Doctor Whooves Episode 2: The Awakening

by Doctor Perseus

Rating: teen
Tags: Twilight Sparkle, Gore, My Little Pony: Friendship is Magic, Doctor Whooves, Princess Luna, Original Character, Adventure, Princess Celestia, Crossover
Length: 11983

The Doctor and Twilight find themselves 1000 years in the future, where a deadly enemy waits for them.

Following an accident with the TARDIS, the Doctor and Twilight find themselves 1000 years in the future. Here they find a futuristic Equestria, a confused Queen Celestia, and a pony from the Doctor and Twilight's future who wants revenge.

Published 2013-01-12 21:00:02 UTC
Last updated 2013-01-12 21:00:02 UTC

The Future

Chapter 1: The Future

Sweet Apple Industries, Ponyville Central, Equestria, Gaia, Spring, 2002 C.E.

The Doctor and Twilight held on tightly as the TARDIS gave one final jolt. The wondrous sound of the TARDIS faded away and the two confused ponies slowly regained their balance. Twilight had never ridden in something as bumpy and wild as the TARDIS and she groaned slightly as her insides finally settled back into place.

"Well that could have gone better!" exclaimed the Doctor.

"Take me back, Doctor! Now's not the time for me to go galloping off on wild adventures!" said Twilight.

"Sorry but the TARDIS needs time to rest. That darn Dalek damaged it to the point where it can only make one trip every few hours."

"Every few hours?!"

"Yeah and even with that I've got to fix some of buttons and levers so that I can properly take you back home. It seems that the TARDIS is stuck on random for right now so, for a while, we'll be jumping through time and space at random."

"Wait a minute! Did you say that we'd be jumping around through space...and time?!"

"Oh yeah. This isn't just a spaceship. It's a time machine too!"

"That's...practically impossible!"

"Oh I'm sure you magical lot have some sort of time traveling spells in your arsenal."

"We do, I've used one, but they're very tricky to pull off."

"Well time machines can be pretty tricky too when they're not working properly."

"So where...or when has it taken us?"

"Don't know. It was set on random. Outside that door could be anywhere in the universe at any time."

"Can...can we take a quick peak?"

"Why not?! The TARDIS needs a couple hours to recharge so I think we can spare a few hours exploring the unknown. This is exciting! A whole new universe for me to explore! We're on the same page here, Twilight Sparkle!"

Twilight chuckled and the two ponies proceeded to walk through the front doors.

They stepped through the doors to find themselves in a long hallway with metal walls. Everything was shining like polished gold.

"Interesting," said the Doctor as he shut and locked the doors to the TARDIS.

"What is this place?" Twilight asked.

"Don't know. Let's find out, shall we? But first!"

The Doctor reached into his suit pockets and sighed.

"Yes! Still got my Sonic Screwdriver and my psychic paper on me!" he exclaimed.

"What's psychic paper?" Twilight asked.

"I'll tell you when we need use of it. Right now, let's find out exactly where and when we are."

Twilight nodded and they continued to walk down the hallway.

They eventually found a doorway leading out of the hallway and they passed through it. The doorway led into a small lounging area.

"I'm guessing that we're in a factory of some sort," Twilight guessed.

"I was thinking the exact same thing myself," said the Doctor. It was just then that they noticed the room was full of futuristic technologies. A high definition TV hung from the wall, three computers stood next to each other on a long desk, several telephones lines the walls, a mysterious metal circle stood in the middle of the room, and several pictures of ponies lines the walls along with the phones. "Amazing! It seems we're in your world, Twilight, but definitely in the future! Look at this! Computers! Televisions! Modern appliances!"

"This stuff is all so...alien. This is our future?" Twilight asked.

"Looks like it. Now all we need to do is find a date. Ah! Here's a newspaper from today!"

The Doctor reached down towards the newspaper and tried to pick it up with his hooves.

"Blast! Damn! Ugh! How do you pick things up with these hooves?!" snapped the Doctor.

Twilight rolled her eyes and said, "I'll just take care of it."

The newspaper lifted off of the ground and the two ponies looked for a date.

"There's the date! Let's see. Today's date is...June 19, 2002," said the Doctor with a smile.

"WHAT?! WE'RE 1000 YEARS IN THE FUTURE?!" screamed a shocked Twilight.

"No need to shout! The last thing we need is someone...uh...somepony coming across us."

"And just who the hay are you two?" asked a southern voice from behind them. The Doctor and Twilight turned around and Twilight's mouth dropped. There, standing a few feet away, was her friend Applejack wearing what appeared to be a lab coat.

"Sorry to barge in like this! We're safety inspectors," said the Doctor. He reached into his pocket and carefully balanced a small black leather wallet in his hooves. He opened it up and presented it to Applejack. "I'm Doctor Smith and this is my plucky assistant, Susan!" Twilight snapped out of her trance for two seconds to shove the Doctor. "She's very temperamental! I apologize if she acts strange or unprofessional."

"Everything seems to check out alright. Okay. Ah guess you're the real deal. Though I have to admit that I've never heard of the North Equestria Health Inspection Company," said Applejack.

"It's new. Princess Celestia founded it."

"Don't you mean Queen Celestia? She's been going by that title for at least 895 years now if I remember correctly."

"What? Oh! Yes! That's what I meant to say! Sorry! I forgot to have my dosage of morning coffee."

"Oh I've been there partner! Take care you two!"

Applejack nodded to the two visitors and stepped onto the metal circle. There was a series of three dings and Applejack disappeared.

"Why it's a teleportation pad! Ingenious! It's amazing what you ponies were able to invent in only 1000 years!" exclaimed the Doctor as he bent down to examine the pad. He looked up at Twilight to see that she was still in a daze. "You alright there, Twilight?"

"That...that pony we just saw," she breathed.

"I liked her. Definitely a southern pony."

"She's my friend, Applejack."

"What?"

"I have a friend back in my time named Applejack. She runs a farm outside of Ponyville called Sweet Apple Acres. That pony we saw was her! But it couldn't have been her if we're 1000 years in the future! Besides, she didn't even recognize me."

"Let's see what type of factory this is."

The Doctor stood up and beckoned Twilight onto the pad.

"Where are we going?" she asked.

"Exploring! That's the best part of time traveling!" replied the Doctor. Twilight looked over towards the wall and noticed a sign.

"Floor Six. Lounge Room 29."

"This pad must rely on thought so we just have to think of where we want to go and we're off."

"Doctor, remember floor six, lounge room 29. So we can come back here and find the TARDIS."

"Right. So where do you want to go?"

"Let's follow Applejack. I want to find out how a friend of mine is still alive in 2002 without any memories of me."

"Okay. Follow that Applejack!"

Twilight chuckled slightly as she stepped onto the pad. The Doctor and Twilight closed their eyes, pictured Applejack in their minds, three dings rang out, and...they were off.

Canterlot Castle, Canterlot, Equestria, Gaia, Spring, 2002 C.E.

Two guards, a pegasus and a unicorn, stood guard outside Queen Celestia's bedroom.

"Is it true what the others are saying?" asked the pegasus.

"What are they saying?" asked the unicorn.

"That the Queen is losing her sanity."

"I highly doubt that. She's ruled over Equestria for almost 2002 peaceful years. Sure there have been a few hiccups here and there but I highly doubt that something's going to happen that's going to cause our Queen to go nuts!"

Just then an earth pony guard ran up to them. He was definitely in a hurry.

"Where are you off to in such a rush?" asked the pegasus.

"I need to talk to the Queen, immediately!" said the guard.

"She's sleeping right now. What do you need to tell her?" asked the unicorn.

"That they've found it. One of our men has found the blue box that the Queen has been looking for."

The bedroom door flew open and Celestia stared out from the doorway. Her hair was strewn and a crazy look was etched onto her face.

