Doctor Who, My Little Pony 1. Prologue

Author's Note: I now present the twelfth episode in the tale of Doctor Whooves! Enjoy!

Doctor Whooves: Episode 12

A Dalek in Celestia's Court

Prologue

_**Canterlot Castle, Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

Luna was avoiding Celestia...again. She was sitting quietly in a small room hidden in one of the older parts of the castle. She didn't have to worry about Celestia finding her. Her elder sister had given up trying to find her a while before. Luna missed being happy with her sister. Their relationship had been pretty strained since the disappearance of Twilight Sparkle. She could still remember the moment when she had to tell Celestia about what had happened. She told her everything. The appearance of the mysterious stallion known as the Doctor, the attack on Ponyville by that strange creature that resulted in the death of a pony named Oak Ridges, and, of course, Twilight's disappearance. Since then, Celestia and her hadn't been on "good, sisterly terms". Luna hardly left the castle anymore. Celestia hardly talked to her nowadays and when she did it was always in a somewhat angry tone. Luna didn't hate or blame her sister. She knew she herself was at fault here to some degree. But, Luna felt there was more to this than just Twilight's disappearance.

Celestia seemed to act oddly to Luna's mentioning of the Doctor. Celestia, at first, had acted as if she knew this stallion. Celestia had been acting weirdly of late. Luna had seen her sneaking off to the library multiple times to scope out the Equestrian history section. Luna found this behavior to be quite odd. However, Luna felt that there was something else afoot rather than Celestia keeping secrets. The previous night, Luna had felt something odd. It was hard to describe, the feeling, but Luna knew one thing for certain: there was a presence of very powerful magic somewhere in Equestria. Luna had wanted to tell Celestia about it but she still didn't feel completely comfortable around her sister.

"I'm sorry, my sister. I'm sorry, Twilight," Luna whispered softly to herself. She said this to herself every single day. It made her feel slightly better but she knew that no matter how much she said it, it would never make that much of a difference. Suddenly, an alien sound began echoing up from the city below. Luna listened carefully. She knew this sound. She had heard it before. In fact, she remembered when and where she had last heard it exactly: five months ago in the home of Twilight Sparkle. It was the sound that bizarre box owned by the Doctor made when it appeared. "Could it be? Could...could it really be Twilight and _him_? Have they returned?"

Luna jumped up and looked out the window. She could hear the sound emanating clearly now due to magically enhancing her hearing. A smile appeared on her face.

"Twilight! She's back! She _has_ to be!" Luna cheered. She then flew out of the window and down towards the city. She was so happy that she didn't noticed a space of rippling air situated in the room she had just left. A metallic voice began emanating from the rip in space and time.

"PRINCESS LUNA! MUST FIND PRINCESS LUNA!" cried the voice. "EXTERMINATE! EXTERMINATE!"


	2. Five Minutes Later

Chapter 1: Five Minutes Later

_**Performance Square, Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

The TARDIS doors opened and the Doctor happily trotted through them. Twilight, Derpy, Trixie, and the others followed close behind him.

"There you go!" said the Doctor. "Canterlot, 1002 C.E.!"

He suddenly realized that he was being watched by a group of confused ponies. The TARDIS had parked itself right in the middle of a makeshift stage. The crowd stood up and began clapping their hooves.

"That was quite an amazing trick there!" stated a wealthy stallion.

"Oh yes it was! Though, didn't she say that she was going to perform the Master's Rejuvenation Spell?" a mare stated. Trixie blushed slightly before stepping in front of the Doctor.

"Thank you! Thank you! This has been the Great and Powerful Trixie!" she said as she bowed before the audience.

"And the Doctor!" the Doctor exclaimed. Trixie turned back at him and couldn't help but chuckle. "Sorry. The opportunity was too good to pass up!"

"Wait a second!" exclaimed Derpy, who had picked up a newspaper that had been lying on the ground a couple feet away. "This is the day after we defeated Thalia! This is the day we left!"

"I told you I would get you back no more than five minutes later. I always keep my promises...for the most part."

"So everything we did, the _Queen Philippine_, the future Rainbow Dash, the Weeping Angels, the Reapers, and everything else...took only five minutes?!" Rainbow Dash asked.

"According to this current time period, yes."

"Whoa! That's trippy!" Pinkie Pie exclaimed.

"Ah don't know about the rest of y'all but I'm ready to head back to Ponyville. Ah really want to see Big Mac, Apple Bloom, and Granny Smith after everything that just happened," said Applejack. The farm pony sighed again. She was still recovering from the whole incident with her parents. She would need some time to heal.

"Understood!" said the Doctor.

"I guess I'll be seeing you around, Doctor," said Trixie.

"I guess so."

The Doctor and the others were about to leave when something landed on the ground a few feet away.

"Princess Luna!" Twilight exclaimed. The surrounding ponies bowed at the appearance of the blue alicorn. Luna ignored them. She rushed over to Twilight and gave her a huge hug.

"Oh, Twilight Sparkle! It's true! You've returned! My sister will be so pleased!" Luna exclaimed. She then turned to the Doctor and scowled. "I know you have something to do with Twilight's disappearance. I demand that you tell me what happened at once!"

It took a few seconds to realize what was happening. Twilight and Spike looked at each other awkwardly. They had forgotten to send a message to the Princesses following the defeat of Thalia and since this was only a day after the dark clone's defeat, the Princesses were still unaware of what had taken place in Ponyville.

"Princess Luna, please don't be angry with the Doctor. I can explain everything."

"_We_ can all explain everything," Rarity added.

"I'll vouch for the Doctor's innocence in terms of whatever crime he's being accused of!" Trixie stated as she raised one of her hooves.

"We must head up to the castle at once. When we get up there, you can explain the whole situation to my sister and I. Hopefully...this will help end the strain between Celestia and myself," said Luna. The Doctor could only feel a twinge of guilt at the sound of Luna's last statement.

_**Canterlot Castle, Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

Celestia was in the library...again. She had spent the last several months refreshing her memory of Equestrian history. There had to be something about him hidden somewhere in these pages. There just had to be. Celestia suddenly thought of her younger sister.

"Luna...why am I so angry at you?" she whispered to herself. "Why do I punish you for the mistakes of somepony else?"

"More conflicting feelings, Princess?" asked an unfamiliar voice. Celestia turned around to see a mare that she had never seen before approaching her. The mare had a dark red coat, a purple mane, blue eyes, and a cutie mark that consisted of a purple feather with a curved tip. She wore a large, pink, brim hat with a single feather extending from it. "You seem to be having a lot of those recently."

"Who are you, and how did you get this far into the castle?" Celestia asked. The mare chuckled before looking at a strange device wrapped around one of her hooves.

"Ah, I see. You haven't met me yet. Well, you have now but you don't really _know_ me yet."

"Explain yourself! Who are you?!"

"Calm down, your majesty! Name's Matilda. I'm just a passerby. Hmm...looking up some old history, eh? I guess you've yet to recover your memories of the Doctor."

Celestia's eyes widened. Did this mare know the Doctor?!

"You know the Doctor?!"

"Yes. I know him very well. Though, by this point in time, he doesn't know me very well. Time's complicated like that."

"Where is he?!"

"Don't get yourself worked up! He's here in Canterlot. If I have the time correct he, Twilight, and their friends are on their way up to the castle with Princess Luna as we speak."

"Luna."

"I remember this. You've been cross with her, haven't you?"

"I guess...wait...why am I discussing this with you? I don't even know you!"

"Because you already trust me. I have that effect on ponies...and people...and whatever else I come across. I just have that special charm. I get it from my parents."

Matilda then turned towards a nearby clock and jumped.

"Oh! I better go! I have to go get help!" Matilda exclaimed.

"Help for what?!" Celestia asked.

"You'll find out soon enough. Let's see. It's mid-November now. There's at least a little bit under a month and a half left before it happens."

"Before what happens?!"

"Don't worry yourself over it. The Doctor's going to take care of it. Here, this will help you with what's _about_ to happen."

Matilda produced a tin canister from her hat and tossed it at the Princess. Celestia caught it with her magic.

"What is this?"

"A portable cage."

"What's it for?"

"A little pest that's found its way into the castle. See ya later!"

Before Celestia could ask anymore questions, the mare clicked something on her device and disappeared in a flash of light. Celestia wanted to stay and think about what Matilda had said but she didn't have time. Twilight Sparkle was back and she had brought the Doctor with her.

_**Outside Canterlot Castle, Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

Twilight had only just passed through the Canterlot Castle gates when somepony ran up and wrapped her up in a big hug.

"Twiley!" Shining Armor exclaimed.

"Shining Armor!" Twilight exclaimed as she hugged her brother back.

"Where in Celestia's name have you been?! You just disappeared into thin air for five months!"

"She's been traveling with us and the Doctor!" said Derpy with a smile.

"The Doctor?"

Shining Armor turned to face the Doctor. The suited stallion walked forward and shook his hoof.

"It's a pleasure to meet you...again!" he said. "Twilight told me that you fulfilled your dream and I'm glad that you did!"

Shining looked back to Twilight.

"It's a long story," she said.

"Well you better tell it to Princess Celestia. Maybe your reappearance will snap her back to her usual self," said Shining.

"What do you mean by that?" Spike asked.

"You'll see," said Luna. That's when the doors to the castle opened wide. There stood Princess Celestia. She slowly walked down the steps and approached the group of ponies. "Sister...it's Twilight Sparkle! She's returned!"

Celestia smiled at the sight of her prized pupil.

"Twilight...I am glad to see that you are alive and well. You're friends and I have wondered non-stop about your whereabouts," said Celestia. That's when she turned and noticed the Doctor. It was true...it really _was_ him! He looked almost like he did the night he came and visited her almost two years previously.

"Hello, Princess Celestia! I must say that it's very nice meeting your present self. I met your future self and she was a bit loopy, but I suppose that was from the possession. Oops! Look at me! Going on about spoilers! I do hope you're not going to banish me to the Moon or something because, if you'll give me a chance, I'll happily explain to you about what happened five months ago," he said. Celestia took in a deep breath and nodded.

"Very well. I will let you explain your case."

Everypony was ready to head inside. This was it. All the loose ends were going to be tied up. However, fate had other plans as, at that very moment, a violent explosion ripped through the entrance courtyard. Celestia and Luna were quick to produce a pair of magical protection fields. The ground shook underneath them and the Doctor fell to the ground.

"What the hay was that?!" Rainbow Dash asked.

"We're under attack!" stated Shining Armor.

_"No! You think?!_" asked Trixie sarcastically.

Just then, an odd creature began emerging from the smoke and fire that surrounded them. The Doctor's eyes widened, along with the eyes of his fellow companions.

"Impossible!" the Doctor breathed.

"It can't be!" Twilight croaked.

"Not again!" Spike groaned. The Doctor stood up and pulled out his Sonic Screwdriver as a Dalek emerged from the cloud of smoke.

"It's that thing again!" Luna stated. Celestia felt a pain rush through her head. She didn't know what was happening but this creature that she had never seen before was causing her to experience physical pain. "Celestia? My sister, what's the matter?"

"I...don't...know," Celestia groaned. "I'm...sorry...my...sister."

"PRINCESS LUNA!" cried the Dalek. Luna turned to face the metallic creature. It's death ray aimed itself at the blue alicorn. "LUNA FOUND! TARGET FOUND! EXTERMINATE! EXTERMINATE! EXTERMINATE!"


	3. Awkward Encounters

Chapter 2: Awkward Encounters

_**Outside Canterlot Castle, Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

Celestia's head was ringing. This pain she felt, it was beginning to feel more along the lines of a psychological pain rather than a physical one. Her mind wanted to tell her something. Something was hidden away deep within her subconscious. This creature was the key to her unlocking the source of this pain...but this creature was also after her sister.

"EXTERMINATE!" cried the Dalek as it edged forward.

"Run, my sister!" Celestia groaned. "It is after you!"

"No! I'm not running away!" Luna stated. The Doctor jumped in between the two Princesses and the Dalek.

"Looks like I'll never be able to be rid of you, will I?" he asked as he aimed his Sonic Screwdriver.

"STEP ASIDE, DOCTOR!" the Dalek ordered.

"A Dalek telling me to move rather than threatening to kill me? That's strange."

"STAND ASIDE! MUST EXTERMINATE PRINCESS LUNA! EXTERMINATE! EXTERMINATE!"

"But why Princess Luna of all ponies? Why her?"

"YOU SHOULD KNOW, DOCTOR! YOU SHOULD KNOW VERY WELL!"

"But I don't! I don't understand! When did your species become so confusing?!"

"STAND ASIDE, DOCTOR!"

"I'm afraid that I can't do that, Dalek."

Without any warning, the Dalek shot a beam of energy at the Doctor. The Doctor felt a searing pain rush through his body.

"DOCTOR!" cried Twilight and Derpy. The Doctor fell the ground, expecting to feel the sensation of regeneration come over him...but no such feeling occurred. He quickly realized that all the ray had done was temporarily stun his legs.

"I can't walk," he stated as he looked up at the Doctor. "You paralyzed me!"

"ONLY TEMPORARILY! YOU WERE BEING A NUISANCE!" stated the Dalek as it began approaching Luna. "MUST EXTERMINATE PRINCESS LUNA! MUST EXTERMINATE!"

"A Dalek shot me...but not with the intention to kill. Something's not right here."

Luna produced a force field around the Dalek but the metallic beast managed to phase its way through the magical barrier.

"Impossible!" Luna exclaimed.

"USE THE CAGE!" cried a voice from nowhere. The Doctor looked towards the front gate. A white stallion with a red mane and a smiley face cutie mark was standing on the other side. He was dressed up like a clown and was waving his forelegs frantically in the air. "USE THE PORTABLE CAGE!"

"A Dalek didn't try to kill me and now a clown pony is yelling at me about cages," the Doctor sighed. "Is this some sort of drug-induced dream or something?"

Celestia, however, knew what the clown was walking about. She produced the metal canister given to her by Matilda and gave it to Luna.

"What is this?" Luna asked.

"A portable cage," Celestia responded. Another surge of pain rushed through her head and she passed out.

"EXTERMINATE! EXTERMINATE!" cried the Dalek. Luna, with a sense of urgency, grabbed the canister and tossed it at the Dalek. Just before the Dalek fired at her, the canister struck its body and instantly trapped the Dalek in a steel cage surrounded by an odd, magical barrier. The Dalek fired through the cage bars but the magical barrier simply caused the death blast to fade away. "WHAT IS THIS?! WHAT IS THIS?! EXPLAIN! EXPLAIN!"

"I'd never thought I'd say this but I actually agree with the Dalek here," said the Doctor as Twilight and Derpy helped him up. "I would like an explanation to what's going on here."

"I think we all would," said Luna.

_**Canterlot Castle, Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

The Doctor and Celestia had been taken to the hospital ward in the castle. The caged Dalek was taken down to the dungeons until further notice. The Dalek continued to scream and holler for Luna's extermination while Twilight explained to the Princess exactly what happened five months ago. Derpy, Pinkie Pie, and Fluttershy went to keep the Doctor company in the hospital ward.

"Too many things aren't adding up," said the Doctor as he lied on one of the hospital beds.

"Do you think there could be more dimensional rips at work here?" Derpy asked.

"Maybe. We'll only be able to learn the details once we interrogate that Dalek."

"How are your legs feeling?" Fluttershy asked.

"Better. I have some feeling back but I won't be able to walk normally for a little bit."

"I broke my leg once while I was playing with Carrot Cake. She accidentally brought a bookcase down on it. It didn't feel so good," said Pinkie Pie.

"That's an...interesting story."

"I have others! Do you want to hear the one about how Equestria was founded?!"

"It's not what you think. It's just the story of how she got her cutie mark," Fluttershy whispered.

"Maybe later, Pinkie Pie," the Doctor replied with a smile.

"Okie-dokie-lokie!" Pinkie exclaimed as she bounced over to the sleeping Celestia. "I wonder what happened to the Princess."

"That's another thing that puzzles me. Why did Princess Celestia pass out?"

"The Dalek must have had something to do with it," said Derpy.

"But how? The Dalek didn't even shoot anything at her," Fluttershy added. The Doctor began scratching his head and thinking when, suddenly, the door to the hospital ward burst open. Fluttershy nearly jumped for the sky. "Oh my!"

In walked the clown pony who had told them about the portable cage.

"Hey Doctor! How're ya feeling?" he asked as he trotted over next to the bed.

"I'm not sure anymore," the Doctor replied as he rested his head down.

"Good thing I was there to remind you about the portable cage, eh?"

"How _did_ you know about what the portable cage was anyway?" Derpy asked.

"The Doctor should know that. We've only used them several hundred times whenever we've had to face off against the Daleks!"

"Do I know you?" the Doctor asked.

"Do you have amnesia or something? It's me! You know! Monty!"

"Who?"

"Monty! Full name: Montague. Sometimes known as Monty the Masterful! Ring any bells?"

"Nope."

"You must have it bad. Did you forget Opal too or something?"

"Opal? You know Opal?"

"Oh so you remember my wife but you don't remember me. Nice, Doctor. Real nice!"

"Wait..._you're_ Opal's husband?"

"Yes! Well, we were only boyfriend and girlfriend the last time you saw us but, as you can see, we finally got hitched. We even have two children now. Twins, they are. Francis Capulet and Julianna Capulet. We took the last name from somepony on Opal's side of the family. Juliet, I think her first name was."

The Doctor thought back to the last time he saw Opal. He _did_ remember her mentioning that she had a husband and two children.

"I have a reason for not knowing you, Monty," said the Doctor. "The adventures I had with you and Opal haven't happened yet for me."

"Huh?"

"I've only come across Opal twice so far. Once in 987 and once in Ponyville here in 1002."

"More of the wibbly wobbly timey wimey stuff?"

"Pretty much."

"So...this is the first time that you've ever met me?"

"Yeah."

"This must have been pretty awkward for you."

"A little bit."

Monty cleared his throat and took a few steps back.

"Sorry about that."

"Don't worry about it. I've had plenty of awkward encounters in my life. This is not that different from others."

"That's good."

Monty then turned to the others and cleared his throat again.

"I guess you're friends of the Doctor too?" he asked.

"Yes indeed!" chirped Pinkie Pie. "I'm Pinkie Pie!"

"I'm Fluttershy," said Fluttershy and she slightly hid behind Derpy.

"Fitting name," Monty chuckled. He then turned to Derpy. "And you are?"

"Derpy. Derpy Hooves," she replied.

"Oh."

Monty then proceeded to give the same, melancholy look that Opal had given Derpy when she had first met her.

"Is something wrong?" Derpy asked.

"Oh! Uh...nothing. Nothing's wrong...at all."

"Whatever you say," said a suspicious Pinkie Pie. Just then, Celestia began to stir.

"Princess?" Fluttershy asked. The Doctor tried to get up but he hadn't regained full control over his legs yet.

"Luna...where's Luna?" Celestia asked.

"She's fine, your majesty. She's with Twilight and the others," said Derpy.

"And what of that creature?"

"It's down in the dungeons," Pinkie Pie replied.

"And the Doctor?"

"Right here!" the Doctor replied as Monty helped him out of bed.

"You're luck you're not dead, Doctor! Come to think of it, why didn't the Dalek kill you?" Monty asked.

"I don't know. That's what I want to find out. Help me down to the dungeons. I have a few questions for our trigger-happy friend."

"Wait, Doctor," said Celestia. "You owe me an explanation."

"I'm afraid that will have to wait until after I've gotten some answers from the Dalek."

"Then at least answer me this one question."

"Okay."

"Why did you appear in my bedroom two years ago?"

Everypony turned to face the Doctor. The Doctor turned to Monty, let out a sigh, and then turned back to Celestia.

"I'm afraid I don't know yet, your majesty, for that hasn't happened to me yet."

"What do you mean?"

"I'm a time traveler. I live events out of chronological order. The Doctor who visited you two years ago was the future version of myself."

"A future version of you...in the past?"

"I know it's complicated. Why don't we discuss this later, your majesty?"

Before Celestia could ask anything else, Monty helped the Doctor limp out of the hospital ward. Derpy was right behind them.

"We'll stay with you, Princess Celestia!" said Pinkie.

"Are you two able to explain to me about what happened five months ago?" the Princess asked.

"We'll try our best," Fluttershy replied softly.


	4. The Doctor Interrogates a Dalek

Chapter 3: The Doctor Interrogates a Dalek

_**Canterlot Castle Dungeons, Underneath Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

The Doctor slowly limped down the stairs that led to the dungeon. Derpy walked next to him and Monty walked behind him. It was a spiral staircase, which made it no easier for the slightly walking-impaired Doctor.

"Confound these steps!" the Doctor snapped. "Why did Celestia have to make this staircase descend in a spiral?!"

"Maybe she likes spiral staircases," Monty guessed.

"Well bah to her assumed fascination with spiral staircases!"

"Doctor, I think the Dalek's stun ray has made you a bit loopy," said Derpy.

"What?! Nah! I'm perfectly fine! I am a bit hungry though. I could eat anything right now...well, except for pears. Anything but pears!"

"Fine. We'll get some lunch after everything is sorted out."

"Thank you, Derpy."

They eventually reached the bottom of the staircase. The Dalek's screams echoed from down the dank hallway before them.

"Charming place," said Monty.

"Well it _is_ a dungeon for heavens sakes!" stated the Doctor.

"I was able to work that much out for myself, thank you very much. Are you sure you're okay, Doctor?"

"No, I'm not okay! A Dalek has appeared and has tried to kill Princess Luna, I've been stunned and am currently quite famished, and I keep running into ponies that know me before I know them! If it were Christmastime I would have to say a catchphrase from my old friend Ebenezer Scrooge!"

"Who's Ebenezer Scrooge?"

"And what's Christmastime?" Derpy asked.

"Oh bother! Let's just find the Dalek already!" the Doctor snapped.

"I guess he gets loopy when he gets stunned," Derpy whispered to Monty.

"He must have grown out of it because that never happened when Opal and I traveled with him," Monty whispered back.

It didn't take them that long to find the Dalek. It was still trapped in its magical cage which had now been placed inside one of the dungeon cells.

"Hello, Dalek," said the Doctor as he approached the cell door.

"RELEASE ME! I MUST COMPLETE THE TASK! I MUST EXTERMINATE PRINCESS LUNA! EXTERMINATE! EXTERMINATE!" the Dalek yelled.

"But why? Why Princess Luna?"

"RELEASE ME AT ONCE! MUST EXTERMINATE! EXTERMINATE!"

"They really like the word _exterminate_," Derpy whispered to Monty. Monty nodded as he let out a great sigh.

"You have _no_ idea!" he stated.

"I want answers, Dalek. Why didn't you kill me? Every Dalek in existence hates and fears me with a passion. Why not shoot to kill?"

"YOU WERE INTRUDING IN MY TASK! I SIMPLY PUSHED YOU OUT OF THE WAY! I NEED TO COMPLETE THE TASK! I NEED TO EXTERMINATE PRINCESS LUNA OF EQUESTRIA!" the Dalek shouted.

"A Dalek who puts killing somepony else over trying to kill _the_ Doctor? That's not Dalek-like."

"IT IS VERY DALEK-LIKE!"

"No it isn't. I've faced off against the Daleks countless times ever since I first encountered your race back when I used to travel with Susan and her teachers. I know your race. Your race is built upon nothing but evil, purification, and the extermination of other species. I've been a thorn in your side for a long time. It would be any Dalek's dream to be the one to rid the universe of the Doctor. You had your chance to kill me. You had your chance to become a hero among your people. And yet, you put the task of killing a blue alicorn from Equestria over taking the chance to kill the greatest enemy the Dalek race has ever known. Now all I can ask is, 'Why?' I can obviously see that you're not like other Daleks."

"I AM THE SAME AS MY BRETHREN! I HAVE BEEN GIVEN THIS TASK FOR A REASON! I WAS THE BEST THAT THE DALEK FORCES COULD OFFER!"

"But what reason were you given this task?! Why are the Daleks so interested in the death of an alicorn from another universe? I can only guess that Luna has never even come across your race before today."

"IT WAS THE TASK I WAS GIVEN! SHE IS THE LAST ONE STANDING IN BETWEEN US AND THE DAWN OF A NEW EMPIRE!"

"Ah! Now we're getting somewhere! Now what exactly is this _great, new empire_ of yours?"

"YOU SHOULD KNOW, DOCTOR!"

"If I did know I wouldn't be interrogating you right now."

The Dalek began to stutter slightly and sparks shot off its armor.

"I DO NOT UNDERSTAND! YOU SHOULD KNOW! YOU SHOULD KNOW!"

"But I don't understand!"

"I...YOU...DON'T...LUNA...YOUR...IT...WAS...YOU!"

"Pardon?"

"IT WAS YOU!"

"What are you talking about?"

"IT WAS YOU, DOCTOR, WHO EMPLOYED ME!"

"What?!"

"I REMEMBER CLEARLY NOW! YES! IT WAS YOU, DOCTOR! YOU WERE THE ONE WHO GAVE ME THE TASK TO EXTERMINATE PRINCESS LUNA OF EQUESTRIA!"

_**Canterlot Castle Throne Room, Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

"And that's basically what happened, your majesty," Twilight finished. Luna let out a great sigh and nodded her head.

"I see. Everything makes sense now," she said as she approached the group of ponies. "Come. I think it would be best if we went to check up on my sister."

"I think Trixie and Spike already went ahead," said Rainbow Dash as she looked around for any sign of the magician and the purple dragon.

_**Canterlot Castle Hospital Ward, Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

"And that's the gist of things!" Pinkie Pie finished. Celestia nodded.

"I see...it all makes perfect sense now," Celestia stated. "I guess Luna didn't have much time to consider any other options at the moment rather than protecting the others."

"Princess? Is something wrong?" Fluttershy asked.

"I haven't been a very good sister recently."

"Hello!" chirped a familiar voice. Spike and Trixie entered the hospital ward. Spike smiled as he said, "We were just coming to check up on you and the Doctor, your majesty."

"I'm doing better. Thank you, Spike. But I'm afraid that the Doctor is not here at the moment."

"He's not?! Well where has he run off to?" Trixie asked.

"He went down to the dungeons to speak with the Dalek. Derpy and some stallion named Montague are with him," Pinkie replied.

"Montague? Never heard of him. Does he know the Doctor?" Spike asked.

"It seems like he does," said Fluttershy.

"That stupid time traveling stallion! Running off before anypony could check up on him, and while under the effect of paralysis! I'm going to give him a piece of my mind!" Trixie snapped. She then turned around and strolled out of the hospital ward.

"Should we bring her back?" Spike asked.

"Let her go. She'll have her say and then she'll calm down," Celestia chuckled.

"At least it's only Trixie who's somewhat ticked off at him. Things could have been worse," Spike stated.

"How so?" Pinkie Pie asked.

"Twilight could have been ticked off at him for something."

Pinkie and Fluttershy nodded in agreement.

_**Canterlot Castle Dungeons, Underneath Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

The Doctor, Derpy, and Monty were speechless. What the Dalek was saying made absolutely no sense.

"You're insane! Even by Dalek standards! Why would I order you to kill Princess Luna?! Hell, why would I even work with you in the first place?!" the Doctor snapped.

"BUT IT _WAS_ YOU! I REMEMBER! I HAVE THE PROOF!" the Dalek stated. The Doctor heard the sound of a button click and then a voice began emanating from the Dalek's speaker. It was_ his_ voice.

"I want you to kill Princess Luna. She's been a thorn in my side, as well as yours, for long enough. The time has come for this all to end. Kill her and don't let anypony stand in your way," said the Doctor's voice. The recording ended. It was definitely the Doctor's voice, but something had been different about it. It had sounded darker, gloomier, sadistic, and...somewhat empty. It was as if the Doctor in the recording had experienced more sorrow and agony than that of the present Doctor. None of this made any sense.

"That sounded an awful lot like your voice, Doctor," said Derpy.

"But why would I order a Dalek to kill Luna? Why? That seems completely out of character of myself!" the Doctor stated. The Doctor looked at Monty. He looked a bit uneasy, as if he were hiding something. "Monty, do you have any ideas?"

"Me? No! I'm just as stumped as you!" Monty choked.

"Are you sure? You look like you have something to tell me."

"I...I don't."

"I wouldn't lie to the Doctor if I were you," stated Derpy as she glared at Monty. Monty backed up. The pressure was too much.

"I can't say! I made a promise!"

"To who? And about what?" the Doctor asked.

"I made a promise to Opal...and to you, Doctor." The Doctor fell silent. Monty ran past Derpy. "I'll meet you upstairs!"

Suddenly, he bumped into somepony.

"Ow! Watch where you're going!" snapped Trixie the unicorn. She suddenly realized who she had bumped into. "Wait a minute. You're that clown that told us about the portable cage!"

Monty took a closer look at Trixie.

"Aren't you that unicorn who almost got a town destroyed by an Ursa Minor?" he asked. Trixie rolled her eyes and pushed him aside. She began walking towards the Doctor.

"Uh oh. It looks like somepony's not really happy with you," said Derpy.

"What the hell are you doing down here?!" Trixie snapped at the Doctor.

"Interrogating a Dalek. What are _you_ doing down here?" the Doctor replied.

"To give you a piece of my mind!"

"Can it wait? I'm a bit busy here." The Doctor yelped as a hoof came out of nowhere and swiped across his face. "Oi! What was that for?!"

"For being a smartass! I should give you another slap for coming down here while you're still injured!"

"What are you? My mum?"

"Ugh!"

"I think this Dalek is making everypony loopy," Derpy whispered to Monty.

"Obviously," Monty replied. He turned around towards the doorway leading to the staircase and noticed something odd. "Not these again!"

Derpy turned around to see a dimensional rift situated just a few feet away from them.

"That doesn't look good," she squeaked.

"What doesn't look good?" the Doctor asked, attempting to distract Trixie. The dimensional rift began to stretch and bend. "Oh...this is not good." There was a flash of light and suddenly four Daleks were standing where the rift had been. "Oh...this is not good at all!"

The Daleks pointed their death rays at the four ponies and began advancing on them.

"WHERE IS PRINCESS LUNA! SHE MUST BE EXTERMINATED FOR THE DALEK EMPIRE!" the Daleks stated. "WHERE IS PRINCESS LUNA?! WHERE IS PRINCESS LUNA?!"


	5. Luna Faces Her Fate

Chapter 4: Luna Faces Her Fate

_**Canterlot Castle Throne Room, Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

Luna had taken off towards the hospital ward in quite a hurry, leaving Twilight, Applejack, Rainbow Dash, Rarity, and Shining Armor alone in the throne room.

"I can't believe you've been traveling around with some strange pony all this time," said Shining Armor.

"He may be strange, Shining, but he's an enjoyable kind of strange you know?" Twilight replied with a warm smile.

"Whatever you say, sis. You sure know how to pick them, Twiley."

"What's that supposed to mean?!"

Suddenly, the entire castle shook.

"What on earth was that?!" Rarity exclaimed.

"Ah don't know but it didn't sound good!" said Applejack.

_**Canterlot Castle Dungeons, Underneath Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

"Well you didn't have to do that!" snapped the Doctor as he stared at the charred hole in the dungeon wall. One of the Daleks aimed its death ray towards Trixie and Monty.

"RELEASE OUR BROTHER OR YOUR COMPANIONS WILL DIE!" snapped the head Dalek.

"Don't do it, Doctor!" said Monty.

"Oh what's the point anyway?! There's four Daleks out. One more isn't going to make things that different!" sighed the Doctor. He pulled out his Screwdriver and walked over to the cell. He unlocked the cell door and deactivated the cage. The once-caged Dalek rolled forward.

"NOW WE MUST FINISH THE JOB! EXTERMINATE PRINCESS LUNA!" announced the Dalek.

