• Published 8th Jan 2023
  • 3,285 Views, 485 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 2

What is the one thing evil cannot face - not ever? Itself.

- The 5th Doctor


Princess Celestia knew that war with humanity would eventually happen since the race was incapable of peace. The barrier, something she hadn’t planned but took advantage of upon seeing its power, had provided a better means to defend Equestria while conquering the planet so that the plan for a better future for her ponies would be complete.

It was too late to save their old world, something Celestia regretted deeply in her heart, but it was a necessary evil to save her kingdom.

The Conversion Potion was both a means and an excuse to turn the humans into ponies while taking over their territory one by one with the barrier. War was going to come when the humans eventually either figured out the truth or the non-converters were too desperate to remain as themselves. But humanity would be no more and their dark history would fade into oblivion as they embraced their new and better lives.

They would be ponies. They would see the light. A world of only ponies with no threats. Just peace and harmony that would last forever. A true heaven on earth that would be made for all her subjects.

It was only when this was complete did Princess Celestia plan on stepping down, letting Luna, Cadence, Twilight, and Flurry Heart rule and guide their new home into a golden age. With her immortality gone, Celestia knew she would last maybe two hundred or three hundred more years before finally entering into her eternal sleep with a peaceful smile. When all the fighting was done and the work was over, she would be more than willing to enter the void knowing that her ponies would live in paradise.

However, things didn’t go as planned.

The humans weren’t converting fast enough with too much hesitation or suspicions. It didn’t help that the newfoals were acting too weird and, in some cases, outright extreme in their anti-human/pro-pony behavior.

Princess Celestia knew there would be some side effects in creating the complex potion, but she never imagined it would be like this. One of many things she would have to fix after the war. Eventually, the humans found out the truth and Celestia knew there was no other choice but to use force. She had hoped the war would be over in a year or two, but it seemed this was going to be a long fight.

But the one thing she had never expected was for her ponies to actually side against her. And this included Lyra Heartstrings.

When Princess Celestia received word that Lyra Heartstrings had gotten away again, she was furious. The upstart unicorn had been a problem Celestia suspected the moment she published that book of hers about her travels in the human world, but she never expected her to outright rebel like this.

Lyra had once been one of Twilight’s friends from her student’s early years as her apprentice. An often energetic and unorthodox unicorn if there ever was one from the times Twilight talked about her old friends back in those days. Of course, Lyra soon left the group after finishing her high school level education and moved to Ponyville.

Most of Twilight’s old friends did so either moving on to schools in specialized fields such as Minuette and dentistry or just went into the job market like the others. Lyra had become a freelance lyre player while living in Ponyville and that was the last Celestria really heard of her.

At least until they arrived on Earth and she became one of humanity’s biggest fans.

Celestia had tried to silence her in the usual ways. Having her followers denounce her and debate her, but either they were incompetent or Lyra had a silver tongue because she gathered more followers with every argument.

She then had the audacity to outright call Celestia a tyrant for her actions when she declared war on humanity. The last thing she needed was a bleeding heart leading a rebellion. Princess Celestia had enough of those in the early years of Equestria and shortly after Luna’s banishment. She would not have one when the fate of her entire subjects was on the line and so she announced the arrest warrant for Lyra Heartstrings for treason.

But the unicorn had managed to evade arrest for so long. The only reason she hadn’t put in a kill order for the unicorn was out of fear of making her a martyr to those that supported her in secret.

Her most vocal supporters were already arrested and thrown in jail. Perhaps she would put them in reeducation camps to clear their minds of the nonsense that they had been poisoned with. I should never have allowed one pony to step foot on those human lands. It completely opened them to ideals detrimental to Harmony and Friendship.

Naturally, Princess Celestia had been angry when she heard that Lyra escaped again, this time at Appleloosa. But then when she was told how she escaped according to the witnesses, the sun-alicorn quickly dismissed the messenger as her mind went into overdrive.

Immediately, she had teleported to her private chambers, locked it, and warded the place with such strong spells that even Discord would have problems teleporting in.

She quickly went for the ancient archives she had kept hidden outside of the Canterlot Library that had been too dangerous to expose to the public. Not even her fellow alicorns knew of these scrolls and tomes. Celestia spent nearly an hour digging through them all until she found the one she needed.

