiting for the carriage to move again, and after it obliged, she counted to ten, then leaped out of the window. She felt herself collide with the ground, but quickly regained her balance. She was outside of the crowd, but not far from her destination. She quickly made her way toward the entrance, following the crowd as they trailed the Princesses.

The Doctor was back on the street, and proceeding to hail a carriage. When one finally pulled up, he stepped inside, not noticing the other pony occupying it. He looked up through the window to the stallions carrying it. “Take me anywhere.”

The other pony took notice of him. She had never encountered him before, but felt she must know him from somewhere. She dismissed the thought, if only for the moment, and began to speak to the earth pony. “Then I suppose you’ll be joining me on my trip to Daffodil’s. Celestia will be taking petitioners after her public address, and I’m very anxious to speak with her.”

Doctor Whooves looked toward the speaker, his breath stopping. She was beautiful. A flowing brown mane, the horn that accompanied all unicorns, grey eyes, and…a cream-colored coat. Of course she’s beautiful. She’d have to be, or else she just couldn’t be called…Doctor.

End Chapter 3

Shadows of the Past: Part Two

Doctor’s Shadows

Chapter 4: Shadows of the Past

Part Two

The white alicorn stood to her full height, glaring across the burning city of Canterlot. The field of magic surrounding it made sure nopony could cross in or out. Not that they could even see the city. It was the perfect plan, and now the whole of the crumbling city could see their glorious ruler, whom they held on the highest pedestal, laughing at their merciless slaughter and ruin.

She took a step back from her survey, speaking in an uncharacteristically low tone, “Now no one can stop me…not even a Doctor.”

Forty years before…

The royal assembly was just beginning, Rarity, of course, mingling seamlessly with the crowd. She had quickly adapted the vernacular of Manehattan. Her movements quietly snaked up towards the front of the assembly hall, and she had a very clear view of the podium, where Celestia would be in mere moments. Celestia…she would have no idea who I am now, would she? Perhaps talking to her wouldn’t be…wise. As Rarity had her quiet thought, Celestia began to make her way into the spotlight. The lights dimmed down.

The carriage must have had a loose wheel to be bumping so much. At least, that’s the sort of thing running through the mind of Doctor Whooves as he stared off into the distance, awkwardly avoiding the gaze of the other pony. How, of all actions, had he made this mistake? He knew her every move. He knew every detail of her existence. How did he forget this?

“You seem troubled.” He looked over at this, scorning himself inwardly. “Are you quite alright?”

“Well enough. Never liked carriages.” His minimal speaking didn’t seem to go noticed, and he sat in quiet pleasure as she nodded, looking out the window. Was it weird that he was admiring her? A bit narcissistic. His brain shrugged, and he began to take in more of his surroundings.

She had a bag. He knew what was in it. A few spare changes of clothes, half of which seemed odd for a mare, a few varieties of food, and probably some tools. The tools were the most often used, of course. A funny idea pressed its way into his head. Maybe I’m psychic today.

He gently cleared his throat, gathering her attention. “I see you have a bag there. A bit over-packed, it seems, for the occasion.”

“Well, I suppose it could be, but, you can never be too prepared, can you?”

He gave a small smile, nodding. “Of course. As you can see, I’m not quite dressed for the situation. Perhaps, in that bag, you might have something I could borrow? It sounds strange to ask, but, what’s more fun than that?”

She gave him an odd stare. Then, as expected, she nodded. She opened the bag, and pulled out a brown suit and overcoat. “You can borrow this…I don’t think I’ll have use for it.”

This brought out a different kind of smile. Not that she would notice the message in his eyes. “You never know.” He took the suit, thanking her in the process. As he pulled the clothing over himself, he looked over her once more. “We should be close by now.” She simply nodded, slipping into her thoughts.

The door was opened for them by a weak-legged filly, who gasped in sight of the unicorn. She walked with him closely, as if using him as a disguise. He knew why. No point letting herself get spotted. This was the day it all tried going wrong. Suddenly, it dawned on him. I’m here because of him! He suddenly stumbled, bringing notice to himself from those around him. He pretended nothing was wrong, and the silent eyes turned away. He looked over at his partner. “What do they call you?”

