Several days had passed since Twilight's regeneration, and her condition had improved immensely. She no longer had a fever, and she'd begun stirring, signalling that she would wake up soon.
Every day, the Doctor sat by Twilight's side, monitoring her to make sure that she slept and recovered. On the morning of her waking, the Doctor realized that he hadn't contacted either of the princesses or Twilight's brother. He stood up from his sitting position on the cushion and made his way into the library's main room downstairs. There, Spike was reading some sort of comic book, frowning in sadness as he read.
"Spike, I need you to send a letter," he said flatly.
He looked up from his comic, saying, "And why should I help you, Doctor?" He nearly spat the name.
"Princess Celestia needs to know what happened, and I'm sure Twilight's brother will want to know as well," said the Doctor, not feeding the fire of Spike's hate by keeping his voice level. Spike glared at him for a second before readying a quill, ink, and the parchment he always kept on hand in case Twilight needed an emergency list or some kind of letter sent.
"Ready," he said coldly.
"Ok, here goes." He cleared his throat before proceeding. "Dear Princess Celestia, I regret to inform you that Twilight had an... accident. While in my care, she suffered a blow from a Dalek laser. No doubt from our experiences in the past, you know the destructive power of their weapons and sadly, she did not survive. However, there is no need for a funeral. Please come as soon as possible, and bring Princess Luna, Princess Cadence, and Shining Armor. Your friend, The Doctor." When he was finished, he turned back to Spike. "Did you get all that?" he asked.
Spike lit the letter on fire, sending it off before saying, "It's on its way." He immediately went back to this comic, ignoring the Doctor in disgust.
Ten minutes later, while the Doctor was cooking some eggs, he heard and felt static fill the library as a massive teleport was made into the central room, bringing with it Princess Celestia, Luna, Cadence, and Shining Armor. He heard hoofsteps coming toward the kitchen and found Princess Celestia standing in the doorway. "Where is she?" she asked with a saddened expression.
"Upstairs," said the Doctor, betraying no emotion whatsoever. He dropped the eggs onto a plate and set them on the counter before going with the princesses up to Twilight's room.
When they arrived and found Twilight sleeping, Shining Armor said softly, "Twili?" When she didn't move, he nearly broke down. Princess Celestia allowed a few tears to flow down her face as she looked on at her fallen student. She moved to Twilight's bed and got a good look at her. When she saw how much she'd changed, she spun back around to the Doctor and glared at him. "What happened to her?" she asked grimly.
"Like I mentioned in the letter, a Dalek happened," he said back, still showing no trace of emotion.
Celestia began walking toward him, gradually picking up the pace as she said, "Just how long ago did this happen?" She was now towering above the Doctor, but he remained unphased and refused move.
"Three days," he said calmly.
"And you didn't contact me sooner?" she asked, feeling slightly betrayed.
"Not at all."
Celestia backed up a little bit before continuing. "Is she dead?"
"Yes," he said back. Before Celestia could speak again, the Doctor said, "but she's someone new now. She's not the same Twilight you knew."
"Why does she look so different?" asked Celestia as she glanced back to Twilight.
"But what does that mean?" asked the Princess, becoming impatient and angrier.
"It means she changed," said the Doctor, raising his voice as he too grew impatient.
"Be specific," ordered the Princess as she gritted her teeth.
"Then kill me and you can see for yourself!" yelled the Doctor as he stamped a hoof down, shocking everyone into complete silence.
Neither Celestia nor the Doctor moved an inch. After a few seconds, the Doctor said, "Do you know what you are? Any of you?" He gestured to Celestia, Luna, Cadence, and Twilight.
"We're the noble race of alicorn's," responded Celestia. "What more?"
"Time lords," he said back without hesitation.
"I beg your pardon?" asked Celestia.
"Don't act stupid. You heard me. The one thing I can't stand is stupidity," he spat.
This took Celestia back, but she pursued her curiosity. "We're one of you? That doesn't make any sense."
"It makes perfect sense when you've lived as long as I have."
"Enough with these riddles," said Luna from behind him. "Please, tell us Doctor. We're alicorns, but how could we possibly be time lords?"
The Doctor sighed deeply before saying, "I watched you both die. Over 2000 years ago, when your parents' cart lost its driver on that hill and you crashed into that chasm."
"What in Equestria are you talking about?" asked Celestia.
"Oh, don't play stupid again," said the Doctor. "It hasn't even been 60 seconds. Need I remind you how much I hate stupid?"
Both Princess Luna and Celestia backed up even more before they lowered their heads nearly simultaneously. "We were so young..." began Celestia.
I remember we were driving on a rough road. Luna and I kept bouncing in our cradles, and our mother did her best to comfort us. Our father, meanwhile, scolded the driver for 'being reckless with foals on board'.
We hit a large stone and lost our driver. I didn't see what happened, but before I knew it, we were tumbling to the bottom of a pit. A remember a very loud crash and some pain. When I woke up, I found that I'd grown wings. I thought that I might be a princess. Of course, Luna and I had been told stories about them, and we thought we were special. But before I could fantasize further, I saw something horrible.
Luna and I were both dead. I saw our bodies and those of our parents, but I didn't know what it meant. And that's when we first met you, Doctor. You came to rescue us with a group of hikers that were in the area. You led them to us, and took us back to Canterlot.
"But I don't see what that has to do with us being related to your people," finished Celestia.
"I studied you all for a very long time after your deaths. Even you, Princess Cadence," said the Doctor, looking over at Twilight's sister-in-law.
"Me?" she asked, surprised. "But I'm not dead. I never died."
"I know that's what you believe, but you're wrong. When your mother was 11 months pregnant with you, she had a miscarriage. You died before you could be born. But when you were removed, you suddenly sprung to life. And with wings no less. Haven't you ever wondered why you're... built differently from other ponies? Why you're so much more slender?"
"No..." muttered Cadence. "That can't be right. It just can't be!"
"But it is," said the Doctor flatly. "I know because I was there in the operating room. I witnessed the conception of all of you, except for Twilight. I still need to know exactly what conditions led to her transformation. I need to learn everything I can about the Elements of Harmony and her 'birth'."
"Huh," came a voice from behind the Doctor and Princess Celestia. "So that's how it works. Who'd have thought?"
Slowly, the Doctor turned around to look at the bed. When he looked, he saw Twilight sitting up, smiling at everyone. "So, what'd I miss?"
"Twili!" shouted Shining Armor. He ran to his little sister and tackled her in a huge hug. "I'm so glad you're okay," he said as he nearly cried.
"Of course I'm okay," she said back. "It's not like I'm dead or anything. Well, not really. Old me is dead, but she had her time. Now it's my turn!" she said excitedly.
Shining Armor backed off to give Twilight some room. Princess Celestia spoke next. "Hello, Twilight," she said as if she was meeting someone brand new. In a sense, she was.
"Hiya, Princess," she said enthusiastically. "What are you all doing here? Did something happen?"
Princess Luna said, "No. We were just meeting someone new."
"Really?" asked Twilight. "Who was that?"
"Let's just say you're very close," said Cadence. Every pony was glad that Twilight was alright and awake, though they had become curious about the Doctor's discoveries as well.
"I thought I knew everyone in Ponyville. Who else is new?" she asked. Instead of answering, the Doctor gave her a big hug.
"It's good to have you back, Twilight Sparkle," he said.
"Did I do something to deserve all these hugs?" she asked happily.
After about a half hour of getting up, and talking for a bit with everyone (who were overjoyed to have her back) Twilight asked the Doctor, "After regenerating, I'm a bit hungry. You wouldn't have happened to make breakfast would you?"
"Well, I did make some eggs, but they're probably a bit cold now. Sorry about that," he said.
"That's okay," said Twilight. "I'll see if I can get Spike to help me make something for every pony."
"Oh!" exclaimed the Doctor. "He doesn't know you're okay! He's still thinks I killed you. And your friends are gonna want to know you're okay, too!" He turned to Princess Luna before asking, "Princess, would you be willing to visit each of Twilight's friends and bring them here?"
"It would be my honor," she replied. In a flash, she teleported out of the room to gather the others.
The Doctor turned to Twilight and said, "You should go down and say something to him. He's been really worried about you."
"Sure," said Twilight. She walked passed everyone and down the stairs. From the room, they could all here Spike's cry of happiness when he saw Twilight was alright. The Doctor chuckled to himself before leading everyone downstairs.
After about ten minutes, Twilight and Spike had started breakfast while the Doctor continued speaking with the others in the main room.
"Doctor," began Cadence, "you said that you all witnessed our conception; our transformation into alicorns. But how does one become an alicorn?"
"I'm still curious about that, too," said Celestia. "I know that it has to do with a unicorn's inner magic capabilities, but I'm clueless as to how the process works exactly."
"You're all very magically adept," began the Doctor. "Princess Celestia, you and Luna can control the sun and moon. Princess Cadence, you can control a pony's emotions. Twilight seems to be a different breed, no pun intended. She seems to have mastery over nearly every magic with more than just a basic understanding of it all. It seems that her strong suit is manipulation over space, hence her knack for teleportation spells and control over her environment. But why can she do that? Why do any of you have the extraordinary magical capabilities that you do in the first place?"
They all sat in puzzlement for a moment before a rapid knocking came on the front door. Every pony looked up for a second and exchanged a glance of curiosity before realizing that it must be Princess Luna and the others. So, the Doctor got up and made his way to the door. He stood slightly off to the side and very quickly hit the latch before sidestepping, allowing the door to swing open and bring an avalanche of ponies with it. Twilight's friends landed in a heap on the other side of the door before picking themselves up.
"Where's Twilight?" asked Pinkie Pie excitedly. "Is she really okay this time? Is she done with her nap?" She grabbed the Doctor by the shoulders and shook him vigorously as she said, "Somepony say something!"
The Doctor struggled away before saying, "Yes, everyone. She's alright. Right now, she's in the kitchen with Spike making some breakfast. You can go and see her if you like." That was all Twilight's friends needed to hear. They rushed to the kitchen and tackled Twilight to the floor in excitement.
Meanwhile, Princess Luna stepped in the room through the front door. "It's a good thing I walked behind them all," she said, amused by their excitement.
"A good thing indeed," chuckled Princess Celestia. "Now, Doctor, why do you think we have such strong magic?"
"I don't know," he said bluntly. "We need to find a connection between you all. But even after fifty years, I only know so much. Argh! What am I missing?" He started pounding his head with a hoof. "Think, Doctor, think!"
Princess Celestia interrupted his train of thought. "Doctor, I may have something. Come meet us in Canterlot when you're ready." At this time, Twilight and her friends walked out of the kitchen carrying food for everyone.
"I hope ya'll are ready to eat yer fill," said Applejack, "'cause Twilight and Spike made a bit too much."
"Actually," said Princess Cadence, "we were just getting ready to go back to Canterlot. We need to find out if there's a connection between all of us," she finished as she motioned to the other princesses. "So I'm sorry, but we can't stay."
"Oh, come on," said Twilight. "You can't even stay for one egg?"
"I'm afraid not," said Princess Celestia. "We must travel there as soon as possible so that I can prepare to present my theory to the Doctor. As much as I would love to stay here with you for a little while, this is where we must part ways."
"Actually," said the Doctor, "we need to know more about Twilight as well. She should come with us."
"Really?!" asked Twilight excitedly, almost like a child would when they heard they were going to an ice cream shop.
"Yes, really," said the Doctor. "If you want, we can take my TARDIS to get there sooner."
"Good idea," said Princess Celestia.
"What's a TARDIS?" asked Princess Cadence.
"Time And Relative Dimensions In Space," said Twilight. "It's basically a time machine."
"That's dumbing it down a bit, don't you think?" asked the Doctor. Twilight chuckled slightly. "Anyway, she's right. It's a 'time machine' that can travel in space. Well, to be honest, it's a space machine that can travel through time, but I suppose they're interchangeable."
"A time machine?" questioned Shining Armor. "There's no way."
"Oh, but there is," said Princess Luna. "Where is your TARDIS parked, Doctor?"
"I moved it out back while Twilight was resting," he said. He began walking toward the back door as he said, "Come along then, everyone."
Twilight turned to follow him, and when no one else followed, she added jokingly, "That means now, slowpokes."
Their entire party followed the Doctor and Twilight out, including Spike and Twilight's friends. The TARDIS sat in the middle of the back yard, it's light from the inside glowing slightly to give it a ghostly appearance, even in broad daylight.
As the others caught up, the Doctor said, "Everyone, inside. We'll be in Canterlot momentarily."
"Oh, I love the TARDIS!" said Twilight excitedly. "It's so BIG on the inside!"
"I will never get tired of that," he mumbled to himself. After everyone had filed in (bringing with them the inevitable 'It's bigger on the inside' from Cadence and Shining Armor), the Doctor approached the console, punched in the correct coordinates, and added, "We're off!" as the TARDIS whirred to life.