A record of all the sightings of a “blue box” that was “bigger on the inside then it was on the outside” that was seen in different parts of not just Equestria’s history but even long before its founding. The tales were all the same. The box appeared along with a pony who called himself “The Doctor” and had companions with him.

However, there were things inside these tales that made no sense. Because sometimes that same “Doctor” and his companions would appear hundreds of years later or before the recording of their first arrival. There were also times when this “Doctor” appeared but with completely different bodies and faces.

Sometimes they were ponies, sometimes they were other races. Most were males, but there were one or two accounts of females. The appearances ranged from everything and anything from an elderly looking earth pony with a grandfatherly figure, to a bright blonde hippogriff that spoke so fast you nearly couldn’t understand her. And the companions were not always the same either: a strange griffin in a kilt that spoke as if he was from lands of Grissgow, a pony wearing a black leather jacket with tons of patches on and holding a metal baseball bat at a time when the sport was decades away from being invented, and there were even reports of a tribal looking dragon with heightened senses and traveling around with a steel skinned dog of all things.

Princess Celestia often dismissed these tales as nothing but ludicrous nonsense, but upon hearing about the blue box moments ago, she began to fear there might be some truth to them. Because the stories tied to this Doctor spoke of how “death” followed in his wake.

It was said that creatures from the stars invaded an ancient city and The Doctor had destroyed them all while the wondrous land burned around him. There was also one where a giant sea creature, lead by some kind of army of “Red Changelings”, had nearly taken over the western griffin lands but he stopped them. And then there was one that spoke of how he had worked with the ancient Abyssian Queen Catfertini in defeating a rising army of the dead led by a trapped evil god known as Sutekh The Destroyer. Many had died, but the Doctor had managed to defeat this evil god by trapping him between “worlds” if what the records were saying was true.

Whatever or whoever this Doctor was he was powerful, dangerous, and destructive as each record talked about him as if he was a warrior death god. One quote in particular stood out and made a cold sweat drip down Celestia’s face:

“He's like fire and ice and rage. He's like the night, and the storm in the heart of the sun. He's ancient and forever. He burns at the center of time and he can see the turn of the universe. And... he's wonderful.”

But it couldn’t be real. It just couldn’t.

For the Doctor to do all this he needed to have some kind of powerful magic, but not all of his so-called “appearances” were of him as a unicorn. Perhaps this is not just one creature? But a network of them? An ancient organization that uses the term “Doctor” as a code word? Or maybe the Doctor is like a traveling knight and his companions are like apprentices with one taking over after the other dies or retires? No, that doesn’t explain how some of them appear so far off in time from each other nor the advanced technology that his companions have.

Celestia needed to know more. The records were dubious at best and outright impossible to believe in. A thought came to her. There was one creature who might know more about The Doctor, if he was real. He was far older than either Celestia or Luna. Much as she hated to rely on him for help, she wanted to know if this “Doctor” was not only real, but also a threat.

Walking out of her chambers, Celestia pulled down the wards and sighed. “Discord? I need to speak to you.”

Talking to yourself was a sign of madness, but somehow the Spirit of Chaos always knew when to appear when someone spoke his name. A second later, he appeared before Celestia with an amused look on his face. “Oh, Celestia. Fancy hearing you call for me. How is the war effort?”

“None of your business,” Celestia started with a glare. “Especially since you’ve not helped in any manner.”

“My dear princess, I am not one for war despite what you might think. It’s a kind of chaos that doesn’t suit my taste,” Discord said as he snapped his fingers and wore a neon rainbow colored shirt with shades and a peace sign necklace. “I like to live in the mellow with peace in my heart.”

“And yet you took over Equestria twice while also aiding Tirek in ruling it a third time,” Celestia pointed out with a deadpan tone.

“Oh, come on. Nobody died,” Discord said with a huff as he snapped his fingers to get rid of his disguise. “If there is one thing I don’t do, Celestia, it's kill. I refuse to do so. Especially for such measures as the one you are doing. Going around converting an entire race into your own little pony cheerleading worship squad? If I didn’t know better I say there is more to this then you are letting others know.”

“That is none of your business,” Celestia growled as she slowly began to calm herself. “I need to know about somepony and you are the only person I can rely on since...well...they might be a threat to Equestria and the war effort.”

“Why sure! I know lots of ponies,” Discord said as a large book titled “Contact Book” appeared in thin air as he opened it up and put on some reading glasses.