"They've found the blue box?" she asked hungrily. "Tell them to bring it to me! Bring it to me now!"

"Yes, your majesty!" said the guard as he ran off.

"Your majesty," said the unicorn. "I'm puzzled. What do you need with a blue box?"

"You'll find out soon enough!" chuckled Celestia as she retreated back into the room. The unicorn and the pegasus stared at each other.

"Maybe the others are right," said the unicorn nervously. "Maybe she is losing her mind!"

The Apple Factory

Chapter 2: The Apple Factory

Sweet Apple Industries, Ponyville Central, Equestria, Gaia, Spring, 2002 C.E.

The delectable smell of sweet apple pies swam through the Doctor and Twilight's noses as they arrived at their random destination.

"That was fun!" said the Doctor.

"That smell. It smells exactly like one of Applejack's pies!" said Twilight. They stepped off the pad and found themselves in a large kitchen. The kitchen was full of ovens, each with around five apple pies baking inside of them. All around the kitchen were boxes filled up to the brim with fresh, ripe apples. "Is this an...apple factory?"

"An entire factory dedicated to packaging apples and making many different assorted goods out of them. Interesting."

"Is this supposed to be the sequel to Sweet Apple Acres or something of that nature?"

The Doctor laughed and they began walking down one of the aisles. The entire kitchen was bristling with the sounds of ovens baking and machines running but there seemed to be nopony in sight. They walked a little bit further into the kitchen before they came across Applejack again.

"Applejack!" Twilight called. Applejack turned towards them and approached happily.

"Howdy there! How can ah help you?" she asked.

"We're the safety inspectors, remember? We met you a few moments ago in Lounge Room 29," said the Doctor.

"You must have met one of my sisters," said Applejack. "And my name's not Applejack. It's Harriet."

"Harriet?" asked a confused Twilight. "Are you a descendant of Applejack's?"

"Are you referring to the Applejack? No. She never had any children...well, no biological children anyway."

"So how come you and your sister look exactly like Applejack?"

"Don't you know this stuff? Ah thought everypony knew this by now."

"We don't get out much," lied the Doctor.

"That makes since. My sisters and ah are clones. Harvested from the DNA of the original Applejack."

Twilight's mouth dropped again and the Doctor pushed it back up.

"Clones?" breathed Twilight.

"Yep! There are around 376 Applejack clones working in the facility today! And there's also around...355 Big Macintosh clones, which ah thought was kind of pointless since we have his own kin co-running the place."

"So who's in charge of Sweet Apple...uh...Acres now?"

"Sweet Apple Acres? It's been Sweet Apple Industries since the Apple Family made it big in 1071! You two really should get out more."

"Well we're out now and that's what matters. Thank you for the information, Harriet. We shall be on our way!" said the Doctor.

"Alrighty then! You just check up on everything and have a nice day!"

The Doctor grabbed Twilight and pulled her down another aisle. They soon found a door and walked through it. The door led out onto a platform that overlooked a massive indoor apple orchard. It was at least three times the size of the apple orchard from Twilight's time and it was all located under one massive roof. The Doctor and Twilight looked down to see various Applejack and Big Macintosh clones bucking apples from the trees and carrying them away in wheelbarrows that levitated one foot off of the ground.

"This is really weird, Doctor," said Twilight.

"I'm still amazed that you ponies managed to do all this in just 1000 years!" said the Doctor happily. "I'm honestly impressed!"

"So much has changed."

"Well a lot can change in 1000 years."

"What if I never get back to my time?"

The Doctor turned towards Twilight and looked her straight in the eye.

"Listen to me, Twilight Sparkle. I'm going to get you home. No matter how long it takes. I will get you home."

"Thank you, Doctor."

"I guess we could start heading back to the TARDIS. That is if you're done exploring."

"I could use a good rest inside that blue box right about now."

"Great! While you get a rest in one of the bedrooms, I can get some time to work on fixing the TARDIS."

"Sounds good."

Just then a pegasus guard with a megaphone flew up towards the platform and said, "Doctor and Twilight Sparkle! You are hereby under arrest under the direct orders of Queen Celestia!"

"What did we do?!" asked Twilight.

"No time for questions! Just run!" said the Doctor. They turned around and ran back through the kitchens. The pegasus guard was in hot pursuit.

"Stop or I will use force!" he yelled.

"Sorry but we don't feel like getting arrested today!"

They made a sharp turn towards the teleportation pad.

"Floor six, lounge room 29!" said Twilight. They jumped on the pad and, following three dings, they were gone.

They stumbled around for a few seconds before jumping off of the pad. Two Applejack clones and a Big Mac clone were having lunch in the room.

"Howdy!" said the Applejack clones. The Doctor and Twilight didn't have time to respond for the pegasus guard had followed them. They burst through the door and ran down the hallway.

"The TARDIS should be around this bend!" said the Doctor. They rounded the bend and found...nothing. The TARDIS was gone. "I swear that we left it right here!"

The pegasus guard was closing in on them.

"Stop!" he ordered. Twilight turned around and shot three magic blasts at him. They were all direct hits and the guard fell to the ground like a bag of sand.

"Sorry. Had to do it," said Twilight. She then turned back to the Doctor and her face fell at the thought of the missing TARDIS. "So...we're stuck here?!"

"Apparently," said the Doctor. Twilight sat down and leaned against the nearby wall.

"Fantastic. I'm trapped in the year 2002 where there are Applejack clones, indoor apple orchards, and teleportation pads! And now I have a bounty on my head!"

"Come on, Twilight. It's not that bad. It's just curious."

"Hmm?"

"Well why would the Queen want us to be arrested?"

"I don't know. Celestia and I have always been close. I don't understand what I might have done...or will do to make her want me jailed."

"Something doesn't feel right. Something is just not right."

Equestrian Academy of Magic and Skills, Ponyville Central, Equestria, Gaia, Spring, 2002 C.E.

Charlie was still in shock when the Headmistress got off the phone.

"Did you say the Doctor and Twilight Sparkle? As in the Doctor and the Twilight Sparkle?!" he asked.

"The very same," replied the Headmistress. "Follow me."

Charlie eagerly trotted after the Headmistress. They left the room and went into an elevator.

"Tell me, Charlie. Have you read any of the stories relating to the many adventures that the Doctor and Twilight Sparkle had together?"

"A few. Not many. But the ones I have read were amazing!"

"Yes. This is a special occasion because today was their first real time trip together."

"It was?"

"And it is. Right around this point they should be at Sweet Apple Industries. Which means we need to act fast."

"Why?"

"Because her forces are sure to be after them soon."

"Whose forces?"

"Thalia's."

Charlie cocked his head and scratched it.

"Who's Thalia?" he asked.

"Exactly. Most of the facts have been changed in the stories. The writers were complete idiots. There's actually several stories about them that are complete fiction. I can assure you, Charlie, that the Doctor and Twilight Sparkle never fought off a horde of dragons the size of skyscrapers," said the Headmistress.

"Man! That was one of my favorite stories!"

The elevator came to a halt and they emerged at one of the lower levels of the Academy. They walked down a couple more hallways until they reached a simple room that contained little more than a sofa, a table, and a teleportation pad. There were three dings and the large form of Queen Luna appeared before them.

"Your majesty," said the Headmistress.

"It is good to see you again. Have you alerted Crisp?" asked Luna.

"Yes. His men should be looking for them as we speak."

"Good. My sister has been slipping in and out of madness constantly now. Her castle must be impenetrable by this point."

"She probably has the TARDIS by now. We must hurry. Thalia will be getting her clutches on them soon enough!"

"Right!"

Just then an alicorn pony around Charlie's age appeared before them. She looked an awful lot like the Headmistress except she had a blue coat, indigo hair, and violet eyes.