She looked over, a gleam in her eyes. “Call me Doctor, please.”

“Ah, really? I’m a doctor too. Went to Canterlot for my education. Travel a lot nowadays.”

She nodded, hearing commonality. “I travel too. All over. You’d be surprised where I’ve been.”

He grinned, and was tempted to issue a challenge, before Celestia took the stage. The hall quieted down, and he surveyed the room. Where was that horrid creature? He would know better than herself. He smirked as the thought ran through his mind. He saw a small red unicorn nearing the front, slowly. His face turned to a frown. He leaned in for a whisper.

“Doesn’t that red unicorn remind you of someone…prominent?”

The mare turned to see who it was he spoke of, and caught the view. “Yes…I think I’ll go talk to him. Don’t wait on me. I may find myself quite interested.” She walked away, and he slipped back into the crowd. A new era of her life was on its way. But enough of that. Let’s hear this grand speech.

Celestia eyed the crowd nervously. She had more on her mind than a simple ‘I’m here for you’ speech. Changelings had been seen crossing the borders. Anypony could be one. She had all of her guards identifying people from afar. If someone came in with no proper ID, she would know…she hoped. She amplified her voice, and began to speak.

“Hello, noble subjects. I have come here today to offer words of encouragement and pride. This establishment has been teaching young fillies the arts of fine clothing and cosmetics for many years, each time, gaining more and more awards. I have never known a fashion school to break so many records in all my years.”

She paused. Her heart wasn’t in this. She appreciated the talents of all young ponies, but this seemed so trivial compared to the security of Equestria. She gently shooed off such thoughts and went on.

“The lives of many ponies have changed here, and it continues to inspire many young ones all around Equestria. Fillies dream of the day they can come here, to the proud and energetic city of Manehattan, and learn at institutions such as this one. If Manehattan were to keep this up, maybe one day, it could even become the capital.”

I could never leave Canterlot. Too many memories…but it gives them hope…why do I feel so anxious?

The rest of the speech went on similarly, boasting how great Manehattan was doing. A great applause and cheering erupted from the crowd, which had been very moved by the praise. They always were, in Celestia’s memory.

“In an hour or two, I will be in the grand hall to hold court. Please attend if you wish to speak.” She smiled brightly, and walked off the stage.

Rarity was confused. That didn’t feel like she thought it should have. There wasn’t the same heart she was used to hearing from the Regent of the Sun. She would have to attend the royal court. She couldn’t let this stand. Especially with people in so much trouble in the future. The Doctor did say that the solution was here. She walked off into the crowd as it shuffled out. Bumping into a man cloaked in brown.

“Found you! Good. See that cream-colored unicorn? Follow her. After a time, she should be able to get you home. I’ll be at the court. Have fun. Keep safe.” He began to wander off before Rarity gripped him tightly.

“I demand to go with you!” Her eyes shown with fury at the denial.

“Not this time. You’re needed at home. Tell your friends that Canterlot is still there. That we can still save everyone. And…find my wife.”

Rarity looked at him with a burning glare, but after a moment, it softened. He was just thinking of his wife. She had to appreciate the romantic side of him. “Oh…of course, dear. I’ll go. I promise, everything will go perfectly. Good luck.”

The Doctor nodded, giving Rarity a small hug, and running off. He had a plan. And she needed to go home.

Cour t was in session. He was third in line now. Rarity was off towards a good way home, and a big shock. So now, here he was. Making a bad decision. Should be fun. He smiled politely as people shuffled in and out. It was his turn now. He felt sorry for those behind him. Who knew if they would get their time or not.

Celestia looked at him as he walked in. She could see something…different about him. She couldn’t place it. Then she saw his eyes. Those…empty eyes. Like the void. “Hello, sir. What is it you wish to speak of?”