“Well, their name is The Doctor and I-”

In a split second, a voice shouted across all of Equestria both with rage and horror.


Celestia found herself nearly thrown off her hooves before staring at Discord in shock and horror as a look of absolute fury was on his face. For a second, Celestia was about to yell at him, but he towered over her and continued to shout with such anger that the palace shook in place. “THE DOCTOR?! THE FUCKING DOCTOR?! WHAT DID YOU DO, CELESTIA?! TELL ME NOW OR SO HELP ME I WILL TURN THE ENTIRE PALACE UPSIDE DOWN AND FORCE EVERY PONY IN THE ENTIRE CITY TO SUFFER OUTRIGHT INSANITY IF YOU DO NOT TELL ME?!”

“Calm down, Discord!” Celestia screamed, but she was now starting to panic as Discord began to pace and looked ready to tear his head off.

“Calm down?! CALM DOWN?! You tell me that The Doctor is here?! THE COMING STORM?! And you are telling me he is going to be fighting you?! Do yourself a favor and slit your own throat right now because as far as I am concerned you just lost the entire war this very second!” Discord shouted before shaking his head. “Do you have...any idea...ANY IDEA...what you have just unleashed on yourself?! On Equestria?! First thing I am doing is getting Fluttershy and getting the fuck out of here!”

A cold sweat then dripped down on Celestia’s neck as she realized something. “Are you...are you afraid of him?”

Discord froze before slowly paling and looking at Celestia with such terror in her eyes she compared it to a prisoner just about to be executed. “Afraid? No, I am terrified. The Doctor is not a pony, Celestia. He is a storm. A storm that will consume all in his path. This being, this creature, has saved and ended more lives than anyone can imagine. When you want monsters to have nightmares? You mention his name. When you need demons to cry in terror? You talk about him. When you need the impossible to be done? You hope he is there. If there is no hope and you have to pray to someone? Pray The Doctor comes because he will be the one to deliver you into salvation. If I am a God then the Doctor is a Titan. He’s...he’s...there are no words to describe him other than to hope you are not in his way or you will be suffering a fate worse than death.”

“But what is he?!” Celestia screamed in desperation.

“...He’s a Time Pony,” Discord sighed with a heavy despairing tone. “An alien. A member of a race of beings as old as the universe itself. Equestria is not even a single half percent to the power and advancement of the Time Ponies. Even my kind, the Draconequus, were nothing compared to them and we could manipulate reality itself. They are the masters of time and space with powers beyond understanding. And The Doctor is the most well known of them all. Because out of all the Time Ponies, he is the one that has had the most impact on the entire universe.”

Discord looked out the window and continued to talk as if he was lost in his own world. “The Doctor has saved countless worlds and races from utter destruction, but also destroyed so many. Species across time and space worship him, love him, respect him, hate him, fear him, or outright curse him. But none can deny their overall awe of him.” He turned to Celestia with a serious expression. “There are evils in the universe of ours that are far deadlier, sinister, and terrible then anything you or Twilight’s gang have ever faced. You know those ‘Ancient Evils’ trapped in Tartarus? Most of them were put there thanks to the Doctor. The ones that survived him anyway. Just a whisper of his name is enough to make them shriek in fear and hide in their cells out of terror that he will come back to finish the job.”

“...Is he that powerful?” Celestia whispered in horror as Discord just laughed.

“Do you know why there is only one of my kind, Celestia? Because they are all dead,” Discord whispered as he closed his eyes. “I am the last of my kind. I am not from Equestria or your planet. I was from a planet known as Lokina. I only came here because my planet was destroyed by a race we couldn’t defeat. They were known as The Daleks. They are the most evil things in the galaxy. Tens of thousands of worlds and species were completely exterminated by their armies, even ones more powerful than my own. For all our powers of warping reality, we were no match for them. They killed all without a care. They take no survivors. Their entire goal is to kill all life in the galaxy until they are the only ones who remain. I watched as all my people died off one by one until my parents used their entire power to send me to a new world in a ritual. Your world.”

Celestia’s mind went into overdrive. The fact that life existed outside of their original world was mind boggling, let alone how many civilizations there were. Suddenly, she felt like a speck in the universe. The fact that there were races and worlds more powerful than she could have imagined was terrifying and made her wonder if this universe had such similar things.

Discord being from another world was also another shocker, not to mention being the last of his kind. He always kept changing his origin story and there was no other record of a being like him in the entire history of their world. To hear he was the last of his kind by these Daleks, who sounded so evil they made humanity look like doves, also made her feel sympathy for Discord.

“But do you want to know something? The Daleks fear one being above all else. The one being who has, time and time again, stopped them and ruined them. Saving countless others from their deadly power to the point that Daleks go mad even encountering him,” Discord said as he sharply turned to a paling Celestia. “And that is The Doctor. They call him Ka Faraq Gatri which means Destroyer of Worlds.”

“...What do I do?” Celestia whispered in horror as the full weight of the situation now hit her. This creature of terrible and outright dangerous power had all but declared his intentions upon rescuing Lyra Heartstrings. It was clear where he stood on the side of this war. And Celestia was this close to losing her bladder because of it. If this was a being that even Discord feared then what horrors could he unleash upon Equestria?

“What did you do is the question,” Discord growled. “The Doctor has defended this planet and Equestria his entire life. The one planet he always treasured even above his own home. He has protected it far longer than you can imagine against threats beyond counting. Twilight and her friends are nothing compared to the adventures and events The Doctor has taken part in for this planet. If it weren't for him, your entire world would have been destroyed dozens of times over. It’s one of the reasons I never sought a fight with him. I knew I would lose in a minute's notice.”

Then why didn’t he do anything about the Sun dying? Celestia wanted to shout but was unable to voice her words as Discord continued to glare over her.

“So for him to side against you? Against Equestria? You must have done something very bad. Worse than imagined. I am this tempted to pry it out of you, but I don't have time to deal with you. I’m going to get Fluttershy and I am taking her, whether she likes it or not, as far away from here as possible. I’ll even try her friends since I owe them that much, but I have a feeling that they either won’t believe me or won’t abandon you since out of all six of them, only Fluttershy has ever outright spoken against this war. Pinkie Pie and Rarity I suspect hate the war as well, but they’re too cowardly to say anything. Rainbow Dash and Applejack are outright fanatics so I figure their lost causes. And Twilight? Well, I guess she’s still your lap dog even after giving her wings.”

“Do not call her that!” Celestia shouted, finding her voice back. “And do not dare to leave Equestria with Fluttershy! We need her and I have more questions!”

“No, Celestia. The moment you made The Doctor your enemy, you lost this war. It’s a matter of when now. Not if or how. Just when. If you have any brains in your head, Celestia, I suggest you surrender right now and spare Equestria and your subjects whatever horrors are to come. Because as far as I am concerned, you are all dead ponies walking. Goodbye.”

And just like that Discord vanished. Celestia just stood there in a stunned state of silence for nearly twenty minutes before calling on her guards.

She needed to gather the element, the war council, and her fellow princesses and fast.

Time was not on her side.



Lyra just stared at the planet Earth in awe as she stood on its moon, breathing despite being in outer space. The Doctor had told her of some kind of shield the TARDIS had been projecting. Another amazing thing the ship could do that she was finding hard to keep track of. The Doctor had suggested this place after she learned...so much good...and so much bad.

Learning that there were aliens was amazing. Learning about a pony who traveled through time and space was amazing. Learning that he had saved so many lives and done so many adventures that would make Daring Doo blush was amazing.

Learning that her world was now destroyed thanks to the Princesses and Elements was not.

That had been hard. She cried for hours and The Doctor held her. He told her about the future Equestria and the world should have had, all the good and bad, all the companions he had come to love and the civilizations that he enjoyed visiting.

It was all gone now.

Snuffed out forever.

All because of that bucking bitch and her cult of brainwashed worshippers.

If Lyra ever needed more of an excuse to rebel, she now had it.

“Beautiful, isn’t it?” The Doctor asked, walking up to her as they continued to gaze on. “Billions of lives trying to live on this planet and they are all at risk because of a madmare.”

“We can’t let it happen,” Lyra whispered with fury yet also pain. “Not like what happened back home.”

“No, we won’t,” The Doctor said with such steel in his tone that it made Lyra shiver. He looked so young, but sounded so ancient. “Come. We have work to do.”

“What are we going to do?” Lyra asked as The Doctor returned to the The TARDIS.

“We’re going to war.”

Author's Note:

Another chapter added. Feel free to help out at the Negotations-Verse TV TRopes Page: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse