• Published 8th Jan 2023
  • 3,542 Views, 489 Comments

Regeneration - Rated Ponystar



The Doctor has to stop the Conversion War and save humanity from Celestia's madness, but a worse evil is playing everyone as pawns for a greater plot

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Regeneration Part 5

There is good and there is evil. I left Gallifrey to answer a question of my own. By any analysis, evil should always win. Good is not a practical survival strategy - it requires loyalty, self-sacrifice and love. And so, why does good prevail? What keeps the balance between good and evil in this appalling universe? Is there some kind of logic? Some mysterious force?

- The 1st Doctor

+}{+

Fluttershy had been surprised but grateful to see the U.N. soldiers arriving to help them. She learned that Big Macintosh and the rest of their unit had surrendered peacefully without any more loss of life. Although Fluttershy knew she was now part of a war, that didn't mean she enjoyed seeing death befall anyone, regardless of the side it fell under. Especially from those she once called friends.

The Element of Kindness watched as the various Earth Pony soldiers, stripped of their armor, were being held in a line in cuffs thick enough to keep them from doing anything rash just in case. Numerous Osprey had arrived to start escorting the prisoners and the refugees from Equestria to safety. The former calmly did so though they weren't happy about being captured based on their expressions. She even saw Big Mac glance at her, but he only sighed and turned away before being led by his fellow soldiers. Perhaps when this was all over, she could talk to him?

Meanwhile, the ponies that had been her charge from Van Hoofer to here in Osaka all looked at Fluttershy with grateful eyes and thankful expressions before they were sent off into safety. The only ones who refused to go were Derpy, Dinky, Flash Sentry, and Carrot Top, all because they wanted answers regarding their saviors.

Seeing Lyra again, alive and well, was a relief for Fluttershy. She had always felt that, deep down, Lyra was right about humanity but Fluttershy had been too afraid at first to say anything since she was scared of alienating her friends. The war, however, made that fear slowly fade away and replaced it with a resolve to do what was right instead of doing what was expected. When Discord begged her to leave Equestria, and she saw the seriousness in his eyes, the Element of Kindness knew it was finally time to go. Learning what happened to their old-world only solidified her determination to end this war and stop Celestia.

Fluttershy still couldn't believe that the princess she had admired, respected, and loved for most of her life was such a monster. This was the princess who had playfully let her hang out with Philomena. The same one who held faith in her redeeming Discord. And the one who treated her as part of the family during celebrations and events. It just made no sense to Fluttershy why Princess Celestia would be so...heartless and cruel, but sometimes the truth was too hidden to see.

Pushing aside her thoughts, Fluttershy and her companions soon found themselves meeting the strange stallion who had been the one that had changed so much in such a short time: The Doctor.

The one who Discord was most afraid of and told Fluttershy that he was beyond understanding. Yet this one being, who made her best friend weak in the knees, looked like any other stallion she had ever met. He talked to the Major-General for a bit before Lyra finally got his attention, and he eventually turned around and saw them. That's when Fluttershy looked into his eyes...

"Fluttershy? Are you...crying?" Flash Sentry asked, getting everypony's attention as she just stood there, sobbing silently as she stared into the confused Doctor's eyes.

Fluttershy had always known she had a unique talent for seeing aspects of all sorts of creatures through their eyes. It worked on ponies as well, which is why she could always tell a stranger's best and worst characteristics by looking directly at them.

When she looked at Twilight, she saw wisdom, excitement, passion, and a gentle soul who was lonely at times because she felt so different from others.

Rainbow Dash? Determination, bravery, a fear of failure, and a need to stand out to prove she was somepony and not a nopony.

Applejack was similar to Rainbow Dash but had more confidence, and heartache from the losses she had suffered at a young age that drove her to work hard.

Rarity was beautiful on the inside as she was on the outside. She was a charitable and loving soul that wanted to unleash the true potential of not just those around her but also in herself. Yet, there was a particular obsession with this mindset that was somewhat scary.