He smiled, almost cruelly, as he put his plan into action. “Time, Celestia.” He knew this was not how to address someone like her, and he knew where it would lead. All part of the plan.

Her eyes narrowed. “Excuse me? You may wish to elaborate.” The guards drew in closer to their princess.

“It’s been so long since you were a filly. A princess, as always, but as a filly? You were always so quiet, weren’t you. When was it you became so outspoken?”

He wasn’t speaking standard Equestrian, based on the perplexed looks of her guardsmen. She understood it though, as if it were her own spoken words. She felt a sharp pain in her head. Something missing that she couldn’t understand.

“I just know I’ll regret this next part…” He ran quickly up to her, avoiding guards, and hitting Celestia hard in the head with his own.

A throbbing pain surged through her, and she saw what he wanted her to. War crimes, death, new life, time itself. He had sent the worst parts of him into her mind, and even when it wasn’t him, she knew it was. The guards saw Celestia go into shock and knocked the Doctor to the ground, quickly making an arrest.

She’s seen the worst now…what no one else can see. How will she respond?

Celestia rose from her shock, anger searing in her look. “You….monstrous being. I condemn you to the deepest depths of Canterlot’s dungeons, until such a time as I see fit to release such a thing upon this land."

He hid a smile, looking down at the ground. He wondered if that changeling situation had been dealt with. I wonder if that’s what happened. An elaborate plot of revenge. Poeti-oh look, a hoof.

The guard smashed his head into the ground, knocking him unconscious.

The next day…

Rarity carried the wounded mare into her TARDIS, per her instructions. The doors closed and Rarity sat the Doctor down. It had baffled Rarity what she had heard and seen over those last hours. She now was starting to piece together what her Doctor already knew. It’s the changelings. She looked over at the Doctor, clutching her wound and looking at Rarity, tears in her eyes.

“Rarity…I wish I could know you more. We could have been good friends.” She turned to the console, programming the next destination. “Now, who knows?”

A sudden wave of what Rarity equated to fire washed over the room. When she looked back, the mare she had met hours before was changing under this burning blanket of energy. “Dear Celestia…”

The mare shouted one last thing before the change was completed, and Rarity could scarcely hear what she understood as “Dear Celestia, I have a-“

The final blast cut her off and the transformation ended. Rarity blinked, and breathed out the words, “Doctor Whooves…”

“What was that? Ew, gross, my tongue is bigger.” He peered down his underbelly, making an assessment. “Thought so. Let’s go, shall we?” He flicked a switch, ignoring Rarity’s state of shock.

It’s like she’s…just gone.

Then she heard the brakes.

End Chapter 4.

Shadows of Deceit

Doctor’s Shadows

Chapter 5: Shadows of Deceit

The doors swung open and Rarity was quickly moved through them. The Doctor had no interest in why she wanted to go back to her normal life. He was excited to learn all about his new body, and who he was. Like a child, she thought to herself. She could see a group of ponies up ahead, standing over something, and looking down at it.

Her approach brought the attention of the others upon her. She noted the faces. Her friends. Almost everyone. No Fluttershy. Maybe they haven’t made it there yet…

Only as she took the last few steps did she see what had planted the downtrodden looks on their faces. The body of Derpy Hooves. And something else…was that her daughter? As she gazed down upon the black, hard-shelled creature that was clinging to its lifeless ‘mother’, she couldn’t help but feel a mix of terror and disgust.

“What do we do with it?” The voice issued itself, or felt that way, from Rainbow Dash.

Applejack spoke up in return. “It’s a she. It’s Derpy’s daughter. We gotta protect ‘er. She’s got nopony left.”

“Where’s the Doctor? He can take care of…her.”

“We don’t know that, Sugarcube…he could be just as…bad.”

Rainbow Dash silenced herself, looking down at the blackened creature in its slumber. “Well…we need to find

Fluttershy then. Doctor Whooves visited her more than anypony else. He even donated a shed.”

Everypony nodded, but the question could be seen easily on everypony’s faces. Where was Fluttershy?