"Yes Mother?" asked the pony as she approached the Headmistress.

"Juliet. I want you and Charlie to head on over to Sweet Apple Industries. Go into Crisp's office. Queen Luna and I have some business to attend to," said the Headmistress.

"Wait. I'm going too?" asked a stunned Charlie.

"Of course! My daughter can't go alone!"

"But what are you and the Queen going to do?"

"Something important. We need to acquire something."

Before Charlie could ask anymore questions he was grabbed by Juliet and pulled onto the pad.

"Action first. Questions second," said the excited alicorn. Three dings rang out and they were off.

Sweet Apple Industries, Ponyville Central, Equestria, Gaia, Spring, 2002 C.E.

Twilight sighed as she and the Doctor found themselves at another dead end.

"I wish I could just teleport out of here!" said Twilight.

"Why can't you do just that?" asked the Doctor.

"Something's affecting my magic. It's blocking me from doing anything major like teleportations."

"Figures. We better find a teleportation pad soon before another one of the Queen's guards shows up."

They turned around another bend to find a group of four Applejack clones.

"Howdy there! Are y’all looking for something?" asked the largest of the four.

"Is there a teleportation pad near here?" asked Twilight.

"Just inside this room," said the second clone.

"Thanks," said the Doctor. The two ponies ran through the doorway only to find a stairwell instead of a room. Four sets of hooves then pushed against their backs and knocked them down the stairs.

"Have a nice fall!" laughed one of the clones sadistically before shutting the door and locking it.

"It was a trap!" said the Doctor.

"No. Really?" asked Twilight sarcastically. The two ponies got up and examined the area around them. There was nothing there except the stairwell behind them and a long tunnel ahead of them lit up with lanterns. "This must lead to the basement."

The Doctor ran up towards the door and pulled out his Sonic Screwdriver with his teeth. He clicked the button with his tongue and aimed it at the door. The Sonic Screwdriver emitted its strange sound but the door refused to open.

"Should've guessed that they wouldn't have made it that easy!" he said as he stored his Screwdriver away.

"Now what?" asked Twilight.

"We follow the tunnel. Who knows? It might lead us to the TARDIS."

"Or to our deaths."

"That too."

They turned to each other, shrugged their shoulders nervously, and began their trek down the tunnel.

The Lower Chambers, Underneath Ponyville Central, Equestria, Gaia, Spring, 2002 C.E.

Water trickled down the walls of the room as two Applejack clones worked near a large tub of water.

"She's almost ready," said a clone named Patricia.

"Ah agree," said another one named Annabeth. "All we need now is the final ingredient."

The two clones turned to each other and laughed sadistically.

"Twilight Sparkle!" they laughed. A swarm of bubbles formed on the surface of the water as they continued to laugh.

What Lies Beneath

Chapter 3: What Lies Beneath

Sweet Apple Industries, Ponyville Central, Equestria, Gaia, Spring, 2002 C.E.

Charlie and Juliet stumbled off of the teleportation pad to find themselves being stared down by a yellow-coated stallion. He was tall, had a strong frame, had a billowing brown mane, and had two deep brown eyes.

"I assume that your mother sent you," said Crisp Oaks.

"Yes," said Juliet.

"Okay. We better head down then."

"Down? Down where?" asked Charlie.

"Under the city."

Charlie gulped. He hated going underground. He was a pegasus. He needed the air and the sky. Being underground just gave him the creeps. Charlie, Juliet, and Crisp left the office and began walking down a nearby hallway.

"The bad AJ's have already been locked up," Crisp stated.

"That bad AJ's?" Charlie asked.

"You know. It's a good thing that this particular trip of the Doctor and Twilight Sparkle was written down. I was eventually able to catch all of the Applejack clones that went rogue."

"Rogue?"

"Yes. From what I've calculated there are only two clones left unaccounted for. They're probably helping Thalia."

"Who's Thalia?"

"Yeah," said Juliet. "Who exactly is this Thalia?"

"You'll find out soon enough. She's a real nasty piece of work that one," replied Crisp. "We ponies used to think she died all those years ago but she didn't. She's been waiting. Planning. And now the last piece of the puzzle has arrived."

"And what is this last piece of the puzzle?"

"It should be obvious."

"The Doctor and Twilight Sparkle," breathed Charlie.

"Exactly. I'm pretty sure that they're already on their way down."

They went around another bend until they came to a door surrounded by five guards.

"Mr. Oaks! We're ready to proceed if you are!" stated a unicorn guard.

"Hurry! Hurry! Down we go!" Crisp ordered.

"Down we go," groaned Charlie as they passed through the door leading towards the basement.

The Lower Chambers, Underneath Ponyville Central, Equestria, Gaia, Spring, 2002 C.E.

"AH!" Twilight screamed. "Something touched my back!"

"Don't worry. It's just an old spider web," said the Doctor.

"Oh...well if it's just a web-"

"Don't move! I think that web still has some inhabitants."

Twilight began jumping and bucking around until the webs finally came off.

"Ugh! I wish there were another way out of here!"

"I do wonder how far down we've traveled."

"These tunnels must be ancient. Look at the bricks. They're all old and covered with grime and...more cobwebs."

"Well compared to you these bricks are brand new, considering the fact that you were born over 1000 years ago."

"Is that supposed to make me feel better?"

"I was just trying to be witty."

"Well please stop. You're not making this any easier for me."

"Fine."

The two ponies fell silent as they walked deeper and deeper into the caverns below Ponyville Central. They eventually found themselves in a massive chamber that was designed like the interior of a castle tower. A pool of swirling water sat in the middle of the chamber.

"We must be down with the sewage," guessed the Doctor.

"Lovely," said Twilight. Then they heard it. Voices. Muffled conversations echoing throughout the tunnels. "There must be somepony else here."

"Well lets find that certain somepony and see if they know any way out."

They walked alongside the pool of sewage until they found the tunnel where the voices were emanating from. They entered the tunnel and followed the voices until they found themselves at a dead end.

"Hello?" Twilight asked.

"How odd. Voices and nopony here. I'd have my guard up if I were you, Twilight," said the Doctor. The sound of stones falling into water echoed from behind and they turned around to see two cloaked ponies walking towards them. "Uh. Hello there. Yes. Do you know a way out of here?"

"There is no way out of here," said one of the cloaked ponies. The voice sounded somewhat female and southern but it also sounded warped and somewhat male.

"The tunnels go on into infinity," said the other cloaked pony.

"Who are you?" Twilight asked.

"We are friends. We are her friends. We are your friends," they said together. The Doctor and Twilight turned towards each other and then back to the ponies.

"Excuse me but who is this her that you're referring to?" asked the Doctor.

"She desires friends. She desires the air and the light. She desires you, Doctor and Twilight."

"Doctor...I really don't think they're going to help us," said Twilight.

"She wants your help. She wants your friendship."

"They're barring us in!"

"She wants your skin. She wants your blood."

"Definitely not friendly," choked the Doctor.

"She wants your life. She wants your death."

The ponies pulled knives out from their cloaks and clutched them in their mouths.

"Twilight, you remember that thing you did to the guard up above?" asked the Doctor.

"Yeah," said Twilight.

"Would it be too much trouble for you to do it now?"

Twilight aimed her horn at the cloaked ponies and fired. The spell hit them but they seemed unaffected.

"She wants your life. She wants your death," they repeated.

"Damn! Where's a secret passage when you need it?" asked the Doctor. The Doctor and Twilight pressed up against the wall behind them and the wall suddenly turned around like a revolving door. Once the wall was done turning they found themselves in a medium-sized room that resembled that of an underground laboratory. "Now what's all this?"

They looked through the room and saw several different operating tables, tubs of water, and boxes of various sizes.

"What's in here?" Twilight asked as she approached one of the boxes. She opened it and yelped.