Pinkie Pie was harder to look into as you could see the joy, happiness, and fun in her eyes, but there was also a hint of madness, sorrow, and something darker hidden behind it.

Others she couldn't really read, like Princess Celestia, Luna, or even Discord at times, but she could get glimpses of how lonely they were deep down inside

And when she looked into The Doctor? All she could do was ask one question.

How?

How could somepony like this live with what was inside them?

There was so much pain.

So much sorrow.

So much fear.

It was like looking into a black hole that swallowed everything. Fluttershy wanted to run. Run away and never look at anything again, but she couldn't. The amount of darkness this pony had seen was enough to make her heartache.

And yet...there was something else.

There was kindness.

There was courage.

There was determination.

Most importantly, there was hope. Like a supernova bursting inside that swirling cyclone of darkness. A light that refused to go out no matter how dim things were. A force of will that continued on despite having lived for so long. Because it was searching for something. It was trying to prove something. It was like looking into the heart of meaning itself.

He held so much struggle in his soul, yet you couldn't tell by just looking at his confused face. One that had a smile that spoke both a lie and a truth. So Fluttershy did the only thing she could do. She ran up and hugged him.

The Doctor was shocked, but she whispered only two words when she looked at him with her crying eyes. "I'm sorry."

At that moment, he went silent and realized she knew.

She may not have known how, why, or what was behind his eyes, but she didn't care. She felt it. And this creature was perhaps the most amazing and tragic figure in the universe for having that burden. Pressing her head against his chest, she whispered again, "I'm so sorry."

"... It's alright," The Doctor whispered as he stroked her hair and slowly looked at his amulet, which showed the green jewel glowing. "I'm used to it."

That only made her cry harder.

+}{+

"Holy manure!" Carrot Top cried out as they all entered the TARDIS together. "It's bigger on the inside than it is on the outside!"

The Doctor smiled as his newest companions all stared in awe at the TARDIS while Lyra just smirked and asked, "Is everypony always like that when they come in here the first time?"

"Pretty much," The Doctor said as he chuckled and pressed a few buttons. "And they always say that same line. Well, sometimes they say it differently like Clara did."

"Another of your past companions?" Lyra asked curiously.

"Yes, but..." The Doctor paused and took a deep breath. "Not one I want to think about at the moment."

Lyra blinked and then looked around the TARDIS as the others continued to look around in awe. Flash Sentry and Dinky were checking out the tactical map of the current war around Earth while pointing at various locations.

Carrot Top was gazing into the glowing white circle lights and probably wondering what they were used for (Lyra sometimes wondered the same thing). Fluttershy looked into the other corridors with wide eyes, no doubt wondering how far the TARDIS really went. Derpy was over at the tea set happily eating a pair of muffins that had just appeared out of nowhere, so Lyra chalked it up to something the TARDIS did.

"Have you ever had this many ponies in your TARDIS before?" Lyra asked as The Doctor continued to work.

"Not often," He admitted with a shrug. "There was that time in my tenth life when I had to stop Davros and the Daleks from stealing Equus and using it to destroy the universe. That was a hairy situation."

"...And they didn't stay with you?" Lyra asked, which made The Doctor pause. As Lyra sighed and asked, he stood there, frozen, "Doctor? What happens to your companions? You said it yourself. You're very old, but you talk about all your past companions like a grandfather talks about his children. Yet, you always seem to be so alone. What happened to them?"

Lyra worried she said something wrong for a moment, but she was too curious. The Doctor had spent two thousand or more years wandering the galaxy of their old dimension, fighting evil and saving lives.

"But never alone! Always with someone! Others who I am proud to call my friends, comrades, family, and more! The Doctor and his Companions! Legends throughout time itself!"

That was what he said to her.

Sighing, The Doctor gave a sad smile as he looked at Lyra and shook his head. "They never stay forever. I'm a Time Pony, Lyra. I don't age. I regenerate. Even more so now that I'm pretty much unable to stop regenerating. Don't ask. It's a long story. At some point, the adventures I have with those I travel with come to an end."

He closed his eyes. "Some...had to be left behind so they could grow up..."

***

During all the years I've been taking care of you, you in return have been taking care of me.”

Oh, Grandfather, I belong with you!”

Not any longer, Susan. You are still my grandchild and always will be. But now, you're a mare too. I want you to belong somewhere, to have roots of your own. With David, you will be able to find those roots and live normally like any mare should do. Believe me, my dear, your future lies with David and not with a silly old buffer like me. One day, I shall come back. Yes, I shall come back. Until then, there must be no regrets, no tears, no anxieties. Just go forward in all your beliefs and prove to me that I am not mistaken in mine. Goodbye, Susan. Goodbye, my dear.”

***

“Others were taken away against their will...”

***

Goodbye, Jamie.”

But Doctor, surely we can't just-”

Goodbye, Jamie.”

I'll never forget you, you know.”

I won't forget you! Goodbye, Zoe.”

Will we ever meet again?”

Again? Now, Zoe, you know that time is relative.”

***

“Others realized they couldn’t stay forever, especially when they wanted something more...”

***

“Because the thing is, it's like my friend Vicky. She lived with this bloke, student housing, there were five of them all packed in, and this bloke was called Sean. And she loved him. She did. She completely adored him. Spent all day long talking about him.”

“Is this going anywhere?”

“Yes. Because he never looked at her twice. I mean, he liked her, but that was it. And she wasted years pining after him. Years of her life. Because while he was around, she never looked at anyone else. And I told her, I always said to her, time and time again, I said, get out. So this is me, getting out.”

***

“A few couldn’t stay anymore because it all became too much...”

***

“My Aunt Vanessa said, when I became an airline stewardess, "If you stop enjoying it, give it up."

“Tegan...”

“It's stopped being fun, Doctor! Goodbye.”

***

“Some died...”

***

“…Adric…

***

“Some were lost...”

***

“You look after him, and you be a good girl, and you look after him.”

“You are creating a fixed time. I will never be able to see you again!”

“I'll be fine. I'll be with him.”

“Amy, please, just come back into the TARDIS. Come along, Pond, please.”

“Raggedy man...goodbye!”

“NOOO!”

***

“And others... well...”

“Dear Doctor. It’s been such a long journey for both of us. I never, ever wanted it to end, but end it has. We both know that. A long time ago now, I said you were the oddest man I’d ever met. You’re that still. You’re the best stallion I’ve ever met too. But we’ve chanced our luck once too often, I think, so I’m bailing out. Escape strategy number five. I’m going to disappear. There’s no freedom like being dead. I can go anywhere, be anyone I want. Just like a Time Pony really. Don’t look for me, please. But remember me. I’ll remember you, always.

With love, The Filly Who Never Was.”

***

“But some...went on to find happiness...”

***

Don't go too far away, will you? And if you do, come back and see us sometime.

“Yes.”

Thank you. Lovely.”

Save me a piece of wedding cake. Oh, I nearly forgot. Your wedding present.”

It's beautiful. Thank you, Doctor.”

Hey, Jo, come and drink a toast to the happy couple.”

But that's us!”

Aye, so it is. Don't worry, Doctor. I'll look after her.”

***

“Others needed to leave to continue their lives...”

***

“You’ll come to our graduation, won’t you, Doctor?!”

“Of course, Silvy. Wouldn’t miss it for the world.”

“So long as the world isn’t at risk of being blown up, right Doc?”

“Yes, Gallus. We’ll try to avoid that next time.”

***

“Some are waiting for me to come back...”

***

“Do you really have to go, Doctor?”

“Sorry, Izzy, but I have to check up on something. But don’t worry. I’ll be back soon. Be in a minute, day, week, month or year? I will return. And the six of us will have more adventures awaiting us when I do!”

“Woohoo!”

***

“And there are plenty who will always be there willing to go with me for another adventure...”

***

“Wicked...”