The dungeons had been dark, damp, and hard to breathe in, but he had made it. 40 years in solitude. Forty entire years of staying still, never letting anyone see him move, never speaking, never even letting himself shift unless for food. It had to be worth it.

About an hour ago, he had received a cellmate. The invasion had begun, but based on the lack of tremors or earth-shaking explosions, it hadn’t truly entered full swing. It was probably a surprise attack, in the final preparations.

The large mare across the room awoke. He heard her faintly muttering. After a few moments of listening to her call out in the darkness, he began to move. His muscles ached under the pressure. It had been far too long, he realized, since his last movement. It would take some readjusting.

The mare, who had easily identified herself, merely in speaking, as the princess of the night, now quieted, watching the movement in the corner of the room. She quickly went into the Royal Canterlot accent, and slipped into the archaic language of a thousand years before. “Who art thou who approaches?”

He remained unfazed, and looked down upon the lowered form of Luna. She rose to her full height, ready for defense. His throat was coarse and dry from disuse, and he barely scratched out the words. “Hello. I’m the Doctor.”

Luna was taken aback by his address. He did not bow; he did not show any apprehension. Yet, he still seemed to stay behind the line of disrespect, and even seemed to command respect for himself. She lowered her voice, speaking in a sweeter tone. “Well then…Doctor of what?”

“Everything.” It was a simple word, and that was where he left off. He removed the bindings that held back her magic, and she removed her chains. “And you are Princess Luna, of the Night. Some of the best adventures are at night. Thank you.”

Luna began to feel more secure…she now only wondered why she was in the dungeon. It matters not, she decided, looking over her fellow captive. He looked well worn down. The food wasn’t the best this far down into the dungeons. Not to mention his waning physique. Most prisoners tried to keep up their strength. He seemed quite odd.

“Would you mind…maybe teleporting us to the confiscation lockers? I seem to be missing a few things.”

She did not know what to do. He was deep in the dungeons. It must have been bad, whatever he had done. But he seemed very kind. He had freed her. He was her only means to knowing what had happened, it would seem. She agreed, and her magical aura surrounded them, filling the Doctor with warmth he hadn’t felt in years.

The office was filled with lockers, and each locker held many boxes, which held different prisoner’s items. He found box number 76. His box. He opened it and retrieved his suit, his saddlebags, and most importantly, his screwdriver. He had put it at just the right frequency to bring his love back into his life, when he needed it.

Therefore, he put it away. It wasn’t time yet. He had to figure out what to do about Luna. Where is everyone anyways? How are they planning to move an entire city?

The cottage had all of its lights on, yet no one was coming to the door. Even with knocking, no nervous squeaks could be heard from inside, and no movement. Naturally, the door had to be bucked in. Applejack’s hind legs appeared where the door had once stood, and everyone rushed inside, ready to combat any ponynappers or other threats to their friend. The house remained quiet however. It seemed as if no one was home, but there were hundreds of candles lit up around the house.

“Fluttershy!” Rainbow Dash shouted into the silence of the home. No response. The tension between them thickened, as they all began to worry for their shy friend. She was Fluttershy, how could she survive being alone in the darkness, or worse, with something in the darkness.

As they all stood there, somepony else walked in behind them. “’Ey. What are all’a you doin’ here?”

A quick turn accompanied a view of four stallions, carrying large, empty saddlebags and dressed in black. Another one spoke up. “I thought it was just one mare s’posed to be here.”

Applejack returned from surprise quickly, and acknowledged the threat in similar fashion. Readying herself for a fight, she practically growled out her words. “What’s yer business here?”

The stallions chuckled to themselves, receiving, at a surprisingly quick speed, a powerful blow to the jaw of the foremost member of their group. The stallion in question failed to pick himself up, catching the full alert of his companions.

The last of the burglars fell to the ground, Applejack standing over him. Her friends were not quite surprised that she had handled the majority of that fight on her own. It came as great relief that they happened to be there instead of Fluttershy. But where was she?

Canterlot Castle…that morning…

Luna had never known a Doctor to act as if there was equality between them, but here it was. The Doctor, as he had asked to be called, was a strange man. She felt some sort of familiarity. They reached the throne room of the castle.

“Here we are, Princess. Shouldn’t be long now.”

“For what?”

“I don’t know yet.” He smiled as Princess Celestia entered from the door behind her particular throne. Something was already wrong. Oh, good, it’s starting quickly.

Celestia showed signs of a start as she spotted Luna in the room. “Ah, Luna, I was wondering where you were.” She slipped her eyes over to the Doctor in the room. “Who is he?”

Luna studied the other alicorn carefully. “He is a prisoner from down in the dungeons…you should know that, he was too deep to have been placed there without your orders.”

Celestia nodded carefully. “Ah, yes…”

“Well, Celestia, why not tell Luna why I was in there?” His lack of titles in his address caught both Princesses off guard, but Luna cared more about the question itself.

“I had been wondering that, yes.”

“Well,” Celestia began her statement calmly, but quickly began deteriorating as she found herself to be caught. “He was...bad.”

Doctor Whooves stepped forward. “Where did you put her, Nightshade?”

The room shattered.

Ponyville…present…

The five mares were now venturing back into town, where torches had been lit back up, and the townsponies, now calm and no longer in panic mode, were gathered in front of Town Hall. Mayor Mare was addressing the crowd. She went mostly ignored by the girls as they sheltered their still sleeping bundle of…love.

As they walked into the Carousel Boutique, where Rarity had told of an extra room where Sweetie Belle would stay on her visits, they were deciding on what to do with her.

Rarity had already made a decision. “We’ve known her long enough to know she means no harm, so she may stay here.”

“We don’t know that it’s really even her though!” Twilight was behind this outburst, having finally recovered from her shock and worry.

“I do. I don’t know why, but I know she is. She’s just looking a bit different is all. She stays here.” With that, Rarity took up the bundle in her magic and would say no more. The young changeling was still unconscious, but breathing steadily. Rarity gently placed her into a small, makeshift crib. She then sighed, and left the room, under the curious gazes of her friends.

Rather than stay under their scrutiny, Rarity walked up the stairs, into her room, and shut the door. She looked over at Canterlot, or where it should have been, and let out another sigh. I failed him…but if I can keep his daughter safe maybe I’ll be forgiven. Suddenly, the spot she was looking at in the sky exploded.

End Ch. 5

Shadows of Circumstance

Doctor’s Shadows

Chapter 6: Shadows of Circumstance

Derpy walked into the TARDIS, her daughter and husband following behind. “Where are we going?” Her face shone with a look of worry. Dinky simply looked around, taking in the view.

“I’m going to drop you off an hour from now, near town hall. Wait until Twilight Sparkle or someone else comes by, then go with them. Alright?” He fiddled with the console as he spoke, finishing the sentence along with the input.

“Ok…are you ok?” His appearance was becoming raggedy. She hadn’t seen him like this in a long time. She was beginning to think it may have been a long time since he saw her…

“Yeah. Always, dear.” He put on a smile, or maybe a grimace, and turned away. After a moment of silent thought, he moved to his daughter, wrapping his forehooves around her. He took a moment to whisper a few words, then got up to kiss his wife. The doors swung open, and he motioned towards them.

“Goodbye, Doctor.”

“Goodbye, Muffin.”

It was.

Canterlot Castle…present…

The walls of the castle had blown apart. The green fire that caused it had apparently spread out, forming a barrier around the city. So this is how it happened? Interesting spell. The Doctor noted that the sun was already dark…oh no. I couldn’t stop it. He cursed himself as he stood. He saw a large white alicorn standing on the top of the rubble overlooking the gruesome scene of the city. It had progressed so fast. I have to get out of here.

Luna leapt to her feet as she awoke next to the still unknown earth pony. She said nothing as she surveyed the situation. Her eyes settled on what was supposedly not really her sister. As this being turned around, it became clearer. Her walk was more aggressive in nature, and as she came closer, a malicious look came into her eyes. Luna stood stoic.