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

"There...there are mutilated animals in these boxes!"

The Doctor approached the box that Twilight had been examining and gave a look of repulsion. The box was filled with the cut up bodies of young forest animals. The smell was horrendous and Twilight nearly gave up the contents of her stomach.

"Fluttershy would have a heart attack if she saw this place," said a sickened Twilight. "What the hay is this place, Doctor?"

"A lab. Obviously home to some illegal activities," said the Doctor. Twilight backed up a few feet and suddenly felt something small and sharp go into her neck.

"Sleep dreams, Twiley," cackled one of the cloaked ponies, who had just injected an anesthetic into Twilight via needle.

"Twilight!" cried the surprised Doctor.

"Ms. Thalia! He's ready for you!" called the second clone as they vanished into another secret passage with the unconscious Twilight. The Doctor looked around as various dead animals, now obviously being possessed by something, stood up from their boxed graves and slowly crawled towards the Doctor.

"After this I hope Twilight and I end up on a tropical island!" he choked as the creatures drew closer.

The Upper Lower Chambers, Underneath Ponyville Central, Equestria, Gaia, Spring, 2002 C.E.

It was incredibly damp underground. Charlie didn't like it but he somehow found comfort about it while he was around Juliet. She certainly was pretty. Charlie shook his head and turned away from Juliet. This was no time to develop a crush. He was underground and trying to help save the Doctor and the Twilight Sparkle from a mysterious villain named Thalia. They soon reached the very bottom of Sweet Apple Industries' basement.

"Okay. The main Lower Chambers are through this door here," said Crisp. The guards nodded and proceeded to open up the door. As soon as the door opened, however, a horde of disfigured animals fell through.

"You shall not pass!" they screamed.

"What in Celestia has she been doing down there?!"

"Take them!" yelled one of the guards. The guards then began kicking and fighting their way through the animal zombies.

"Charlie! Juliet! Stay behind me!" Crisp ordered. The two of them did as they were told. Then a series of dead hands reached up through the floor and grabbed Juliet. She began to sink through a hole in the floor.

"Juliet!" cried Charlie as he grabbed onto her. Crisp tried to grab onto them but a possessed fox jumped onto him and caused him to smash into a back wall. Charlie held his breath and he and Juliet were pulled into the earth below.

The Lower Chambers, Underneath Ponyville Central, Equestria, Gaia, Spring, 2002 C.E.

The animals were close now. The Doctor had resorted to kicking and punching at them with his hooves. It wouldn't be long before they managed to consume him. Just then a nearby wall exploded and a pile of mud, brick, and animals poured in. The animals attacking the Doctor were knocked aside as the dirt poured it. The slide of dirt stopped and the Doctor realized that there were two ponies in the dirt.

"Are you alright?!" he asked as he ran to their aid.

"Could've been worse," choked the pegasus.

"I'm glad that my mom went to the trouble of teaching me that spell," said the alicorn. The two ponies looked up at the Doctor and their eyes widened. "Oh my Celestia! It's you!"

"Yeah! It's me! Uh...do I know you?" said the surprised Doctor.

The ponies hopped up and each shook the Doctor's hoof vigorously.

"My name's Charlie Kemp," said the pegasus. "I'm a huge fan of your adventures!"

"I'm Juliet," said the alicorn. "Juliet Sparkle."

"Wait a minute. Juliet Sparkle?" asked the Doctor. "You can't possibly be related to-"

"Yes. Twilight Sparkle's my ancestor."

"Well Juliet Sparkle. The pleasure is all mine. And it's also nice to meet you, Charlie Kemp. I thank you very much for rescuing me from the animal zombies but, not to brag or anything, I probably could have finished them off on my own."

"Excuse me but...where's Twilight?" asked Charlie.

"Damn! I nearly forgot! Some cloaked ponies took her to God knows where!"

"They've taken her to Thalia," said Juliet.

"Thalia? Who the hell is Thalia?"

"We...don't know that either," coughed Charlie. "It seems that only the Headmistress, Queen Luna, and Crisp Oaks know who this Thalia pony is."

"Well, whoever she is, she's endangered my friend. I promised her that I'd get her home and by a Queen Victoria's werewolf blood I'm going to keep that promise!"

"So where do we start looking?"

"No idea."

"I have an idea! Queen Luna and my mother were talking earlier about Queen Celestia having possession over the TARDIS," said Juliet.

"Celestia's the one who stole my TARIDS?! That's a bit rude."

"They've been talking about how there's something horribly wrong with Queen Celestia and I believe this Thalia pony has something to do with it. So I'm guessing that where your TARDIS is-"

"That's where Twilight should be too! Brilliant!"

"But how are we going to get to Canterlot? We're all the way underground with no means of getting back to the surface," said Charlie.

"I think I know how to get there quickly," said Juliet.

The Crystal Caverns, Underneath Canterlot, Equestria, Gaia, Spring, 2002 C.E.

Twilight awoke to find herself strapped to an operating table by tough, metal bonds. There was a long cut on her left foreleg and blood was slowly oozing out of it. It hurt slightly but it wasn't agonizing. She turned left to see the cloaked ponies holding a medium-sized jar filled with...her blood. The ponies looked over at Twilight and giggled.

"You're awake," they said together. "Now the fun can commence."

The ponies poured the bottle of Twilight's blood into a large tub of water. There was something in the water and it began to jerk around after the sudden exposure to blood. Suddenly the tub exploded and the ponies were knocked back. A beam of white light circled around the form of a thin pony. The pony danced in the light and Twilight's blood began orbiting around the pony like rings. The blood was absorbed into the pony's body and there was a second, and brighter, explosion of light.

Soon the light show was over and a mare unicorn stood in the middle of the room. Twilight noticed that the cloaked ponies laying on the ground were more Applejack clones. Her attention then turned back towards the mare. The mare raised her head and Twilight gasped. The mare...was her. This clone of Twilight was very different. She had a pale white coat, hair and eyes as black as night, and a smile that could make even the meanest of dragons shiver in fear. Twilight stared at the clone as she laughed and slowly approached the bound Twilight. She leaned against the table and brought her face only a few centimeters from Twilight's.

"Hello, Twilight Sparkle," she said. "It's good to see you again after all these years. You and your Doctor have foiled me time and time again...but this time I win! Your Doctor is dead, you are weak, and I, Thalia, am strong! Enjoy these last few breathes of air, Twilight, because soon you won't have to worry about breathing anymore."

A Flaw in the Plan

Chapter 4: A Flaw in the Plan

Old Barnaby Station, Underneath Ponyville Central, Equestria, Gaia, Spring, 2002 C.E.

The Doctor, Charlie, and Juliet fought their way through another wall of cobwebs and found themselves standing on the platform of an old subway station. The station was built into the side of an underground chamber and the chamber was large enough to hold three train yards. Several different old train tracks were laid out throughout the chamber but the only one that led out of there was a single track that ran alongside the platform.

"This station used to be used constantly but it got shut down after the depression of the 1640's," said Juliet. "The cars were specifically made to be moved by either unicorns or alicorns. And, luckily, there happens to be a car right here."

The train car that Juliet pointed to resembled that of a trolley that the Doctor had seen riding through San Francisco.

"Truly marvelous! I'm still impressed by how much you lot have advanced in just this short amount of time!" exclaimed the Doctor. They then entered the trolley and Juliet walked up to the front.

"Now, according to what I've read, these trains can go really fast so we should be in Canterlot in at least half an hour."

"Then let's go! Allons-y!"

Juliet nodded and her horn began to glow. The train car slowly moved forward and soon they were racing down the track. The Doctor and Charlie sat down across from each other to wait out the ride.

"So what were two doing down here, again?" asked the Doctor.