"EXTERMINATE! EXTERMINATE!" cried the Daleks together. Three of the Daleks began heading towards the staircase while two of the Daleks remained.

"GET INTO THE CELL!" ordered the remaining Daleks.

"You know, it's kind of pointless. I can just Sonic our way out of the cell," said the Doctor as he presented his Screwdriver.

"Don't tell them that!" Trixie snapped.

"IT MATTERS NOT! YOU WILL DIE IF YOU TRY TO ESCAPE!" stated one of the Daleks.

"Now hang on. Why would you kill me? Aren't I the one who sent you to complete the task in the first place?" the Doctor asked.

"WHAT BECOMES OF YOU DOES NOT MATTER TO US! WE DO THIS TASK IN NAME OF THE DOCTOR! THAT IS WHAT IS IMPORTANT!"

"Okay. I'm confused now. You don't care about what happens to me, the Doctor, but you care greatly about fulfilling the task given to you by your master, the Doctor."

"THAT IS CORRECT!"

"But I'm the Doctor."

"THAT IS OBVIOUS!"

"And your master's the Doctor."

"ALSO OBVIOUS!"

"But you don't care what happens to me, your master (or apparent future master in this case) the Doctor."

"YOU ARE NOT OUR MASTER! THE DOCTOR IS!"

"But _I'm_ the Doctor!"

"YES YOU ARE. BUT THE DOCTOR IS OUR MASTER AND WE OBEY ONLY HIM!" A series of sparks shot from the Dalek's armor. "NOW GET INTO THE CELL, DOCTOR, FOR YOU CANNOT INTERFERE IN THE COMPLETION OF THE TASK GIVEN TO US BY THE DOCTOR!"

The Doctor, Derpy, Trixie, and Monty walked into the cell. The door was shut tight behind them.

"I didn't make heads or tails of what that thing was saying," Trixie admitted.

"You're not alone," Derpy sighed. She turned towards the Doctor. "Doctor, are you okay?"

"No I'm not, Derpy. I'm stumped. I'm completely and totally stumped," replied the Doctor. "I'm rarely stumped. Strange feeling. I don't like it. Let's start hypothesizing so that I can escape this cursed curse of stumpedness!"

"_Stumpedness_ isn't a word, Doctor," said Monty.

"Well it is now because I just invented it! Ha!"

"Whatever you say, Doctor."

"So I'm the master of these Daleks and yet I'm not their master."

"I think I have a headache," said Derpy.

"I can tell. Your eyes are inverting again."

"What? Oh! Not again!"

"Have you gotten somepony to take a look at that?" Monty asked.

"Sadly, yes."

"Alrighty then! Any ideas about what the flying jelly baby is going on?!" the Doctor asked with a forced smile.

"Maybe the Doctor in charge of them isn't you at all."

"I think I see where you're going with this, Ms. Hooves! Please continue."

"Well, you know how the TARDIS has begun to gain the ability to travel through dimensions? Well, what if, the Doctor in charge of these Daleks is a Doctor from another universe?"

"Oh ho! I knew I made a smart choice in bringing you along with me, Ms. Hooves! Yes! That certainly sounds like a very possible scenario!"

"Okay, so we've come up with a possible idea. Now what? That _Dalek_ is heading up to kill Princess Luna and we're stuck down here with those two watching us," Trixie stated.

"Maybe we're not so trapped after all."

"Do I detect a plan up your sleeve?" Monty asked.

"Possibly."

The Doctor smiled like a devious little schoolboy.

_**Canterlot Castle Hospital Ward, Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

Luna walked calmly into the hospital ward. Celestia was standing up now.

"Sister! You are feeling better, yes?" Luna asked.

"Better than I was earlier, though I still have a few pains in my head," Celestia replied. The two sisters fell silent as they stared at each other.

"We'll be outside if you need us," Spike said awkwardly as he, Pinkie Pie, and Fluttershy slowly walked out of the hospital ward and shut the doors behind them. Once she found that she was alone with Celestia, Luna smiled and chuckled.

"It's been a while since we've been alone together, Celestia," she said. Celestia looked down and sighed deeply.

"Luna...I...I just wanted to say that-"

"I know. I forgive you, sister."

"It's not enough. I want to say it, Luna."

"Okay then. I'm listening."

"I...I'm sorry, Luna. For everything. I haven't been a very good sister of late. I've been troubled recently by the possible recollection of lost memories. Memories I wish dearly to remember but can't for some reason. I was angry about the possible death of Twilight, my prized pupil. I took my frustration out on you, my sister. It was not fair for me to do such a thing, especially to you of all ponies. You've suffered long enough because of my mistakes. I'm sorry, my sister. I'm sorry, Luna. I'm so, _so_ very sorry."

Luna smiled again.

"Like I said, I forgive you," she said with a happy gleam in her eye. The two sisters walked forward and hugged each other. Suddenly, Celestia collapsed onto the floor. "Celestia?!"

Luna knelt down next to her weakened, elder sister.

"The battle...it's not going so well," Celestia groaned.

"What are you talking about?!"

"The battle...we're losing. We're losing. Wait. There's...a box."

Celestia watched as the hospital ward disappeared around her. She found herself standing on top of a high hill situated just a few miles away from the base of the mountain the held Canterlot. She was wearing a golden suit of armor with an Equestrian symbol painted on the side.

"Here they come!" she cried. An army of armored Canterlot guards was around her. A sea of Changelings was flying towards them at incredible speeds. "Brace yourselves!" Suddenly, she heard an odd noise. She turned towards a small forest located about a mile away. A strange light was emitting from it, as well as an alien sound. She recognized that sound. She had heard that sound before. "Can it be?" A small, blue box appeared just on the edge of the forest. "Doctor. I'm glad you decided to arrive now of all times. Equestria needs you, now more than ever."

The vision faded and Celestia found herself back in the hospital ward. Luna was kneeling down next to her.

"My sister...are you okay?" Luna asked. Celestia grabbed onto her younger sister in order to regain her balance.

"Sorry, Luna. I was just...reliving old memories," she replied.

"It looked like you were having a heart attack!"

"It must have, for it felt like I was."

The two sisters jumped at the sound of a scream emanating from outside. Spike, Pinkie, and Fluttershy burst back into the ward.

"We have a problem!" Pinkie shrieked.

"What sort of problem?" Luna asked.

"Take a guess," Spike gulped.

"EXTERMINATE! PRINCESS LUNA! MUST EXTERMINATE PRINCESS LUNA!" echoed the voice of a Dalek. Celestia turned towards her sister.

"Sister, you must flee! Now!" she ordered.

"No, Celestia!" Luna stated. "I'm not running from this!"

"Please, sister! I just got you back! I don't want to lose you!"

"These creatures are obviously persistent. They won't give up until they find me! They'll continue to chase me, ruining the lives of innocent ponies in the process. It ends here, sister! If I am meant to die at their hoof, then I guess I just have to face my fate!"

"Luna."

"This ends here, sister."

Luna turned around and ran out of the ward. Celestia looked after her sister and, after a second of thought, raced after her.

"I don't think Daleks have hooves," said Pinkie Pie.

_**Canterlot Castle Throne Room, Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

Twilight tried to trap the Daleks in a force field but it was no use. Like the first Dalek, they had the strange ability to phase through magical barriers.

"How do we stop them?!" Rarity asked.

"I don't know!" Twilight replied.

"Whatever you do, don't tell them about where Princess Luna is!" Shining Armor whispered into the mares' ears, just out of earshot of the Daleks.

"WHERE IS THE PRINCESS?!" asked the Daleks. "YOU WILL TELL US WHERE THE PRINCESS IS!"

"She's on a coffee break!" Rainbow Dash choked.

"Really? Is that the best excuse you could come up with?" Twilight asked.

"Oh shut up, egghead!"

"Gals, now's not the time for arguing!" said Applejack. The Daleks continued to advance on them.

"YOU WILL TELL US WHERE THE PRINCESS IS OR WE WILL BE FORCED TO EXTERMINATE YOU!" the Daleks ordered.

"I don't want to be exterminated, and _especially_ not looking like _this_!" Rarity stated.

"You look fine, Rarity! Now's not the time to worry about how you look!" said Shining Armor in the most polite/annoyed tone he could manage.

"Hey!" called a familiar voice. The Daleks turned to see Princess Luna standing a few feet away. "You looking for me?!"

"PRINCESS LUNA!" cried the Daleks. More sparks shot off from their armor.

"I'm right here! Come and get me!"

"EXTERMINATE! EXTERMINATE!"

The Daleks aimed their death rays at Luna and fired. Luna dodged the attacks and sent a series of magical blasts back at the Daleks. One Dalek was hit by a spell that sent it flying through the air and into the wall. The Daleks continued to fire at Luna.

"LUNA!" cried Celestia as she raced into the room.

"Why are you here?!" Luna asked. A Dalek fired but the sisters dodged the attack.

"I'm not letting you face these creatures on your own!"

"EXTERMINATE! EXTERMINATE!" cried the Daleks as they fired at them. Celestia and Luna returned fire. Their magical blasts meet the death rays in mid-air, sending a shockwave through the room. Sparks began flying off of the Daleks' armor. "NO! WE MUST NOT FAIL! WE MUST NOT LET THE DOCTOR DOWN!"

"The Doctor? What are they talking about?" Twilight asked. The Daleks fired again and the sisters followed suit. This time, their blasts met and interconnected. Celestia and Luna quickly found themselves in a life-or-death tug-of-war in which they pushed their magical blasts against the death rays of the Daleks.

"Hold on, Luna!" cried Celestia.

"I am!" cried Luna.

"EXTERMINATE! EXTERMINATE!" cried the Daleks. The collision of energies was too much and another, larger shockwave rocked the throne room. Sparks began flying off the Daleks' armor. Celestia felt a familiar pain in her head as she fell to the floor.

The throne room disappeared and she found herself staring through what appeared to be a telescope. The Doctor appeared before her, only he didn't look like the Doctor she knew. His hair was black, he had a black bow tie, his eyes were sunken in, he had a gray coat, and he had a pair of large, menacing, pegasi wings.

"Doctor?" Celestia asked. It was apparent that the Doctor couldn't hear her.

"I want you to kill Princess Luna. She's been a thorn in my side, as well as yours, for long enough. The time has come for this all to end. Kill her and don't let anypony stand in your way," said the Doctor.

"YES, MASTER! WE SHALL COMPLETE THE TASK THAT YOU HAVE ASSIGNED US!" came the voice of a Dalek.

"Good. Good."

The Doctor let out a cold laugh as the vision faded.

Celestia was lying on the floor of the throne room. Luna was once again engaged in battle with the Daleks.

"MUST EXTERMINATE PRINCESS LUNA! MUST EXTERMINATE!" cried the Daleks.

"L...Luna," croaked Celestia as she reached for her sister.

"Daleks! Cease fire!" ordered a cold, controlling voice. Celestia instantly recognized the voice. It was the voice of the Doctor, but not her Doctor. It was the voice of the Doctor she had seen in her vision. She looked and saw the Doctor strolling into the throne room. Thankfully, he looked like his normal self: chestnut coat, brown mane, blue suit, red tie, and no wings. Derpy, Trixie, and Monty were walking behind him, as well as two Daleks. "Put down your weapons, Daleks! Your master commands you to do so!"

Celestia didn't like the voice that the Doctor was using. It was too...out-of-character in relation to his normal personality. But, for some reason, the Doctor's empty voice seemed to work as the Daleks stopped attacking Luna. Spike, Pinkie Pie, and Fluttershy walked into the throne room after the two other Daleks.

"Doctor?" Twilight asked.

"Sorry about the grim voice, everypony. Talking like this is the only way in which I can control them."

Sparks flew off of the Daleks' armor.

"WE DO NOT UNDERSTAND!" they stated.

"Listen here! You are to not do anything unless I tell you to do so! Is that clear?!"

"YES! IT IS CLEAR, MASTER!"

"Good!"

The Daleks lowered their weapons and fell silent.

"Doctor? What did you just do? Why were you talking like that?" Twilight asked as she approached the Doctor.

"Brilliant, he was!" stated Monty. "He came up with an excellent plan!"

"And that was?" Rainbow Dash asked.

"Well, these Daleks appear to be working for an alternate, darker version of myself. I heard a recording of this darker me through one of the Daleks' speakers. It didn't take long for me to see that these Daleks are somewhat confused about things. I simply mimicked the voice of my darker self and _voila_! The Daleks obey every command I give them!" the Doctor replied in his normal voice.

"I'm a little bit confused but good job, Doctor!" stated Twilight.

"Well, it wasn't that hard of a plan to concoct."

"So now what are we supposed to do with _them_?" Trixie asked.

"Lock them up and try to figure out exactly why they were sent here by a darker me to kill Luna."

Celestia's head was still hurting as she stood up. She had heard everything that the Doctor had said. It was confusing and yet it made perfect sense. She looked and noticed that one of the Daleks was emitting a sea of sparks. Its death ray began to raise up and point towards Luna.

"EX...TERM...IN...ATE!" the Dalek croaked.

"L...Luna," Celestia warned. Luna didn't hear her sister's weakened voice. These visions had drained a lot of strength from Celestia. The Dalek's death ray was now aimed straight at Luna. "L...Luna!" Luna was still unable to hear Celestia's weakened voice. The Dalek shot out a couple more sparks before firing its death ray at Luna. The beam of energy shot across the throne room and towards the unsuspecting, blue alicorn. Celestia, using the last bit of her strength, rushed towards her sister. "LUNA!"

Luna turned just in time to see the death ray rushing towards her. She then felt a violent shove as Celestia pushed her out of the way. Celestia let out a cry of pain as the death ray collided with her body.


	6. A Spiritual Rescue

Chapter 5: A Spiritual Rescue

_**Canterlot Castle Throne Room, Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

Luna's eyes widened as the body of her sister fell to the ground right in front of her. It couldn't be. It just couldn't be. Celestia couldn't be dead. Her sister _could not_ be dead!

"NO! What did I tell you about not doing anything?!" the Doctor snapped at the Daleks in his colder voice. "All of you shall remain still until I say so! No shooting! Nothing!"

"BUT WE CANNOT LISTEN TO YOU...AND YET WE MUST!" cried the Dalek that had shot Celestia. Another shower of sparks shot off its armor before it fell silent again.

"Princess Celestia!" Twilight cried. Luna knelt down next to her sister and balanced her head in her forehooves. "Doctor...this can't be! We've been to the future! We know that Celestia still lives in the future! She can't die here! It's impossible!"

"I know, Twilight. Something's not right here...and I have a feeling that something else is going to fix it," the Doctor replied in his normal voice.

"Don't die on me, Celestia!" Luna cried as she stared deep into her sister's black, lifeless eyes.

_**Unknown Place, Unknown Time**_

Celestia opened her eyes to find herself standing in what appeared to be the throne room at night. She was alone.

"Luna? Twilight? Doctor? Is anypony here?" she asked. She remembered the Dalek shooting her and a familiar pain rung through her head. "Am I...dead?"

"Not quite," replied a familiar voice. Celestia looked into the darkness to see the familiar, blue eyes of her sister staring back at her.

"Luna?!"

"Yes and no. I am Princess Luna but not the one that you are thinking of."

"I do not understand."

"Maybe the best way for me to help you understand is if I show you."

Celestia watched as a figure emerged from the darkness. She didn't know what to think. She knew that the creature before her was Luna...but it certainly wasn't the Luna she knew.

A human woman stood before her. She had long, flowing, blue hair that glimmered like the night sky. Her eyes were night blue and carried a sharp gaze. Her skin was incredibly fair. A black crown sat on top of her head. She wore a deep blue tunic with dark blue pants and a long, gray cloak. A silver rapier hung from a holster connected to a black belt wrapped around her waste, which had Celestia's Luna's cutie mark imprinted on it. The last thing Celestia noticed was a long, silver wand sticking out of one of the pockets in the woman's tunic.

"What...what are you?" Celestia asked. Another pain shot through her head. The woman approached her.

"I told you, Celestia. I'm Princess Luna," she said.

"You...you can't be Luna. You're not even the same species as her!"

"But I am her, just from another reality. Members of _my_ species are known as human beings."

Another pain shot through Celestia's head.

"Human...beings. I...I think I've seen them before."

"Of course you have. You've seen me. You've seen...well I guess I shouldn't go into that just yet."

"Why are you here?"

"I'm here to make amends to the wrongs done against you and my ponified self."

"What do you mean?"

"The Daleks that went after your Luna were incredibly confused. I can only assume that the dimensional rifts didn't take kindly to their minds. They were befuddled."

"Befuddled?"

"Yes. You see, the Daleks _were_ after Princess Luna but not your Luna."

"They...they were after you!"

"Exactly."

"But why?"

"It's complicated."

"Is...is it true that the Doctor sent them?"

"Yes and no. _A_ Doctor sent them but not the Doctor who's been fighting alongside you."

"So...there's more than one Doctor?"

"Yes. It's complicated and I don't have much time to explain. I'm reaching through not only dimensions but time as well to talk to you."

"You said that I'm not quite dead. Is this true?"

"Yes. You're not going to die, Celestia. You're going to live on. I've come here to help your lost spirit return to its body."

"How are you to do that?"

"Well, unlike your Luna, I've had some practice in the spiritual arts as well as the magical. Nothing dark, I promise you."

Celestia sighed. She couldn't be happier. She wasn't dead...but something else was troubling her.

"So...is this other Doctor a threat to me, my friends and family, and my kingdom?" she asked. The human Luna sighed.

"If you want an honest answer then...yes. He is a threat to you," replied the human Luna. "But don't worry, Celestia. As long as you're allies with the Doctor and as long as you have that odd stallion by your side, you will always triumph against anything the cosmos throws at your home." Luna the human suddenly began to fade away. "Oh man! I better make this fast! Listen to me, Celestia, tell the Doctor to follows the rifts."

"Follow the rifts?"

"Yes! The dimensional rifts! They're the key to everything that's going to happen! A war is on the horizon, Celestia! Don't anticipate when this war is going to happen or what the outcome is going to be! Just make sure the Doctor is there to help you. As long as Equestria is an ally of the Doctor, you'll never have a short supply of allies to fight alongside you!" Luna the human placed her hands against Celestia's head. "Now this may sting a bit. I'm going to send you back to your body! You still have a lot to do, Princess, and a stupid Dalek shall not bear your downfall!" Celestia watched as the dark throne room began to slowly disappear into darkness. "And, one more thing, I've noticed that you've been struggling with some lost memories. I think, as a special bonus, I can give you one last jolt to allow you to finally remember what you lost."

Celestia closed her eyes and cried out as her body began to glow like the sun and vibrate like an earthquake.

_**Silent Forest, South of Canterlot, Equestria, Gaia, Autumn, 53 C.E.**_

Celestia walked through the forest quietly. The air smelled of oak and maple and colorful leaves fell to the ground slowly. The city of Canterlot could be seen shining far above the forest. The Princess fell silent as an odd sound began emanating through the trees. She knew this sound. She knew it all too well. She turned as a familiar, blue box appeared a few feet behind her. The doors of the box opened and out stepped a familiar, chestnut stallion in a black suit.

"It's nice to see you again, Doctor," said Celestia as the Doctor approached her. He seemed sad about something. "What happened to your blue suit, Doctor? I think that fit you quite nicely. No offence, but this new black outfit of yours doesn't really go with you."

"It's nice to see you too, Celestia," the Doctor replied grimly. "Don't worry, I still have the blue suit. I just felt like wearing this one for a little bit."

"What's the reason?"

"I...I lost somepony. Somepony I really care for."

"I'm sorry, Doctor. Death is never an easy thing to get over."

"No. Death didn't take her. What took my friend was something much crueler than death."

"What could be worse than having somepony you care for dearly die?"

"The unknown. That's what's worse. I've lost her..._literally_. She's gone and now it's incredibly probable that I'll never see her again."

"But there _is_ a chance that you'll find her, right?"

"Of course there is! That's what I'm doing! I'm searching for her. I'll never give up, Princess Celestia. I will _never_ give up!"

"I wish you all the luck in the universe, Doctor."

"Thank you, Celestia. Well...I guess I better be off then." The Doctor turned around and began walking back to the TARDIS. At the last second, he turned around and said, "Before I go, I have something to tell you."

"And that would be?"

"There's a storm coming, Celestia. Not even a year from now, there's going to be a giant cloud of evil rushing over that horizon to destroy everything that you hold dear. It's going to be a rough fight...but don't worry. I'll be there to help save your country."

"I've already lost a lot, Doctor. I've lost most of my friends. I've lost my parents. I've even lost...my sister. But I will not loose Equestria! I shall be ready for this storm when it arrives! And you better live up to your promise!"

"Don't I always, Celestia? And, besides, I know I'm going to keep my promise because I've already fulfilled it!"

"What? Oh. Right. Wibbly wobbly timey wimey."

"Never gets old, does it?!"

"No. I guess it doesn't."

"Goodbye, Celestia."

"Goodbye, Doctor."

The Doctor strolled into the TARDIS and shut the doors. Celestia gave a small smile as the TARDIS disappeared, leaving her alone in the forest once again.

_**Canterlot Castle Throne Room, Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

Celestia opened her eyes to find everypony looking down at her.

"Celestia?!" cried Luna. Luna grabbed her sister and hugged her tightly. "You're alive! You're alive!"

"Yes...I guess I am," Celestia said with a loud sigh.

"But how?" asked a shocked Twilight. "You were hit by that Dalek's death ray!"

"It's complicated."

"You can tell us the details when you're feeling better!" said Luna.

"Aw! We have to wait?" Pinkie Pie asked.

"So Celestia just came back from the dead. I guess nothing's going to separate these sisters, eh Doctor?" Monty asked.

"No. I guess not," the Doctor said with a smile. "So, what are we to do with our unwanted, metal attackers?"

"I'll take care of them," said a flirtatious voice. Everypony turned to see a red-coated mare with a purple mane walking towards them.

"Matilda?!" asked the Doctor and Twilight.

"The one and only."

"But...how...why...what...what are you doing here?!" asked Twilight.

"I just popped in to take care of your Dalek infestation. Don't worry. I know exactly where to send these unwanted guests of yours."

"So _this_ is Matilda," said Fluttershy.

"I see this, for some of you, is our first meeting. Don't worry, you'll get to know me quite well in the future."

"Yay," said Applejack sarcastically. Matilda rounded up the Daleks while Luna helped Celestia up.

"It...it's you! The mare who gave me the portable cage!" Celestia exclaimed.

"Your welcome," said Matilda as she finished rounding up the Daleks.

"Wait. How did you know to bring the portable cage here?" Rainbow Dash asked. Matilda turned towards the Doctor.

"Doctor?"

"Wibbly wobbly timey wimey!" the Doctor sang with a smile.

"There's you answer, Ms. Dash!"

"That's not an answer! That's a rhyme!" Rainbow snapped.

"Are you saying that rhymes can't be answers?"

"No need to discriminate against the rhymes, Rainbow Dash!" teased the Doctor.

"Don't tell me you've decided to become like her, Doctor!" said an annoyed Derpy with a smile.

"You know what they say. If you can't beat them, join them."

"Good choice, Doctor," said Matilda. "Well I better get these Daleks back to where they belong. Oh, and Celestia, I believe Princess Luna just provided you with some interesting information that the Doctor would like to hear."

Celestia took in a deep breath as memories of the Doctor flooded her mind. The words of Luna the human, however, remained in place as the main focus at the moment.

"Yes," Celestia replied. "I believe I do have some interesting information."

"Good! Well I'll see you all later! Have a nice day!"

Matilda clicked a few buttons on her vortex manipulator and, in a quick flash of light, she and the Daleks disappeared.

"She sure is quite a character," said Monty.

"Look who's talking, Mr. Clown," said Rarity.

"Look who's talking, Ms. Marshmallow!"

"How _dare_ you!"

"I think everypony can be considered as _quite a character_," Derpy whispered to the Doctor.

"Not going to argue with that one," the Doctor replied with a chuckle.


	7. Homeward Bound

Chapter 6: Homeward Bound

_**Performance Square, Canterlot, Equestria, Gaia, Autumn, 1002 C.E.**_

The TARDIS let out a familiar hum as the Doctor approached it.

"Ah! There you are, TARDIS! Nice to see you again!" he said happily. "Oh dear, I think I really have become slightly loopy. Oh well. Nothing a nice drink and a long nap can't fix!"

The Doctor fell silent. All he could think about was what Celestia had told him. He was happy that she was alive and well and that she had finally made amends with Luna, but the news she brought about was nowhere near cheerful. Apparently there was a war on the horizon and the dimensional rifts had something to do with it. Then, of course, there was the whole deal involving the human Luna and the other, darker Doctor. There was so much to think about. The Doctor turned back to the others and he could tell that they were just as worried as he was.

"So...what are we supposed to do now?" Derpy asked.

"Celestia was pretty vague in what she told us. I can only think that she kept a few, particular details from us," said Twilight.

"Why would she do that?" Spike asked.

"Spoilers!" chimed Rainbow Dash and Pinkie Pie.

"Of course," Applejack sighed.

"I don't know about the rest of you but I'm ready to get back to old Ponyville!" said Rarity.

"Home sounds pretty good right about now," said Fluttershy.

"You're leaving already?" asked Shining Armor, who was accompanied by Trixie and Monty.

"Yes. We've been traveling around for a while now and we're all ready to head home," Twilight replied.

"I wish you could stay longer. You weren't even able to see Cadance."

"I think it's obvious that we were a little preoccupied." Twilight giggled before hugging her brother. "Take care, BBBFF."

"Take care, Twiley."

"I guess this is goodbye for now," said Trixie. She shuffled her hooves awkwardly. "I'm glad I got pulled into your TARDIS, Doctor."

"I'm glad about that too. May our paths cross again in the future, Trixie," said the Doctor as he extended a hoof. Trixie shook it professionally. "Say, have you ever thought about a career in writing?"

"Not really. Why do you ask?"

"Oh nothing! Just a suggestion."

"Sure. Whatever you say, Doctor."

Trixie then proceeded to say goodbye to the others while the Doctor turned his attention to Monty.

"You knew about my dark self, didn't you?" the Doctor asked.

"Yes. I wish I could tell you more...but I made a promise," Monty replied.

"Best to keep your mouth shut for the time being. Don't want to risk spoiling anything in a negative way."

"I guess. Opal's probably still in Ponyville. Send her home if you run across her there. The kids are starting to miss her."

"And you too?"

"Of course!"

"Take care, Monty. I have a feeling that we're going to cross paths again."

"As long as Opal's life continues to intertwine with yours, you'll always find me somewhere either in the action or somewhere in the background."

"Will you always be dressed up as a clown?"

"It counts on what mood I'm in."

The Doctor chuckled as he shook hooves with Monty. He then turned back towards his companions.

"So is everypony ready to head back to good, old Ponyville?" the Doctor asked.

"Definitely!" replied the companions.

"So, Doctor. What are your plans from here on out?" Twilight asked.

"Oh, I don't know. I think I might want to take a short break from traveling. Maybe kick back and relax for a while. I guess this would be a good opportunity to keep the promise I made to you oh so long ago, Twilight."

"You mean you're going to stay in Ponyville and take things slow for a little bit?"

"Why not? Everypony needs some R&R every once in a while, even me."

"You can stay in the library. I have an extra guest room in the basement that would be perfect for you."

"Sounds perfect, Ms. Sparkle." The Doctor looked and noticed that Derpy seemed somewhat disappointed about something. "I can see that you still have a lust for adventure, Ms. Hooves."

"I guess you could say that," she replied.

"Don't worry. We'll be off traveling through space and time once again. You, me, Twilight, and whoever else decides to join us. Does that sound fun?"

Derpy and Twilight exchanged sharp glances but then smiled at each other.

"Yeah," said Twilight.

"That sounds good," Derpy finished.

"We're ready!" Pinkie called from within the TARDIS. The Doctor looked and realized that everypony else had entered the TARDIS aside from him, Twilight, and Derpy. The stallion, the unicorn, and the pegasus couldn't help but chuckle as they entered the TARDIS. Trixie, Monty, and Shining Armor watched in silence as the TARDIS slowly disappeared.

_**Canterlot Castle Royal Quarters, Canterlot, Equestria, Gaia, Winter, 1003 C.E.**_

Princess Luna the human opened her eyes following the end of her connection with the ponified Celestia.

"That went better than I thought it would," she said to herself.

"That's good," said a familiar voice. Luna turned around to see none other than Matilda standing there. A group of bound Daleks was standing next to her. "Special delivery for the Princess."

"Thank you, Matilda. This should be the last of the Daleks."

"You owe me big time! Do you realize how long it took for me to track all of this rogue Daleks down?"

"Enough to warrant a vacation, I would guess."

"My whole life's a vacation. A paid one wouldn't make a difference."

"Besides, you don't even officially work for me so I can't give you vacations anyway."

"Too true." Matilda fell silent and shuffled her legs. "You know what? There are times where I wish I could spill the beans to the younger Doctor about what's to come."

"I felt the same way you feel when I was talking to Celestia's ponified counterpart." Luna became stiff and lowered her head. "It was wonderful...hearing her voice again. Even if the Celestia I talked to wasn't my sister...she still made me feel the way I did around my own Celestia."

"You miss her dearly, don't you?"

"More than anything."

"I can help you see her again." Matilda presented the vortex manipulator to Luna the human. "And all with the click of a button."

"It wouldn't be the same and it would have too many risks. No. We best not do that."

"Okay. I understand."

"Can you fetch Spike for me? I need to discuss some plans with him about what to do next in the Restoration Movement. There's a lot of work to be done."

"Of course. And, remember, I'll always be just a call away if you need anything."

"Thank you." Matilda began to leave. Luna then suddenly said, "Wait. Could you promise me one last thing?"

"Of course, Luna. Anything."

"Could you make sure that nothing ever separates my pony self from her sister? Make sure nothing drives them apart. Make sure no harm falls on them. Make sure to aid the Doctor in any way you can so that their Equestria can continue to thrive and recover quicker than mine."

"I promise. Have a nice day, Princess-"

"I've decided to change my title to _Queen_ Luna. I think it's about time. It's not like I have anybody ruling over or alongside me anymore."

"Right. Have a nice day, Queen Luna."

Matilda walked out of the room and Queen Luna sat down on the edge of her bed. When she knew that Matilda was out of earshot, she lowered her face into her hands and silently wept.

To be continued...

Author's Note: I just wanted to note something here involving my future writing plans for Doctor Whooves. With the completion of this episode I am now halfway through the first season of my Doctor Whooves series. This, I feel, is the perfect point for me to take a short hiatus from the series. I promise not to have you all wait too long for the next episode but I've been writing practically nothing but Doctor Whooves for a while now and I'm starting to feel a little bit burnt out. That's why I've decided to go on a short hiatus. I also want to start working on another fanfic that I've been dying to start writing for a while now as well as maybe write some more spontaneous one-shots. If any of you are wondering when I'm planning on returning to Doctor Whooves, well I plan on returning to writing the series normally in around a month or so, even if I'm not done with my other fanfic project. But, in honor of the Doctor Who 2012 Christmas special premier, I am planning on writing and uploading the prologue of my next Doctor Whooves episode on Christmas Day just so you guys will have something to hold onto until I officially return to the series. So, for now, I'll say that I'm planning on returning to writing and uploading Doctor Whooves episodes in my normal routine at around January 15, which is exactly a month from now (obviously). Lastly, I'd like to thank you all for reading and enjoying my series and sending me feedback. I really do enjoy hearing your thoughts and opinions of my series and I hope you all continue to enjoy this series of mine. So I guess there's no better way for me to end this author's note than by saying the following:

The Doctor will return in Doctor Whooves Episode 13: Clockwork and the Doctor!


End file.

Doctor Who, My Little Pony, Adventure, Sci-Fi