“Now that the plan is so far in motion, neither of you can stop me.” She turned to the Doctor. “Even you are powerless now. No TARDIS. No helper…I think I’ll be rid of you now.” Fire consumed her form, and there stood a large changeling, whose structure resembled that of a stallion.

If not for all of the holes and the shell…and wings. As Doctor Whooves was lost in thought, Luna rushed forward, smashing into the changeling warlord. It was taken as the perfect opportunity to escape. He pulled the screwdriver from his bags and sent off the frequency.

As the TARDIS began appearing in the room, he heard the words that would set off the next hour of his time. “Just try and save your wife, Doctor!”

The TARDIS…one meta-temporal hour later…

The Doctor watched his wife and daughter exit, sighing in relief. As far as he was concerned, they should be safe now. He had checked the safest locations to drop her off at beforehoof. No reason to worry. Now, it was time for the next phase of his plan. I need to collect Fluttershy. Her friends will come looking, so I need to send along a distraction. He gripped a lever in his teeth and pulled, sending himself through time once again. Raider ponies will do. Any one of those girls could probably handle themselves…probably.

He stopped off and popped the door open, staring happily into the faces of a group of stallions ransacking the schoolhouse. “Why would you raid a school? There’s a beautiful cottage up near the forest. Race you!” He closed the door again, flipped a few switches, and pushed some buttons. Fluttershy was suddenly standing a few feet away, screaming until her lungs were vacated.

“D-Doctor!”

“I left Rarity somewhere around 962, or so. She’ll probably be in Ponyville again by now. I’m trying to speed things up a bit. Based on the rate things are going, this invasion should last a week before a winner comes out. I plan to end it in a day. Ready?”

Fluttershy dropped.

“…good enough.”

Canterlot Castle…

Luna and the changeling called Nightshade grappled on the shattered remnants of the castle, augmenting their assaults with clashing blasts of color. Luna latched on to Nightshade and her horn lit up. No one may impersonate my sister…we go together.

She released the energy built in her horn, and the world around them seemed to vanish.

The Doctor was supporting a now awake and hyperventilating Fluttershy as he landed the TARDIS. He guided her to the door and kicked it open, seeing the black sky only a moment before witnessing the massive light appear at Canterlot. A concussive blast knocked him, Fluttershy, and, according to the screams heard, many of the residents of Ponyville. As he climbed back onto his hooves, and Fluttershy quivered in his wake, it became apparent that the invasion was, officially, over. The shroud over the land vanished quickly, and the sun shone through.

“This isn’t how it’s supposed to go…Luna should still be fighting…did she win?” He puzzled for a minute, trying to deduce the possible outcome.

“That didn’t look like something a winner would do…” Fluttershy’s voice startled the Doctor from his thoughts. “Oh! Sorry, I just meant that if someone had to do that…maybe they were…losing.”

“Maybe…”

Rarity flew back down the stairs as the shockwave hit her. Her friends had also experienced this, as when she looked around, they were still clambering back onto their hooves. She ignited her horn to give more light to the room, and to fix a few things that had been knocked from place. Namely, the bounty of mirrors that were previously on the wall.

“Rarity, are you alright?” Twilight walked over, a slight limp giving evidence to a sharp impact to her hindlegs.

“Of course, darling, do you need something for that leg?”

“No thanks.” Twilight smiled, the presence and well-being of her friends keeping her spirits somewhat upwards of their earlier slump.

As the rest of the room managed to stand up, and the loose objects were replaced, the attention turned towards the window, as sunlight of all things began pouring through.

Rarity took the first view into the blue sky. Did he do it? The only pony capable of answering that question took that precise moment to enter the room, accompanied by a significantly calmer, though still anxious as always, Fluttershy.

He cleared his throat, and with the attention of the whole room, declared: “Rarity, I have no idea what’s going on.”

End Ch. 6