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!"