The First of Many

by Mudkipman98

Chapter 1

Warning:Thar be spoilers ahead! This chapter conains spoilers for the BBC series, Doctor Who. If you haven't seen "The Name of the Doctor", "The Day of the Doctor", or "The Time of the Doctor", I suggest watching those first before reading on. Otherwise, you'll have quite a lot spoiled for you in only three sentences. You've been warned!

"Oh," said Twilight, using the same voice of 'old Twilight'. "I'm alive. Well what do ya know? Hey Doctor, let's go to the space carnival. I bet they've got great cotton candy! You know what, never mind that. What about the moon?! I've always wanted to go there! Oh! I've got a horn. And wings! That's fascinating! I should write an essay about it!"
As Twilight went into a mad rave about how she had completely obvious body parts that she and everyone else could see (such as legs, hair, a tale, etc.), Spike asked the Doctor, "What happened to her? Is she okay?"
"Oh, Spike!" exclaimed the seemingly crazy Twilight. "You're here! And so's everypony else. What're you all doing here? Oh, that's right. I regenerated 'cause I died! That's it. So you all came to watch me die? Wow, you guys sure are weird. To each their own I suppose."
The Doctor was marveling at Twilight's incomprehensible rave before he was punched to the ground by Applejack. "I said, what in tarnation did you do to her?!"
The time lord stood up, rubbing his cheek. "Ow," he groaned as the feeling came back to his jaw. "You didn't have to do that. Besides, I didn't do anything. This was always going to happen to her at one point or another."
"What's that supposed to mean?" asked Rarity, concerned that her friend was going insane.
"Traveling with me is... dangerous," he began. "And my companions don't always... survive." He began thinking about Amy and Rory before he snapped back to reality.
"So she was..." said Fluttershy, trailing off because she didn't want to say what all of Twilight's friends feared.
The Doctor lowered his head before nodding to them. Fluttershy broke into tears and ran while Rarity chased after her. Rainbow Dash and Applejack were stunned, and Pinkie Pie simply shut her eyes and frowned, too shocked to cry. "I'm sorry," he said. "We were running for our lives--isn't that always the case with me?--when she was shot. By a Dalek 'death laser' as they call it. There was nothing I could do, but it seems that fate may have played a lucky hand in all this."
"I left you all for nearly fifty years. I learned everything about your world, including your rulers. I know why they're alicorns and where they came from. As it happens, they're much like my race," he said, allowing himself a slight chuckle while the remaining three ponies continued to listen. Meanwhile, Twilight was bouncing around excitedly near the fireplace. "When a time lord dies, we don't."
"What?" asked Applejack in confusion. "You don't 'what'?"
"Die," continued the Doctor. "Instead, we regenerate. The person, or pony, that we were dies while our bodies live on. We still have our memories and our souls, but we change our face and become someone, or somepony, new."
"So Twilight isn't Twilight anymore?" asked Rainbow Dash sadly.
"No, she's still Twilight, just not the one you know. It's funny. Before you all met me, I regenerated 14 times.(1) I'm such a different man, I shouldn't even be called 'Doctor' anymore. Once, I renounced that name. But that was a long time ago. The point is, she's still Twilight, but she's changed. She's not the same mare that you all befriended on her first visit to Ponyville, or the mare that helped you all stop Discord. That mare is gone, and now this new Twilight will take her place."
Finally, Rainbow Dash lost it. "But I don't want this 'new Twilight', I want my friend back!" She charged into the Doctor, slamming him into the wall before punching him as hard as she could across the jaw. "Bring her back!" she repeatedly yelled as she continued to assault him. After nearly ten strikes, she lost heart and began whimpering, "Bring her back..." before she gave up and relaxed. This allowed the Doctor to drop to the library floor. He spat out some blood before standing up again.
"Don't you realize I want her back too?!" he yelled, filled with anger. "You know I never quite understood what it was like for my companions to watch me change, to watch me become some other man; to watch me die! But now I do, and it makes me sick. You're not the only ones who've lost someone you care about today!"
He stopped yelling when he saw all three of the ponies and Spike staring to his left. He slowly turned to see Twilight, sitting on the floor with her wings and head drooping. "Do you all really not want me?" she asked with sadness in her voice. "All of you? Do you just want your friend back instead of me?"
All the Doctor could do was walk over to her and embrace her as he said, "Of course I want you. You're still my companion, and I'm not gonna leave you behind just because you changed a little bit."
They sat together for a few minutes before the Doctor felt Twilight go limp. He slowly stood up, setting her down on the floor carefully before turning to her remaining friends. "She's not completely done yet," he said to them. "She's still regenerating, hence the stark raving mad outburst from a few minutes ago. Get her upstairs into bed. She should be fine in a couple of days."
"Days?" asked Pinkie Pie, still without enthusiasm. "How sick is she, Doctor?"
"Yeah," agreed Rainbow Dash. "You're a doctor after all, so tell us what's wrong with her."
"I just got done saying she's still regenerating. First, your body heals, and then your mind. That's why she's so crazy. She's marveling at the fact that she's just been born. Give her time, and I promise you she'll be back up and active in a few days."
"You'd better not be lyin' to me, Doctor," said Applejack. With that, the three remaining ponies carried Twilight upstairs and put her in bed before departing, leaving Spike and the Doctor alone.
"So Twilight's really gone?" asked the baby dragon, holding back tears.
"I'm afraid so, Spike. I'm sorry." That was too much for Spike. He cried as he ran away upstairs, unable to take that the mare who he'd considered a sister was dead.
So now, the Doctor stood alone in the library's main room, the only light being that of the several wax candles and weak light fixture in the ceiling. He hung his head in shame. Through his inability to protect his companion, he'd not only cost Twilight her life, but the lives of her friends. A large part of them had died with her, forever lost with their dear friend.
And now, for the first time in a long time, the Doctor felt loneliness again. Even when he had traveled for fifty years without Twilight, he knew he could always return to her and she'd be waiting for him like nothing had changed whatsoever. But now, she was gone. He had to prepare for another Twilight to take her place. Though of course, no one could replace that fun loving, excitable, intelligent mare he used to know.
Was this what Rose had felt like when he regenerated after the Bad Wolf broadcasting system had been defeated and the Daleks with them? What about when Clara watched him die? Had they felt the emptiness he felt now?
He was shaken from his thoughts when he heard Rarity calling out to him. "Where's Twilight?" she asked worriedly. She had been standing in the doorway with Fluttershy behind her every since she caught up to the pegasus, still crying slightly.
"She's upstairs resting," he said back. "She's not completely done regenerating yet, so she'll need to sleep for a couple of days."
"And she'll be alright afterwards?" asked Fluttershy through sniffles.
"Yes, she'll be alright," said the Doctor, doing his best to smile through the pain in his heart.
That's when they all suddenly heard hoofsteps coming down the stairs. They all turned their heads to see a purple alicorn with navy blue hair and a pink stripe running through it stepping down the stairs, her wings folded to her sides. She stopped at the top before saying, "Ow, my head. Doctor? What happened? Why are we back at the library?"
"What?" exclaimed the Doctor.
"What's going on?" asked Twilight.
"B- Bu- What?"
"Why are we back in Ponyville?"
"Why do you keep saying that?"