***

The Doctor then smiled at Lyra and chuckled. “Yet, for all the pain it sometimes brings I never regret taking any of them aboard. Because they are what makes my life feel like it means something. To think it all started with keeping two school teachers in my TARDIS out of fear of being exposed and it’s become this now. Every one of them I remember and treasure because they changed me and, in turn, I changed them. It’s not all easy and certainly I have regrets...but as one of my closest friends once said...”

***

You know, you act like such a lonely pony. But look at you. You've got the biggest family on Equus.”

***

“...But because of what happened... on Equus,” The Doctor whispered as he closed his eyes and lowered his face. Lyra couldn’t tell, but she was sure he was about to cry or scream from the way his body shook. Maybe both. “With Equestria here...and the world gone in your timeline...most of them are lost...not all...but...too many...far too many...I want to bring them back...I need to bring them back and even if I don’t know how I’m still going to try.”

“And if you cannot?” Lyra asked.

Then he stood still, slowly raised his head, and upon seeing the look in his eyes and the anger despite his calm and stoic expression, Lyra felt nothing but utter fear and terror for a terrible split second when he heard him whisper:

“Then I will avenge them all.”

"Uh, Doctor?" Their conversation was interrupted by Flash Sentry, who was looking at one of the screens on display in the "War Computer." Everypony soon crowded it and looked in horror as it showed a drone's camera of Discord being thrown against the pavement by a combined blast from Twilight, Cadence, and Shining Armor.

"Discord..." Fluttershy whispered in horror.

"Right! No time to waste!" The Doctor shouted as he went back to the TARDIS controls and went to work before the TARDIS started to move again. "No more delays! The time to end this battle is starting now!"

+}{+

Discord always wondered when he would meet his end, and he never thought it would be outside a ramen noodle shop. The battered, bruised, and bleeding draconequus lay in a crater, breathing heavily as he looked above at the sky covered in the ashes of war. Earth had such a pretty sky when you really stopped to look at it. Sure, it didn't seem any different from the sky of any other world, and yet...

Raising his head and sitting up as best as he could, Discord glared at the three ponies who stood nearby, ready to strike. It showed how strong they had become over time and how weak he had gotten. Although he had done his best and gained a few good blows on the three, they could still go on while the rest of their squad was unconscious. Discord didn't even have the strength to summon one last glass of chocolate milk.

"For the last time, Discord. Where is Fluttershy?" Shining Armor stated as he raised his sword. "If you tell me, I'll make your end a quick one."

Discord shook his head. "I'm never going to tell you. Ever. Everything I've done has been for her. I'm not going to betray her again. Never again."

"Tell me, Discord," Princess Cadence asked as she stepped forward. "Are you doing all this just for Fluttershy? If you just care about her, then help us find her, and we can help her. She's not in the right mind if she thinks that what we're doing is wrong."

"Cadence is right, Discord," Twilight said as she pointed to the entire city. "Look, I don't like this war as much as the next pony. I can understand being afraid of what we're doing. But this is for the best. Humanity has proven they cannot continue like they are, or they will destroy themselves. We're offering them a chance to survive and live something better. We're not trying to hurt them. We're trying to save them."

"Save them from what? From having the freedom to choose who they want to be?" Discord grumbled as he slowly sat up and shook his head. "You ponies really don't get it, do you? Do you really think that your way is the best because you happen to be number one in your world? Newsflash, Twilight, you were just the top dog at the moment in history. Before you were the griffins, the dragons, the alicorns, the wolves, and the silurians. History is always about some nation losing power and a new nation regaining it. Your so-called perfect utopia would have fallen eventually, and another nation would take over. I always thought it would be the diamond dogs, but we'll never know since our world is gone."

"That's just a lie, Discord!" Twilight shouted with fury. "Princess Celestia-"

"Can go fuck herself," Discord said, which only made the three angrier, but he didn't care and smirked. "And so can the rest of you. Because you clearly are a bunch of idiots who cannot think for themselves. You're slaves to a madmare, and I hope you regret it forever when your world comes crashing down. As for me? Sure, I'm gonna die. But I'll die as myself and do the right thing."

He chuckled and shook his head. "You want to know something? I did agree to do this all for Fluttershy's sake, but knowing what I know now? I think deep down, I would help humanity even without her blessing. Because I've seen these humans in the best and worst, and I know why I like them. Why is their chaoticness so familiar to me?" He closed his eyes and smiled. "They remind me of my true home. My true people. When I see them, I see the faces of my mother, my father, my childhood friends, and more. I see their potential, even without the means to reshape reality. I saw one world burn from those who sought to destroy them because of who they were. I'm not going to let that happen again."

Pointing at the three, Discord shouted, "Because so long as I breathe, I will sacrifice everything to defend this world from you ponies! Even my life!"

The three were silent as Twilight sighed and stepped forward. With a sympathetic look, she whispered, "Goodbye, Discord."

Twilight began to shine her horn as Discord slowly closed his eyes and prepared for his end. But then...

"Excuse me!" Everypony stopped as a figure walked out of a nearby alley. At first, the ponies feared it was a human but then were confused when they saw a pony walk out with a smile on his face. "Sorry to interrupt this fight. Wow, that's a lot of cotton candy on that sidewalk. And has that shield been turned into a pear? Ugh, I hate pears. Honestly, all this violence really has ruined this nice street." He frowns as he shakes his head in disappointment. "War is just terrible all around, isn't it? You come to a new planet, a new dimension, with so much to learn, and the first thing you discover is death, destruction, and chaos. Millions of worlds are out there, and yet so many of them are always filled with bloodshed. It is a sad thing, really."

"Who are you? Are you from the Guard or the ESS?" Shining Armor asked, looking at him with confusion.

"Sorry, but no."

"This isn't a place for Equestrian citizens to stay!" Princess Cadence warned with concern.

"Sorry, but I am not from Equestria."

"Are you a newfoal?! It's not safe here! You need to get to the containment camps to be properly sent to Equestria!" Twilight warned.

"Wrong answer," the strange pony replied. "I'm not a newfoal. Not even a pony. Not really."

"Then… who are you?" Twilight asked.

The pony chuckled. "Ah yes. Who am I? The one question in the universe that I've heard repeatedly. I even had a cult try to kill me because of it. I... wasn't very nice to them in the end. Kinda deserved it. Did get married for a time thanks to them, so there is that. I wonder if River ever put this in her diary..."

"Um, are you okay?" Shining Armor asked, eyebrow raised. Shaking his head, he said, "Look, it doesn't matter. You shouldn't be here."

"Neither should you," The pony said sternly as he glared at them. Despite just meeting him, the three couldn't help but flinch at how cold the stare he gave them was. "I'm so disappointed in you three. I'm glad Sunny isn't here because if she saw you, as you are now? The poor filly's tears would never end. Especially for you, Twilight Sparkle. You know, even hundreds of years after your death, you would be remembered. All of you. All your friends, adventures, lessons, and deeds. Even after a thousand years, you would be remembered, but all of that wisdom? All those adventures you had? The teaching you discovered and, in turn, gave to the world? Wasted. All wasted. And I really can't help but feel utter pity for how far you have fallen."

There was a long silence as the strange pony continued to look at them before he took something out, some kind of amulet with multiple gems on it. He stared at Discord, looking at him with wide eyes and an open mouth while pointing the amulet at him. The light blue one was shining, making the strange pony smile brightly. "But you, Discord? They say that hard times create strong creatures. Look at you, from villain to anti-hero to hero. But this? I think this is your fondest moment. Proving that, deep down, you're a better creature than you think."

"... It's you," Discord whispered in awe.

"Yes," He replied.

"...Why weren't you there? On that day? That day I lost everything?" Discord asked as he slowly lowered his head and sobbed. "My father. My mother. All of my people..."

The pony sighed in such a way that it reminded the other ponies of how Princess Celestia sighed only because he sounded much older for some reason. The mysterious pony knelt before him and lifted his head up. "Much as the legends like to make me seem like I am a god, the truth is I am not. I am just one old stallion in a box that can only do so much. But when I am there...I always do my best to make others smile. I couldn't save your people, and I am so sorry that I can't bring them back. But I can give you something else. I can give you a future."

"But we changed the future..." Discord whispered in confusion. "The timeline it's...gone..."

"So let's rebuild it or make a new one," The stallion replied with a nod. "It will take time. Maybe it won't ever be like it once was. But if there is one thing I have learned in all my travels, it is that when the dust settles and the nightmare is over? You can rebuild and start again. But only if you let go of the past." He held out his hoof. "There is a mare out there waiting for you and others. And...there was also a stallion... you'd like him...brave and strong...a truly loyal and kind friend...stubborn at times, so narrowly focused on what he thinks he ignores what's around him, and sometimes kind of an idiot, but when you get down to it? You couldn't ask for a better sheriff."

"Who is he?"

"Somepony that doesn't exist now, sadly. But there is a chance for him to come back so long as two certain individuals are alive and well. Because that pony? Far off into the future? His favorite drink is chocolate milk, and animals love him," He answered with a smirk. "So much so that he can understand what they are saying."

Discord slowly looked up and stared at the pony before laughing. He laughed and shook his head before tears began to fall down, yet he still laughed. Discord then took a deep breath. "What's his name?"

"Hitch Trailblazer. Well, Sheriff Hitch Trailblazer if you want to be technical," The stallion said as he helped the chaos spirit up. "And I don't know if I can bring him or those wonderful mares he called friends back or anyone else lost in our old dimension. But I won't stop trying. I never will. And if I cannot? Well, then I'll just try again."

"...So there is a chance?" Discord asked with hope in his heart.

"Always a chance," The stallion said with a wink. "Always time for one."

"...Could somepony explain to me who the buck you are?!" Shining Armor asked, which made the stallion moan.

"Seriously?! We're having a moment here! But if you want to know who I am?" The stallion then marched towards them with a severe glare as his coat raised from the windy breeze. "I happen to be a citizen of the universe that goes wherever I want.

I've traveled through every corner of the galaxy, both past, present, and future.

I've destroyed monsters, brought justice to evil, and stopped the ends of thousands of planets, including yours.

I've been to the darkest places where unimaginable horrors await, and I've seen the birth of new life from its origins.

I've been a warrior, a poet, a healer, a savior, a traveler, a teacher, a husband, father, grandfather, companion, friend, and more words beyond counting.

I'm very old, but I always look younger than I'm supposed to.

I've changed shape, gender, size, race, attitude, likes, dislikes, habits, and more, but my morals and principles have been as unyielding as the universe's expansion.

I keep moving and never look back because I can't.

I do the things needed in our universe, this universe, or any universe because someone has to. And right now, the people of this planet need me.

Who am I?

I'm The Doctor.

And I'm here to stop you."

The three Sparkle family members just looked at each other in surprise and then looked at the one who called himself "The Doctor." The one that Princess Celestia warned them to be wary of.

"Y-You're real?" Princess Cadence said in disbelief as she looked at him. "You look like nothing more than a stallion speaking madness."

"A gentlepony speaking madness, thank you," The Doctor said with a snort. "Besides, anypony remotely interesting is mad, in some way or another." He then rubbed his chin. "Did I say that? Or did someone else say that? Wow, I really am getting old."

"Enough!" Twilight shouted as she stomped her hoof. "Doctor or no Doctor, you are coming with us, and Discord here is-"

"Coming with me," The Doctor said with a smile. "Sorry, but this fine chaotic spirit of a mad creature is now officially my patient. I'll send you the bill and the letter of recommendation for treatment later. Though for you three? My suggestion is to stop listening to brainless stupidity and listen to your reasoning for once."

"And what are you going to do about it?" Shining Armor stated as he pointed at the three of them with his hoof. "There are three of us, and you clearly have no means of defeating us."

"Oh, I'm not here to defeat you. Not yet anyway. That comes with time," The Doctor said with a shrug. "I'm actually here to escape in about three simple moves."

"Three moves?" Twilight asked.

"Yes, here is move one," He then tossed a strange green-scaled object that was round yet square on the ground. "Here is move two." The Doctor then pulled out a fuzzy pink pair of earmuffs from his coat pocket and put them on his head. He then pulled out his Sonic Screwdriver and smiled. "And here is move three."

He quickly pointed it at the object, which instantly caused a window-shattering vibration sound to echo across five streets. Everypony, including the unconscious ponies who woke up immediately, screamed and held their ears as they struggled to stay on their hooves, but their heads felt like they were being pounded with jackhammers.

The Doctor whistled and, flying down at top speed, Derpy, Fluttershy, and Flash Sentry, all wearing earmuffs, rushed out of the alley while holding a stretcher before settling down next to Discord, the only one who wasn't affected and just looked around in confusion.

"Flutters..." Discord whispered with a smile as he held his best friend's hoof.

"Hey, Dizzy," Fluttershy whispered back with an even bigger smile as she and the others put him on the stretcher and rushed around the way they came.

Twilight, gritting her teeth, attempted to follow and screamed out Fluttershy's name, who looked back and saw her former friend, but soon turned tail and continued to run until they were out of sight. Finally, the sound shortly died, and Twilight instantly rushed after them with her wings. She just managed to turn the corner when something blue disappeared, and she screamed in frustration before blasting the ground.

+}{+

"What was that?" Flash Sentry asked as he took off his own earmuffs while The Doctor concentrated on the TARDIS. "We had our ears protected, but it still felt like a ringing in my ears."

"Ice Warrior sonic grenade," The Doctor answered as he worked on the console. "Usually, those can implode your eardrums, but I lowered the intensity to make the experience like having a dreadful headache."

"Why wasn't I affected?" Discord asked as he lay on the stretcher while Dinky, Carrot Top, and Fluttershy started using first aid kids to bandage him.

"Frequency I used only affects equine type sentients. Now please hold still." The Doctor walked over with a syringe and poked Discord's arm before drawing some blood. Smiling, The Doctor walked back to the TARDIS and put the needle in a slot before typing in some calculations. "And done! Eureka! A full-on cure for the Conversion Potion that can be used on anyone!"

"Wait, what?!" Everyone but Lyra shouted in shock.

"You just made a cure for the Conversion Potion in just a few minutes?!" Dinky asked in disbelief. "That potion took Twilight and the other scientists years to create!"

"Well, technically, I've been working on it for a few weeks," The Doctor said as he continued to work without looking at everypony. "But if you think that's impressive? Wait until you see my next trick."

He then pressed a button, and Major-General Highmoore appeared from his home base on one of the screens of the TARDIS. "Major-General? Are you and your forces prepared?"

"We are, but are you sure about this?" Major-General Highmoore asked.

"Major-General, in a few hours, we will be having sake and sushi to celebrate our victory. Just tell your men to get ready!" The Major-General nodded before signing off.

"So what now? What's the plan?" Lyra asked, with excitement on her face, "What can we do to help?"

"Make yourself a cup of tea, have a few biscuits, and sit down to relax," The Doctor said with a toothy grin. "Because you're about to see a show like never before."

Author's Note:

Seriously, I am glad I finally got to write The Doctor. He's one of my favorite characters of all time (When the writing is good) and I just love seeing him outwit opponents. And yes all those flashbacks are actual moments where The Doctor and various companions say their farewells to each other. Except the one with Gallus and Silverstream and Izzy, that's just to show that The Doctor has had adventures off screen. If you are wondering who my top three Doctors are its 7th (Sylvester McCoy), 3rd (Jon Pertwee), and 11th (Matt Smith)

As always, please help out at the NegotationsVerse TV Tropes Page. We even have a Regeneration Focus section: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse