Not Quite The Last

by Mudkipman98

Rating: everyone
Tags: Doctor Whooves, Twilight Sparkle, My Little Pony: Friendship is Magic, Sad, Tragedy, Slice of Life, Crossover
Length: 2901

When Twilight faces imminent death, the Doctor reveals to her a secret about herself that she could never have guessed in her wildest dreams.

When Twilight faces imminent death, the Doctor reveals to her a secret about herself that she could never have guessed in her wildest dreams.

Sequel now up! Click Me!

Published 2014-01-21 03:00:02 UTC
Last updated 2014-01-21 03:00:02 UTC

A New Beginning

VEEEEEM! VEEEEEEM! VEEEEEM!

The hallway of the Dalek capital ship sizzled as each of three plasma projectiles arced through the air, barely missing Twilight Sparkle and the Doctor as they sprinted for the TARDIS which sat only 50 feet away.

"Exterminate! Exterminate!" shouted the Daleks as they pursued their greatest enemy. "Stop the Doctor at all costs!"

As Twilight and the Doctor approached the TARDIS, the time lord dug out his key with his mouth and threw it into the lock with perfect accuracy, allowing it to slip in while Twilight used her magic to turn it and open the blue box's doors.

A few more Dalek plasma beams struck near the time travelers, slowing them down slightly before they reached the safety of the TARDIS. As they crossed the threshold into the time machine, the Doctor moved to shut the doors before being shot at with another blast of plasma. He sidestepped to avoid the buzzing projectile, then shut the doors in one, swift movement.

Allowed to relax for a second now that he and his companion were safe, he dug out his sonic screwdriver and pointed it behind him with a hoof to activate the TARDIS and put it in flight. He took a moment to rest his head against the doors as he spoke. "Well, *huf* that was a *huf* close one, eh Twilight? Twilight?" he asked again when he received no response. He turned around froze when he saw her.

A large burn stretched across her chest where the Dalek laser has struck, blackening and charring her flesh and fur as it cracked and fell off. "I'm sorry, Doctor," said Twilight weakly. "I think they got me." As she began to stumble, the Doctor rushed over to her and caught her before she could fall.

"Twilight? Twilight, look at me," he said frantically. He turned her head to face him, looking into her eyes as they rolled back in her head. He began to shake her saying, "Twilight, stay awake. Stay awake! Focus on me!" A bit of relief passed over him when her eyes began to slightly focus on his face again. "There you go," he said, still full of worry. "Now don't take your eyes off me."

He carefully dragged her over to the railing and propped her up against it. He then rushed over to the TARDIS console and put it on a flight path straight to Twilight's present time back in Equestria. He moved back to her and knelt down so they were face to face. "Hold on," he said. "You're gonna survive this. I promise." Twilight returned a slight smile to the time lord. "Now, let me have a look at you."

The Doctor moved her forelegs out of the way so he could get a good look at the wound. The longer he looked, the more he couldn't quite believe what he saw. It had started to heal. She was no longer bleeding, and the destroyed flesh had begun to reform and reconstruct while the damaged cells began to fall off, dropping onto the TARDIS floor. With this recovery, Twilight began to shift and move again. When she managed to focus on the Doctor in front of her, she jumped a little in surprise.

"Doctor, what are you doing? What happened?" she said as if nothing was wrong. As far as she was concerned, nothing was. The Doctor backed up as his expression darkened.

"Nothing," he said coldly as he stood up. "Nothing's wrong." He walked over to the console and flipped a few levers.

Twilight stood up and walked over to him. "That's funny," she said in a concerned tone, "because it doesn't sound like nothing's wrong. You look like you've just seen a ghost."

It felt like a taunt to the Doctor, but he endured it. "So go on," she said. "Tell me what's wrong."

"Firstly," he began slowly, "we're going back to your time."

"Why's that?" she asked. He ignored the question.

"Second, there's something I need to tell you," he said as he began walking around the console. When he stood at the opposite end of it, across from Twilight, he said in a flat tone, "You're dead."

Silence hung in the room for a few seconds before Twilight responded. "What?" ,unsure whether she'd heard him correctly.

"In fact, you've been dead for quite a long time now." As Twilight was trying to process what she'd heard, he said, "You might want to take a seat." She obeyed and sat down on the TARDIS floor.

"Do you remember when I left you for a few days? After your... transformation into an alicorn?"

"Yes," she said back. "Why?"

"When I left you, you only went three days without seeing me. But for me, it was nearly fifty years."

"Fifty?!" asked Twilight, jumping back to her hooves. "How's that possible?"

"Time travel," he said back without any hesitation and as cold as ever.

"Did you miss me?" asked Twilight back, feeling crushed.

"Every second," he said back, allowing himself a short smile before returning back to his somber tone. "During that time, I traveled all across history to every time period I could think of. I learned everything about this planet. About it's history, it's geography, about this country's monarchs, and about you."

"About me?"

"Yes. Do you know where alicorns come from?"

"Are you going to try to explain the birds and the bees to me?" asked Twilight jokingly.

"Twilight, this is serious. You have to listen to me." Twilight lost her jesting mood after he said this. "Now, answer me. Do you know where alicorns come from?"

"Apart from the... um... natural process, no," she said. "I just assumed they were born like any other pony. Am I wrong?"

"Yes," said the Doctor. He began walking toward her as he continued. "Alicorns are not real. They're spiritual beings with a physical form. They never age, and they posses godlike power such as that over the sun and moon, or that over the emotions of others." He was now standing in front of her. "Or, the power to control every possible kind of basic magic with absolute perfection, including that of friendship." He walked past her as he continued to talk.

"When I said that you'd been dead now for quite a long time, that was no exaggeration. How long ago did you become an alicorn again?"

"Nearly four years now," she said.

"Do you remember how it happened?"

"Vaguely. I remember being in the library..."

I had just finished writing Starswirl the Bearded's unfinished spell when suddenly, the Elements of Harmony started acting up. Before I knew it, they were covering me in this strange energy. I remember this blinding light, and then a horrible pain. When it stopped, I was in some sort of strange dimension. Princess Celestia was there, and she even sung a song. At the end, this strange purple magic came out of me, and I started transforming. After that, I woke up back in Ponyville in the street with my friends and the Princess. After that, I found you back at the library. You and I talked for a bit and you were wearing a scarf of all things. You told me I was 'magnificent', and that we'd had a great run, then you left and reappeared a few seconds later. But when I talked to you, you seemed completely different, like you were just seeing me again after the last time we'd separated.

"Did I," said the Doctor, phrasing it more like a statement than a question. He stopped at the console and flicked a few more switches. The TARDIS jostled slightly as it touched down. The Doctor then grabbed a striped scarf that was draped over the railing and made for the door. He stepped out, and then moments later stepped back in, sighing and full of sadness. He replaced the scarf, pressed another button and pulled a lever on the console before rejoining Twilight.

It took her a moment, but finally she said in wonderment, "That was you just now. You went back to visit me on that night. But why then? Why now?"

"Because... you aren't going to be around for much longer," he said, "and I wanted you to know just how great you are and just how much you meant to me. Just how much you still mean to me."

"What are you talking about?" asked Twilight, becoming nervous. "Doctor, you're starting to worry me."

"That's good that you're worried. It proves you haven't changed one bit. Yet."

"Doctor, what's going on? Why are you being so cryptic?"

"Because!" shouted the time lord, "... because you're dead, Twilight. You have been since that night. On that night, you died and became who you are today. Oh sure, you're still the same Twilight, but your body died and was replaced with this one. And now..." The Doctor was on the verge of tears. "And now, you're gonna change again and I don't think I can handle it." Tears started to run down his face. "Because that pain you felt, when the elements activated? That was them killing you, destroying your body so your precious princess could make you into a god. Except you're not a god. Not at all." He backed away from her.

"So then what am I?" she asked, desperate to make sense of all the Doctor's ramblings. Suddenly, her hooves began to tingle. In fact, her whole body began tingling slightly. When she looked down at herself, she found that she had begun glowing a little bit.

"You're a time lord," said the Doctor. He walked up to Twilight and put a hoof on her shoulder. The light from her suddenly disappeared as it fed into him, disappearing as soon as it reached his hoof.

"I'm one of your race?" she asked in complete and utter disbelief. "But that's impossible!"

"Then start believing in the impossible, Twilight Sparkle, because it's only going to get more impossible from here on out!" he yelled, the tears now flowing freely from his eyes. "The time lords came into being when they discovered the essence of time itself, the untempered schism. Those bold people stared into the heart of time itself, and through the millennia, they became time lords with the ability to manipulate time with their machines. But you're a different breed. The alicorns of your world came from impossibly strong unicorns with unnatural magic talent. Your princesses, Celestia and Luna? They died when they were only three months old. Their cart was destroyed when it plummeted 5,000 feet into a dark chasm in the middle of nowhere. Their parents were killed, but they lived on and were rescued by a group of hikers that were in the area that saw the cart crash. They were worshipped as gods because of their wings and their horns, and have ruled for over 2000 years. And you are no different. The elements were smart. They killed you because they knew you had the incredible magic in you to successfully become an alicorn, a true time lord. Ever wonder why the princesses don't age? It's because they've been constantly regenerating, and they've got enough juice to last them another 10,000 years, assuming they don't get killed before then. And the saddest thing is you could've joined them. But now, it's too late for you. You've already started your regeneration cycle. Every time you age to your latest, you will regenerate into a completely new pony. But you see, you can only do this 12 times, and then you're done. You die. And it's all my fault!"

The Doctor fell to the floor and cried for minutes on end. Suddenly, he felt a hoof on his shoulder. When he looked up, he found Twilight staring into his eyes with a compassionate smile. "Cheer up," she said. "It wasn't your fault at all. Besides, you said it yourself. I'll just regenerate. I'll still be me. I'm not going anywhere."

The Doctor stood again before saying, "You really have no idea what regeneration means, do you? You don't just become young again. You die. Not a normal death with a burial, mourning, and some fancy flowers. You, the mare you are right now, dies, and some brand new pony saunters away, only to die in another two hundred years, assuming they don't get killed before that like you just did." The Doctor suddenly stopped and looked up at Twilight.

He hadn't realized it, but she'd started crying herself. "So you're saying I'll never see my friends again?" she sobbed.

Now it was the Doctor's turn. He embraced Twilight in a hug. "No. You'll still be able to see them, whenever you want. But it won't be you. Sure, you'll have your memories. You'll know who you once were, so I suppose you could just act like the Twilight you still know. But you will still be a different pony. I'm sorry." He separated from her then and walked over to the console, leaving her on the floor. "But I can still do one more thing for you before you go. Consider it... your reward."

The Doctor began piloting the TARDIS back to Twilight's current time until it landed. He then dug through a few boxes in the corner of the massive room until he found six purple envelopes. He quickly scribbled a bunch of notes on some paper and put them into the cards, sealing them with wax and a seal that held the pattern of a six pointed star. He put the letters into a hatch near the door and pressed an eject button next to it, sending the letters off to their designated recipients. He moved back to the console, put it into flight, and piloted it back to Twilight's library three hours in the future.

The Doctor walked over to Twilight and helped her up off the floor, leading her to the door and opening it for her. She weakly stepped out into her library's central room, her regeneration nearing its explosive end. When she looked around, she found all five of her friends standing around the TARDIS doors, including Spike as the sixth. They were all holding the purple envelopes, opened and in front of them.

"Heya, Twilight!" cheered Pinkie Pie. "What's up?"

"Yes, dear. Why did you call us here?" asked Rarity. Twilight turned her head to look at the Doctor and he smiled to her. She silently thanked him.

"Are you okay, Twi?" asked Rainbow Dash. "You don't look so good." Twilight's eyes were drooping from exhaustion as her body spent its last.

"I'm fine," she said back, lying to them. "I just wanted to tell you all how much of an honor it's been to have you all as friends. You've been the best to me, and nopony could ask for more."

"Aw, shucks, Twilight," said Applejack. "We're your friends. No need to thank us for that."

"But what do you mean 'it's been' an honor," asked Fluttershy. "It sounds like you're leaving for somewhere without us."

"Fluttershy makes a good point," said Rarity. "Why did you say 'it's been'?"

"Because from what I've heard, I won't see you again. At least not like this," she said back, a tear rolling down her face. "I wanted a chance to say goodbye before I leave."

"What do you mean?" asked Rainbow, worry present in her voice. It was then that Twilight's body began to glow a golden light again.

"Everyone, stand back," commanded the Doctor. He rushed over to them and pushed them back a little bit. "Give her room."

"Twilight, what's going on?" asked Spike. But she couldn't hear him. She was at her breaking point, and any second now she'd regenerate. "Twilight?"

She took one last look at her wonderful friends. The friends who had been there to guide her, to fight beside her, and to be with her as she said, "Goodbye."

All at once, her legs, wings, and head began pumping out golden light, her screams of agony filling the room as her body rode out its transformation.

"What did you do to her?!" asked Applejack to the Doctor, unable to look away from her suffering friend. He didn't respond. Instead, he silently cried as his companion continued to regenerate, the energy from her body spilling out into the room. It shattered the libraries windows and forced open the door. The heat nearly set the building and books on fire, but the others didn't care. They stayed with their friend until the cycle had finished.

As the energy disappeared, Twilight fell to the ground in a heap. In moments, her friends were around her. But they noticed that she looked different. No longer was her coat a deep purple, or her mane a navy blue. Instead, her coat was a very pale purple, and her mane and tail were light purple with a dark purple stripe. She still had her wings and horn which had also changed color to match the rest of her. After a moment, her eyes snapped open and she jumped to her hooves, eyes darting around and quickly examining everything in sight.

After a moment of silence, she said, "Hellooooooo, everypony. I'm Twilight Sparkle, and it's magnificent to meet you!" she finished with a smile.