"Juliet's mother sent us to go down and look for you and Twilight with Crisp Oaks, the head of Sweet Apple Industries," Charlie replied.

"How did they know that we'd be in this time period at all?"

"There are countless stories about you and Twilight Sparkle."

"There are?"

"Yeah. Now, granted, some of the facts have been warped and a majority of the stories are works of fiction, according to the Headmistress, but they're still classic stories."

"If they're so classic then how come you two don't know Thalia or about what's supposed to happen?"

"It's funny. I've read a fair amount of your stories and I have a friend who's completely crazy about you. He's told me about every story and none of them talk about you arriving in this time period."

"Then how could your Headmistress or this Crisp Oaks pony know anything about it?"

"I'm still trying to figure that part out."

"We should be there shortly!" Juliet called. The Doctor and Charlie turned back to each other, laid back in their seats, and waited.

Chariot Pass, Outskirts of Canterlot, Equestria, Gaia, Spring, 2002 C.E.

The Headmistress and Queen Luna stared out upon the grand city of Canterlot. Queen Celestia was no doubt sleeping peacefully in her bedroom. The TARDIS would be close by her.

"You ready, Sarah?" Queen Luna asked. "Are you ready to fulfill history?"

Sarah Sparkle looked down at a large bag hanging around her back and she nodded.

"I've read the story countless times. I know how it's all going to play out," she replied.

"I still don't understand why you've never let anypony else read the story. You've only told your secretary, Crisp, and myself. You haven't even told your daughter about it."

"Like the Doctor said, or says, "Some points in time are fixed and some are in flux." This is a time that's definitely fixed. I have to let it play out like Twilight Sparkle wrote it out. Otherwise time itself would unravel and we'd be caught in a never-ending paradox."

"You've put a lot of thought into this, haven't you?"

"I've read that story hundreds of times since I first read it as a young foal. I read all the stories and have spent years of my life dedicated to studying the history of Equestria, and most notably that of the Doctor and my ancestor. Of course I've put a lot of thought into this."

"Then, if you're ready, let's head down there and finish something that should have been finished years ago."

"I couldn't agree more."

With that, Luna used her magic to open up a small cave entrance that stood on the side of the train tracks leading into Canterlot. Sarah was the first to enter and Luna followed suit, making sure to close the entrance as she entered.

Crystal Station, Underneath Canterlot, Equestria, Gaia, Spring, 2002 C.E.

The train car came to a halt and the trio of heroes hopped out. This station wasn't as big as the one they had previously been in but it was definitely in better shape. The walls were made of solid marble and granite and chunks of glass and crystals shone from the walls. The Doctor wanted to stay and admire the architecture but this was not the time to do so. He had a friend to save.

"So what is this place?" asked the Doctor.

"This place is known as the Crystal Caverns. They used to be used as a dungeon for war criminals in the early years of Equestria. In fact, the spot where Canterlot sits now used to be a massive prison. They were forgotten following the fall of King Discord to the Queens and weren't rediscovered until 1002. It wasn't until 1291 that the Queens decided to start using it as an underground transportation system. But, like I said earlier, the depression of the 1640's caused it to become abandoned again," said Juliet.

"Seems like the perfect place to hide."

"Yeah. It sure gives me the creeps," Charlie croaked. They walked through the interior of the station until they came across a blocked stairwell. "I'm guessing that leads up to the city."

"Used to. There has to be another way out of this station and into the main caverns," said Juliet. They began examining the area and the Doctor pulled out his Sonic Screwdriver. Using it with his mouth was definitely strange but it's something that he was getting used to pretty quickly. He aimed it at a nearby wall of glass and activated it. The light hit the wall and it shook a bit. The wall slid aside to reveal a long and incredibly dark passage.

"This Thalia sure likes to use secret passages," the Doctor chuckled.

"It's pitch black in there!" said Charlie. "We wouldn't be able to see our hooves in front of our faces!"

"I can take care of this," Juliet said. Her horn then began to emit a dim bluish light. "It's not the best illumination spell but at least we won't be blind."

"Perfect!" said the Doctor. "Onwards!"

Charlie gulped as they entered the dark passage.

There wasn't much room inside the passage. In fact, it was only wide enough for two ponies to walk next to each other with a little bit of space between them. Juliet took the lead while the Doctor and Charlie walked behind her.

"You okay?" the Doctor asked Charlie.

"Fine. Could be better though," Charlie responded.

"I take it that you're not fond of being underground."

"I'm not fond of a lot of things."

"Then why did you agree to come and help Twilight and I?"

"The Headmistress kind of sent me. I didn't have much of a choice."

"But you didn't protest."

"How do you know that I didn't protest?"

"The way you're acting. Sure you're unsure, frightened, and somewhat nauseous but you're not constantly complaining or running away from danger. That proves that, somewhere in your mind, you want to be down here."

"I don't know."

"Think about it."

Charlie nodded and looked forward again. The tunnel slowly began to widen out until they came to a large, open room. The Doctor pulled Charlie and Juliet back as an explosion of light began emitting from the room.

"Stay back and keep quiet!" he whispered to the two ponies. "And, Juliet, turn off your horn!"

The light around Juliet's horn faded away and they turned towards the room. The Doctor crept in front of Charlie and Juliet and looked around the corner.

Twilight was there but she was strapped down. There was a pair of cloaked Applejack clones laying unconscious in the corner of the room. In the middle of the room there was a mare. A mare with a pale white coal, night black hair and eyes, and a look very similar to Twilight. It was then that the Doctor realized that this mare was a Twilight clone! The clone laughed and approached Twilight. She then proceeded to gloat in front of Twilight and mock her.

"Enjoy these last few breathes of air, Twilight, because soon you won't have to worry about breathing anymore," she chuckled. The mare walked over to a nearby table and grasped a butcher's knife in her mouth. Twilight struggled at the bonds but she couldn't break free. "This...will be fun."

The Doctor couldn't wait any longer. He stepped out from behind the corner and casually walked over to the spot where a tub of water once stood.

"You know, you should really redecorate this place," he said. The Twilight clone, who had revealed herself to be infamous Thalia, turned around. The knife fell out of her mouth and hit the floor.

"How the hell did you escape my animals?!" she asked.

"I had some help."

Charlie and Juliet emerged from the shadows and stood behind the Doctor.

"How charming. You've formed your own rescue team!" Thalia teased.

"Yeah well I like teams. Teams make everything fun," said the Doctor.

"Yes. They certainly do. You know, this isn't a hiccup at all. Now I can gain the pleasure of killing both you and her!"

"And you can go along and do that shortly but listen to this. It seems to me you've met us before."

"All too many times, Doctor."

"But Twilight and I have yet to meet you before."

"What do you mean by that?"

Thalia picked up the blade and clasped it between her hooves.

"You see...this is Twilight and I's first real trip together. We haven't met you before. You don't exist yet in our timeline."

"You're lying! You're just trying to buy time."

"That may be but listen. If we've yet to meet you that means you don't exist yet. Now, I'm assuming that you're a clone of Twilight, harvested from her DNA. If you don't exist yet from our standpoint and you kill Twilight now...then how will you end up being created?"

"I...I-"

"Exactly! You wouldn't be created! But then, if you were never created, who would be down here to kill Twilight in the first place? Nopony! Don't you understand?! If you kill Twilight or me...then you prevent yourself from existing altogether! And, in the long run, time would fall apart from the paradox."

Thalia looked down at the ground. She had picked up the wrong Twilight. This was a Doctor and Twilight from before her creation. He was right. She was stuck. But...she didn't care.

"What makes you think that I care by this point?!" she snapped.

"Pardon?" asked the Doctor.

"So what if I destroy my existence?! So what if I cause time to unravel! I'm ready to face that in order to finally feel satisfaction for just a few seconds."

"You're completely mad!"

"And whose fault is that, Doctor?! Who drove me to this point?! You did! You and this lavender bitch! It's time to settle a score."

Thalia turned around and raised the blade. Twilight's eyes widened as the blade came down.

It all happened in a flash. The blade was a few inches from Twilight's neck when something yellow flew past and smashed into Thalia. The blade flew through the air and embedded itself in the wall. Charlie didn't know what we was doing but he suddenly found himself fighting against a thrashing evil clone of Twilight Sparkle.

"Kill them!" screamed Thalia. The two Applejack clones sat up, their eyes glowing with black energy, and began advancing on the Doctor and Juliet.

"I'll handle these two. You free Twilight!" said Juliet. The Doctor nodded and pulled out his Sonic Screwdriver. It didn't take long for him to undo Twilight's bonds.

"Thank...thank you, Doctor," Twilight breathed. She had definitely lost a lot of blood and she was slowly losing consciousness.

"Stay with me, Twilight! Stay with me!" pleased the Doctor. Thalia pushed Charlie off of her and threw him into the wall. She then stood up and pointed her face upwards. Her eyes glowed of pure black light.

"Celestia! The time has come! Destroy the city!" she yelled.

Canterlot Castle, Canterlot, Equestria, Gaia, Spring, 2002 C.E.

The pegasus and unicorn guard in front of Celestia's bedroom had begun talking about a new movie coming out when the bedroom door flew open. Celestia's eyes were completely black and an evil smile was etched onto her face.

"Destroy the city," she cackled. "Destroy the city!"

She flew at the guards, shooting several beams of dark energy at them. They dodged the attacks and fled. The unicorn activated his communicator as he ran.

"Celestia's gone insane! She's crazy! She's trying to kill us! We need backup!" he cried. Celestia then proceeded to begin her unwilling destruction of Canterlot Castle.

The Crystal Caverns, Underneath Canterlot, Equestria, Gaia, Spring, 2002 C.E.

"What? Celestia?" asked a woozy Twilight.

"Yes. It took me some time to expand my telepathic influence while I was still weakened but I managed to drive myself deep into Queen Celestia's psyche," Thalia chuckled.

"So now, instead of killing us, you're going to have Celestia destroy the entire city above?!" snapped the Doctor.

"Their blood shall be on your hooves, Doctor! You brought this tragedy on those ponies the day you began your campaign against me!"

There was a bright flash and Thalia was gone.

"Damn! Come on, Twilight!" said the Doctor. Charlie and Juliet were battling the clones but they were incredibly strong.

"How much longer can we hold them off?! Charlie asked.

"Not long!" croaked Juliet. Just then, a nearby wall burst open and a beam of light shot out of the hole. The Applejack clones were caught by the light and they instantly fell apart. Charlie and Juliet turned towards the hole to see that it was none other than Juliet's mother and Queen Luna.

"Mother!" cried Juliet. Sarah had a strange device attached to her hoof that was emitting a lot of steam.

"I knew that you two would be here. How are you?" she asked. Luna looked over and saw the Doctor holding the weak Twilight. Sarah nodded to the Queen and Luna walked over to help.

"Hello again, Doctor," said Luna as she knelt down next to him.

"Princess, I mean Queen Luna? How did you know that we'd be down here?" asked a stunned Doctor.

"Sarah told me. She's known that this would happen for many years."

"How?"

"She's had a story about you and Twilight in her possession for her entire life. Only she has read it."

"Huh."

"What?"

"That was actually for two things. One was for her knowing that this would all happen and the other is the fact that I've just now realized that you and your sister are immortal. My mind has sure been preoccupied with other things."

Luna chuckled and clutched Twilight in her hooves. Her horn began to glow and the wounds on Twilight's body slowly healed.

"Thank...you...Luna," said Twilight as she blacked out.

"So what now?" asked Juliet as she, Sarah, and Charlie approached the Doctor, Twilight, and Luna.

"This device I have is the only thing that can kill Thalia for good," said Sarah as she presented the device on her hoof. "It's a clone destabilizer. It's not a common weapon and it's only used on clones that go rogue."

"Ingenious," said the Doctor.

"Where is she now?" Charlie asked.

"Above in Canterlot. She's probably using Celestia like a puppet now to destroy the city," Sarah replied.

"Luckily the protective spell is down so I can teleport us there," said Luna.

"Then let's go. We need to finish this!" said the Doctor. Everypony nodded. The nods were followed by a bright flash. They were gone.

My Dearest Sarah

Chapter 6: My Dearest Sarah

Equestrian Academy of Magic and Skills, Ponyville Central, Equestria, Gaia, Summer, 2002 C.E.

Sunlight shone through the nearby windows as Twilight opened her eyes. It was definitely a nice sight to see after waking up from a long sleep. She yawned quietly and sat up. She was in a bed. It was nice and cozy but it was incredibly warm. She pulled the sheets off and climbed out of bed. The door opened and in walked the Doctor.

"Good morning! I'm guessing that you feel quite good right about now," he said with a smile.

"Yes. Thank you again...for rescuing me," she cooed.

"Come now. We're friends. I wouldn't just go and leave a friend to die!"

"We're friends?"

"Aren't we? After all we've been through so far I'd only assume that we had some type of positive relationship."

Twilight chuckled and walked towards the Doctor. She gave him a quick hug that came off as both awkward and heartwarming for the both of them. She pulled away and smiled.

"Yes. We're friends."

"Good! I'm sorry to say that you missed the 2002nd Summer Sun Celebration."

"Oh. When was it?"

"Yesterday. Today's June 22, 2002."

"Wait. Wasn't it the 19th? I've been out cold for three days?!"

"Yep! Celestia came by to visit you several times. She's really nice when she's not being brainwashed by half-dead pony clones."

"Where is the Pri...I mean the Queen?"

"She had some political business to attend you. Nothing to worry about. She told me to tell you that it was really nice to see you again...even if you were out cold."

"What about Luna?"

"She's back in Canterlot. Somepony's got to look after things while Celestia's away."

"And Thalia?"

"Took care of her myself. But I wouldn't feel too safe. From what I can assume, this may have been Thalia's final stand but this is definitely not the last time that we're going to run into her."

"We're going to have to face her again?"

"That's one thing that annoys me about time travel. You don't live events or meet people in a normal chronological order. I mean we just finished off a villain who has had a long and rocky history with the two of us and yet this was the first time that we met her."

"Speaking of time travel. Did you find the TARDIS?"

"Yep. It was in Celestia's bedroom. I had it moved into my guest room for the time being."

"Have you fixed it?"

"I've had some time to work on it but, sadly, it's still broken. If we leave now then our next stop will be completely random."

"That's good."

"Excuse me?"

"That's good. That means our next stop will be a surprise. Hopefully it'll be a lot better than this surprise."

"That's the spirit, Twilight Sparkle! I can see us doing this for a long time!"

"But I still wish to return back to my time before I'm an old pony."

"Hey, I said that I'd get you back to 1002 and I promise that I will."

"Thank you."

"Speaking of thank-yous, you have some certain someponies to thank."

The door opened and in walked Charlie, Juliet and Sarah.

"It's nice to see that you're finally awake," said Charlie. He walked up to her and shook her hoof. "Charlie Kemp. It's nice to finally be properly introduced to you."

"The pleasure is also mine," said Twilight happily. Sarah was the next to walk up. She hesitated at first but then grabbed the surprised unicorn in a giant bear hug. "Uh...thank you too."

Sarah pulled away and their eyes met.

"Twilight Sparkle," she uttered. "I have waited so long to meet you."

"Am I famous or something?"

"You have no idea," chuckled the Doctor.

"My name's Sarah," Sarah continued. "Sarah Sparkle. I'm your descendant."

Twilight's eyes widened. She looked closely at Sarah and could just make out the family resemblance.

"And I'm Juliet. Her daughter," said Juliet.

"How...how did you know about the Doctor and I being here?" Twilight asked.

"You wrote it down for me," said Sarah. Sarah reached into her bag and pulled out a stack of several pages. There was a small purple note taped to the top of the stack.

"What is that?"

"It's the only untold story of the Doctor and Twilight Sparkle. It was written by you. It tells a full and highly detailed description about what took place three days ago. I received it as a family heirloom when I was eight years old. I'm the only pony who has ever read this story. Here. Read the note."

Twilight peeled the purple note off of the stack of papers and read it.

"To my dearest Sarah," she read. "This is a story that I've written for you and only you. Nopony before you has read it and nopony other than you shall read it until the following events have transpired. I have no doubt that you will be prepared for these events when they come around. I remember the event clearly for it was not long ago for me. If being with the Doctor has taught me one thing it's this. Time is complicated. Try not to reason or comprehend it. Just take everything as it comes at you. Here's just a little spoiler for things to come. Only tell this story to those who you know will be able to help you in your part to help these future events unfold. I know you will be brilliant. Your loving ancestor, Twilight Sparkle. Date finished - December 1, 1002 C.E."

Twilight looked up from the note. Her eyes were somewhat watery but she was quick to wipe them with her hoof.

"Looks like you have some homework to do, Twilight," said the Doctor as he patted the papers in Sarah's hooves.

"Great," Twilight laughed. "Not only do I have a note to write. I have another note plus a detailed description of an event that happened to me three days ago."

"Don't worry. I can help you with it."

"So...before you two leave," said Sarah. "How about a tour?"

"A tour?" Twilight asked.

"Yes. You are in the most successful academy of skills, magical or otherwise, in the world. And, not only that, you helped found it."

"I...I'm going to found the most successful academy of skills in the world?!"

"Come on, Sarah. Let's not give too much away," said the Doctor.

"Oh...yes. I do apologize," Sarah choked.

Outside the Equestrian Academy of Magic and Skills, Ponyville Central, Equestria, Gaia, Summer, 2002 C.E.

"I still can't believe that Ponyville's going to grow into this," said Twilight as she overlooked the city.

"Technically it's five cities but whatever," said the Doctor.

"Five?"

"Weren't you paying attention? There's Ponyville Central. Then there's Ponyville North, Ponyville South, Ponyville East, and Ponyville West. You certainly need to start listening better."

Twilight laughed and gave the Doctor a friendly shove. The TARDIS stood a few feet away.

"Well it's time to go," said the Doctor as he turned back to Sarah, Charlie, and Juliet.

"Could you come back for a visit sometime?" Charlie asked.

"I never really plan visits. I just sort of go where the wind takes me."

"Are you sure that you don't want to stay any longer?" Juliet asked.

"Sorry but I've got to get Twilight home as well and get some more work done on the TARDIS. Besides, there's a whole universe of time and space just waiting for the Doctor and Twilight Sparkle to venture through!"

"Well I wish you two the best of luck!" said Sarah.

"It was really nice meeting all of you," said Twilight.

"And it was amazing to meet you two!" said Juliet. "You're just as incredible as the stories describe you as!"

"By the way. Who's the pony that wrote the stories about the Doctor and I, anyway?"

"Here it is. I borrowed it from my friend," said Charlie as he handed Twilight a book.

"Let's see. The Countless and Timeless Adventures of the Doctor and Twilight Sparkle. Written by-"

Twilight's eyes widened and she almost dropped the book in disbelief.

"Of all the ponies to write a story about me, why in Celestia did they pick these three?!"

"What is it? Who wrote the book?" asked the Doctor.

"Written by Trixie, Snips, and Snails. Ugh!"

"Who are they?"

"I'll tell you about them later."

Sarah, Charlie, and Juliet laughed as the Doctor and Twilight walked back towards the the TARDIS. The Doctor clapped his hooves and the doors opened.

"Bye!" said Charlie and Juliet together as the Doctor and Twilight walked through the doors. Twilight waved goodbye, tossed the book back to Charlie, and then shut the doors behind her.

"I've been waiting my whole life to see this," said a delighted Sarah. The light on the top of the TARDIS began to flicker and the alien teleportation sound began echoing around it. Then it was gone.

"Where do you think they've gone off to this time?" Juliet asked.

"The TARDIS has only one destination," said Sarah with a smile. "Next stop: everywhere."

To be continued...

Prologue

Doctor Whooves: Episode 2
The Awakening

Prologue

Equestrian Academy of Magic and Skills, Ponyville Central, Equestria, Gaia, Spring, 2002 C.E.

It was high noon and the sun shone brightly down on the metropolitan paradise that was the city of Ponyville Central. The Equestrian Academy of Magic and Skills stood at the northern boundary of the city and was a crowning achievement of architecture, education, and, of course, magic. Within the walls of the Academy there lived hundreds of students who spent years developing their magical abilities under the supervision of some of the most gifted and intelligent ponies in the world. Charlie Kemp was one of these students. He was a 13-year-old pegasus pony with a light yellow coat, short red mane, soothing green eyes, and a laptop cutie mark. He was making the usual trip up to visit the Headmistress.

It was all too common nowadays for Charlie to find himself trotting up to the Headmistress's office due to not paying attention or causing a disruption in class. He wasn't a trouble making pony but he lacked the expected amount of discipline and concentration that the Academy required of its students. It wasn't long until he was walking through the large silver doors that led into the Headmistress's office.

"Headmistress?" he asked grudgingly.

"Charlie. Please have a seat," said the Headmistress. She was beautiful alicorn with a lavender coat, a long deep blue mane, sharp blue eyes, and a cutie mark that consisted of a scroll surrounded by fire. Charlie walked up towards the Headmistress's desk and sat down on a cushion opposite to the side that she was on. "Charlie Kemp. What am I to do with you? This is your third year at the Academy and yet you're still getting monthly, and sometimes weekly, calls to my office!"

"I apologize, Headmistress. But I swear I wasn't messing around on my laptop this time! I was just looking up a word that I didn't understand!"

"Why couldn't you have asked your professor?"

"To be honest...he frightens me a bit."

"Professor Telltale frightens you? I'd hardly call him an intimidating pony to be quite honest."

"He just towers over us. Everypony's afraid of him."

"Really? Is everypony really afraid of him?"

"Okay...maybe it's only a few of us."

"Charlie, you don't have to lie to me. We've been meeting in this office together for the past three years. We don't need to keep secrets between us."

"I guess...I'm just kind of shy."

"There you go. See? That wasn't hard now was it?"

"Not really I guess."

"You need to start branching out more! Here. I'm going to give you a free pass to join our computer club."

"Huh?"

"You have a talent and love for computers. I think the best way for you to break out of your shy streak is to join a club consisting of ponies you can identify with. I've been waiting three years for you to try and puck up the courage to join a club or start making some friends. But, since you've refused to do any of that thus far, I've decided to take some of the matters into my own hooves."

"But...but Headmistress!"

"Don't worry! I'm sure you'll do splendid! My daughter's the founder of that club. I think you two will get along quite nicely. That will be all for now, Charlie. You may return to class."

Charlie gulped, nodded his head, and got up.

The doors swung open and in ran a frantic unicorn mare with her mane and glasses askew.

"Headmistress!" breathed the mare.

"What is it, Beatrice?" asked the Headmistress.

"Do you know what day it is?!"

"It's the 19th of June. What are you so frantic about?!"

"Don't you remember the stories?! June 19, 2002. Today's the day they arrive!"

The Headmistress's eyes widened and she suddenly stood up from her desk.

"Beatrice, I want you to alert Crisp Oaks at Sweet Apple Industries immediately! Tell them to look out for them and be careful! I'm sure that she's going to be waking up pretty soon. And get Queen Luna on the phone!"

Beatrice nodded and ran out of the room.

"Headmistress? What's happening?" Charlie asked.

"You're in luck, Charlie. You're about to meet two very special someponies," said the Headmistress as she reached for her phone.

"Who? Who am I going to meet?"

The Headmistress looked at Charlie, smiled, and replied, "The Doctor and Twilight Sparkle."

The End and Beginning of a Feud

Chapter 5: The End and Beginning of a Feud

Canterlot Castle, Canterlot, Equestria, Gaia, Spring, 2002 C.E.

The castle was in a state of complete panic by the time the Doctor and the others arrived. Sarah put the unconscious Twilight on her back.

"I'll find a safe place for her to rest," she said.

"I'll try to keep my sister at bay," said Luna.

"I guess that leaves Thalia to the Doctor, Juliet, and myself," said Charlie.

"Okay! We've all got a game plan set! Let's go!" exclaimed the Doctor. Sarah ran down the hallway with the unconscious Twilight and Luna took for the skies to prevent the possessed Celestia from destroying any more of the castle and city.

"So where do you think she is?" asked Juliet.

"If I were an insane pony clone desiring to watch the destruction of an entire city I'd probably find the tallest point in the area and watch the show from there," said the Doctor.

"The Belle Lamburg Tower."

"The what?"

"It's an old bell tower that was constructed in the late 1300's. It's the highest pony-made structure in Equestria."

"Where is it?"

"Look up."

The Doctor did what he was told and saw a sturdy tower of stone and metal rising into the sky.

"Huh. How could I have missed that?" he asked himself.

"We need to get up there! Now!" stated Charlie.

"Is there a way up?"

"I visited this place on a field trip once. I believe there's an elevator just around the corner," Juliet replied. "But, Charlie, I'm and alicorn and you're a pegasus. We could just fly up there."

"Huh?" Charlie croaked.

"Brilliant! You two can fly up there and distract her while I use the elevator to go up! I can then finish her off with the clone destabilizer that your mother gave me," said the Doctor.

"My thoughts exactly!" said Juliet. "Are you ready, Charlie?"

"I'm kind of nervous," Charlie admitted.

"Don't be! Just think of this as...a test."

"A test? Really? Is that the best comparison you could come up with?"

"Oh do shut up and let me try to help you! Just think of this whole thing as a really hard test that you have to pass! Don't focus on the collapsing castle, the possessed queen, or the possibility of falling to your death. Just focus on the goal! Get Thalia into the Doctor's shooting range."

"I wouldn't have a choice to back down anyway, right?"

"That's correct. I'll drag you up there myself if you refuse."

"Alright then. It's not like I have anything else to do while the castle's under siege."

"That a boy...er...pony! I'll see you up there!" said the Doctor. Charlie and Juliet took to the skies as the Doctor ran down the hallway in search of the elevator.

The Belle Lamburg Tower, Above Canterlot, Equestria, Gaia, Spring, 2002 C.E.

Thalia leaned against the exterior wall of the bell tower calmly as the city of Canterlot burned underneath her. She had complete control over one of the most powerful alicorns in Equestria and now the entire country, if not the world, would eventually bow down before her. Sure it was a little generic to go after complete world domination but she thought that coming up with a whole new complicated goal would tire her out more excessively than she needed to be. The screams of the ponies below excited her. Their pain and suffering would bring a rise to her fame and fortune. Unless the Doctor interfered again. That annoying pony. He had always been there to foil her. To stop her from obtaining her true purpose in this vast and changing place known as the universe. And he was almost always joined up with that obnoxiously snarky Twilight Sparkle.

Suddenly, Thalia fell back. The mere thought of Twilight sent a strange vision flashing through her mind. It was happening again. She was taking another memory trip. The world around her faded and she collapsed on the ground. The bell tower disappeared and was replaced by that of a simple shop. Sugar Cube Corner. The name popped into Thalia's head. She knew this place. She had been there many times before through the eyes and ears of Twilight Sparkle. She was sitting at a table now. Five others ponies sat around the table. She instantly knew their names. Applejack, Rainbow Dash, Pinkie Pie, Fluttershy, and Rarity. She had run into them several times in the past, all meetings resulted in her trying to kill them, but this meeting through the point of view of Twilight Sparkle was calming. It was even somewhat enjoyable. There was laughter, talk of future parties and events, and just goofing off. She found herself enjoying the memory. It was nice. It was innocent. But it still put her teeth on edge. How dare that Twilight Sparkle have a happy and innocent life while hers was full of change, pain, fighting, and failed dreams! How dare she be happy! How dare the original have more rights and respect than her, labeled under the status of being nothing more than a dark shadow that needs to be bathed in the light of death. In the memory, Pinkie handed Twilight a cupcake and she ate it. Thalia could taste the sweet frosting and the spongy cake. It was too scrumptious for words. That taste. The taste of true friendship and happiness. The taste of a life before the arrival the wondrous and incredible Doctor.

The memory faded away and Thalia found herself laying on the ground of the bell tower room. Two fuzzy figures were examining her.

"Do you think she's dying?" asked a female voice.

"I don't think so," replied a male voice. Thalia's vision returned and she recognized her spectators. They were the two ponies who had been helping the Doctor down in the caverns. Her eyes scanned them and two names popped into her head. Charlie Kemp and Juliet Sparkle. Sparkle?! The alicorn possessed the blood of Twilight Sparkle. Sure, she couldn't kill Twilight...but killing her descendant would be just as satisfying.

She quickly jumped up and attempted to grab the alicorn. The alicorn jumped aside and managed to cut her attacker with her horn.

"Stay away from her!" ordered Charlie as he attempted to kick her. The kick missed and Thalia simply shoved him aside. Juliet looked down towards the spot where she had cut Thalia. There was definitely a rip in the skin but no blood was coming out.

"No blood? How is that possible?!" breathed Juliet.

"Honey, I've been dead for a long time," chuckled Thalia. The wound slowly healed itself and the clone flung herself at the alicorn. Juliet tried to use a few offensive spells on her but they all had little to no effect. Thalia pushed Juliet onto the ground and attempted to choke her. Charlie jumped on the clone's back and bashed her with his wings as hard as he could. "Get off of me you annoying whelp!"

Thalia attempted to buck Charlie off of her back but he held on tightly. She eventually managed to kick him off, sending him into a collision with the side of the Lamburg Bell. The bell emitted a deep and loud ring that shattered the silence around them. The town and chaos seemed to stop as the bell rang out. Even the fighting Luna and Celestia stopped to listen to the bell. Thalia wasn't phased. She grabbed Juliet in a headlock and prepared to snap her neck.

"Just try to escape my grasp!" Thalia gloated. "Just try!"

"I don't have to try," chuckled Juliet. Suddenly there was a flash of light behind Thalia and she felt her body slowly fall apart. Her bones turned to dust, her skin turned to gelatine, her brain turned to jelly, and her mind turned into a vaporous energy doomed to evaporate up towards the sun. The last image Thalia saw was another quick vision. She was laying in the Doctor's arms as he pleaded down to her.

"Stay with me, Twilight. Stay with me," he said. Thalia looked into his eyes. They seemed caring and thoughtful. So sign of hatred or sorrow. They were beautiful eyes. "Stay with me, Thalia. Stay with me."

"But...I can't stay, Doctor," she sighed as her body finally disintegrated into nothing. The Doctor stood there, Sarah's clone destabilizer aimed at the spot where Thalia had been standing. He gave a long sigh and looked over at Charlie and Juliet. Charlie was on the ground, one of his legs had been broken, and Juliet was doing her best to heal him. Juliet looked up at the Doctor and their eyes met.

"It is finished," he said.