• Published 8th Jan 2023
  • 3,286 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 1

Author's Note:

Yup, it's another story to add to the Negotations-Verse series. If you already know about this one, chances are you don't need to read this part. If you haven't, please read. This is an Alternate Universe and Crossover fic for my NegotationsVerse series with Doctor Who. I've always wanted to do a Doctor Whooves fic and when I asked zelkova48, the author of Choice if I could write chapters for them they agreed.

One of those ended up being Regeneration, a popular story in the fic, but as it went forward many believed it should be its own series instead of being part of choice and over time I agreed as well. I talked it over with Zelkova and we agreed to remove the chapters in January and I would start the chapters again as a separate fic. So here we are.

A few things you should know about this before reading it. One, this features an original doctor and not one based on any of the previous Doctors. Second, The Doctor had his adventures (all the canon ones) in the MLP universe and not the Canon Doctor Who universe. Three, I will be making a lot of refrences to the Classic Doctor Who series which is still my favorite over the current one but you'll see them as well.

While eight of the Regeneration Chapters were made before being put down I'm going to repost them once every week instead of all of them in one go.

Thanks for reading and be sure to help out at the Negotations-Verse Page on TV Tropes: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse while also checking all the other Negotations-Verse fics.

I’ll be a story in your head. That’s OK. We’re all stories in the end. Just make it a good one, eh? Cause it was, you know. It was the best. The daft old man who stole a magic box and ran away. Did I ever tell you that I stole it? Well, I borrowed it. I was always going to take it back.

- The 11th Doctor


This was a familiar feeling.

A very familiar one.

He lost track of how many times this had happened in his long life.

Seven? Ten? Thirteen? Twenty-six?

It was almost as bad as how his sixth life ended. Hitting his head as hard as possible on the TARDIS's controls while being blasted by The Rani. Goodness, what an embarrassing way to go. At least Orange Melody hadn't seen it, but that had only left confusion for her when she didn't recognize him in his seventh regeneration at first.

He tried to remember what had happened that caused his TARDIS to act all haywire while the aftereffects of his current regeneration were still sinking in.

First, he remembered who he was: The Doctor. A Time Pony from the planet Gallopfrey, one of the oldest civilizations in the galaxy. Keepers and protectors of time and space.

He was past the year 2,000 in terms of age, and he had managed to regenerate more times than any Time Pony has ever due to a strange mishap that happened in his twelfth life. He had traveled through time and space in his faithful and loving companion known as the TARDIS (Time And Relative Dimension In Space) that could travel to not only alien worlds, but the past, future, and all in-between.

He had fought monsters, alien races, madmen, godlike beings, and even the Loch Ness Monster once. And ever by his side, those who fought with him and helped him along the way were his faithful friends and companions.

They were citizens of Equestria both in the past, present, and future, aliens of different races, and even a robotic dog once or twice. All with different faces, genders, and even races, from ponies to griffins to changelings and more. He had fond memories of many of them but regrets more than one. For they were more than just his friends, they were his family. A family one old stallion in a box would never trade for in his entire near-immortal lifetime.

Speaking of companions, The Doctor then recalled who his latest ones were and what he had just done with them. He, Sunny, and the rest of her friends had stopped the Cyberponies from turning all the pegasi in Zephyr Heights into new weapons for their war machines.

He smiled upon remembering his most recent companions and the first time they met when they both discovered, separately, that ponies were disappearing in the Bridlewood forest thanks to the Vashta Nerada, and they teamed up to stop them. It was clever Izzy who gave him the idea of gathering illumination crystals to create an artificial sun barrier to weaken and destroy them around the areas they had conquered. From there, he offered his TARDIS to them for use and exploration while warning them of the dangers.

After all, more than one companion had died under his watch.

But they all agreed, and the adventures they had were some of his favorites in recent memory. He had said goodbyes to them, needing to check up on something in ancient Equestria, but promised to be back.

The reason for his check-up was when he decided to see how Equestria was doing during the first years of Twilight Sparkle's Alicornation that would eventually lead to her rule. He rarely ever visited that time period in all the years he had been traveling around Equus save for the time he had Silverstream and Gallus as his companions shortly after their second year at the Friendship Academy. Oh, right, he needed to attend their graduation soon. He did promise after they parted upon saving Gallopfrey from the Daleks.

The good thing about being a Time Pony was that you could be there in a flash of a second after not seeing them for about two hundred years. He'd still have to explain the regeneration thing though. That would take time.

Getting up, The Doctor shook his head and cracked his neck. "Well, I still got a head. That's a good sign. Now, let's look at the damage." The good news was that the TARDIS was still in shape. In fact, it strangely didn't look like it had been damaged at all despite all the flare and sparks it was giving a minute ago. "Then again, it could have fixed itself up again. The old girl's done that before. If so, how long was I out?"

He decided to ponder that later. Right now, he wanted to see how he looked. "Well, judging by the voice, I'm male. Again. That's four in a row since the last gender change. Still feel like a pony, but no wings, so that rules out pegasi. I don't feel a magical aura bouncing around in my skull, which rules out unicorn. Earth pony again. I swear I become this more than any other regeneration. I wish I was back in my diamond dog body. That was an interesting experience."

He decided to walk over to the mirror near the TARDIS entrance that he put long ago if something like this happened again. When he arrived, he was pretty interested in what he saw. "Hmm, dark brown mane with an inward shift in the right direction. Still not ginger. Darn. Ash gray-colored coat. Eh, not bad. At least it matches decently with the mane color this time, unlike when I was pure blue with a yellow mane. That didn't look right. The hourglass cutie mark is still there. Eyes are a bit smaller, and that green color? Ehh, I guess it's passable. The nose looks good too. Thank the stars. No freckles or ugly markings. I could honestly pass for a twenty-five-year-old. I swear the older I get, the younger I look more and more in my regenerations."

Clapping his hooves, The Doctor decided to walk over to his TARDIS and check what had happened and where precisely he had landed. "Well, I shouldn't have landed too far from Ponyville. Even if I have a tendency to miss it a lot. We should be about...about...wait, what?"

This couldn't be correct.

These numbers in front of him made no sense because that was impossible.

According to these numbers, which he knew very well, he should be in the middle of a star in the Tralaxia System if his memory of the entire universe coordinates was correct. But that was impossible. He couldn't have missed it by that much.

Deciding to check out what was really going on, he pushed out the TARDIS's sensors and relaxed upon realizing he wasn't in the middle of a star after all, but still in Equestria. Yet, as he looked at the exact coordinate, he paused. This wasn't where Equestria was supposed to be on the planet. In fact, this didn't look like anything from Equus at all. "Has...Has the nation been moved?!"

Now he really needed to get out and find out what was going on.

Practically galloping through the door, The Doctor opened the door and found himself staring into Ponyville just a short distance away. It smelled like Equestria, and the grass tasted like Equestria...but the air was different. No, this was not Equestrian oxygen. Sticking out his tongue, The Doctor calculated what he was tasting and winced. "Ugh, definitely not Equestrian. This is post-industrial revolution pollution type air. That's not supposed to happen for another two centuries! Jeez, how much plastic does this planet have?!"

Shaking his head, if this was not Equus, this was another planet. And if there was industry here, that meant there was another species living on this planet. One that was highly more technologically superior to the ponies of Equestria. This both excited him and unnerved him. It was a mystery that was only getting weirder and weirder. Well, I'm not going to find out what's going on just by standing around.

Rushing back into the TARDIS, The Doctor quickly decided to find the nearest moon he could rest on to get a clear view of the planet while the TARDIS promptly tapped into the communication and networks of the planet. If it was that advance, that is. He soon found a nearby moon about 225,623 miles away and quickly sent the TARDIS there. He felt her land in less than a few seconds and walked out to gasp at the planet. "Oh my..."

It was beautiful.

"Fascinating." Never before since Equus herself had The Doctor seen such a beautiful sight of blue and green. So perfectly mixed together with just the proper formation of continents and landmasses that were evenly split apart for both travel and distance. Waves of oceans as pure blue as sapphires and bright city lights in the distance showed that this was, indeed, an advanced civilization. "Question is, are they hostile or peaceful?"

Were they responsible for bringing Equestria to their planet if it was the former? How would they respond to meeting their new equine neighbors if they were peaceful? Of course, this could also be the work of someone else. A third party that The Doctor either knew or didn't know. I can count at least sixteen different enemies of mine that can do this and have various reasons for it. Although I don't see any starships or planetary defense fortresses. There are just a few space stations that show they are capable of space travel, but nothing beyond their borders. It must be just about discovering atomic energy if they don't use magic. Of course, I could figure out what planet or system this is if...the stars were...wait a minute.

The stars.

He didn't know these stars.

The Doctor had been to nearly every corner of the galaxy, and he knew where every star was. Every consolation, planet, comet, nebula, and more were memories he could recall at any time. And this....this was new. This was not something he had recognized.

A growing dark horror began to feed into The Doctor's heart as he recalled only in specific times when such a thing happened. He rushed into the TARDIS and quickly started doing something he rarely ever did: contact Gallopfrey.

Things might have been much smoother between him and his people, especially after Romana became President, but he still preferred to keep himself as far from his homeworld as possible. He tried the various contact signals, but he got nothing. He then tried the Galactic Federation of United Races's contact signals. Nothing. There was nothing from the Tyroan Empire or the Star Changeling Federation or even space music from the various local alien radio stations.

Nothing but absolute silence.

As if there were no other lifeforms in the entire galaxy.

Save for one.

This one planet where he picked up various broadcasts and focused on one coming from someplace called Britain.

"This is John Smith of B.B.C. news with the latest on the war against Equestria. As viewers know, we recently have entered the second anniversary of the announcement of Princess Celestia's declaration of war for our failures to accept the Magic of Friendship. In reality, our governments discovered her plot to turn humanity into ponies, known as newfoals. This was following the tragic attack on Madrid in Spain, where over sixty thousand people were ponified using the conversion potions, with ten thousand deaths from the attack itself. Reports of an upcoming attack on London proved incorrect as an Equestrian attack force did indeed land on British soil but teleported instead in...Windsor Castle. There are reports of mostly converted humans turned into ponies, but there are casualties...among which... I'm sorry...this is...there are no other words for me to put this. The royal prince and princess, ages two and four, are alive but are now...newfoals. And the rest of the royal family...is gone. Their bodies were respectively given quick deaths...and covered with the flag of our beloved land...All of England and the world is in mourning for these losses...truly...God help us all..."

The Doctor just stood there in silence as he turned to another station. This one is about a battle happening in China where Equestrian forces were turning people in villages into ponies using some kind of potion that The Doctor had never heard before. Speeches in Equestria were being given about how the righteous ponies of Equestria would bring “Light” and “Friendship” to the humans who were misguided and lost in chaos. A blogger on a site called Youtube talking about his best friend turned into a pony and rejected him calling him a sinful human and no longer recognizing him.

There was indeed a force that had been behind this, but it was no alien or extra-dimensional creatures or even cosmic beings. It was Equestria itself.

It had invaded another dimension and was taking over this world.

For once, The Doctor was without words.


Once he had calmed himself, The Doctor tried to process all that had happened. First, it turned out that Equestria had been on this planet for twelve years, but he had only just arrived recently. According to the computer logs, the TARDIS had to adjust to access a power source to travel in this dimension.

This wasn't the first time he had been in such a situation, so The Doctor made sure to have a few means to make sure his TARDIS never lost her power whenever he traveled to parallel worlds. Once it had converted and adjusted itself, it landed in Equestria just as The Doctor finished his regeneration. It took about ten minutes in the TARDIS, but outside it was twelve years.

The second thing was to figure out who this human species was and how this war began so he could end it. He went into both the human lands and the Equestrian lands to get answers. The former was harder to do, especially since this was a new species hostile to pony-looking life. Thankfully, some ponies kept their morality and sided with the humans though there weren't that many. Even in Equestria, some talk of others disapproving of what was going on could be heard, but they were being silenced.

He went first to a public library and spent an entire day reading the whole history of these people as fast as he could both on books and websites. Overall, The Doctor found them overly emotional and warmongering but clever, creative, and filled with potential to do so much good. They were young. Just starting out as a species despite their faults. No doubt they would have evolved better if Equestria had not come. Overall, he felt he would have liked this species if The Doctor had the time to get to know them, but first he had to save them. Save them from a species he had saved multiple times as well.

That had been the other thing he did right after. Figure out what the blue blazes had happened in the time he had left.

What had caused Princess Celestia, Princess Luna, Princess Cadence, Princess Twilight, and the rest of the Elements of Harmony to suddenly do this mad act without even once thinking of the consequences? He had never interacted with them in his entire lifetime traveling through the timeline of Equestria, but this was not how they were supposed to act.

They were supposed to bring a golden age where Equestria soon created a near worldwide government that would last for hundreds of years before the Darkening Era. Yet, even then, the future would be bright afterward. The Doctor himself had seen it and played a part in it.

They were so critical to the planet's future that practically everything they did were fixed time events.

The Doctor feared even doing the slightest bit of interaction would ruin it all save for meeting Silverstream and Gallus, students at the Academy of Friendship. It had been an accident, one The Doctor would never trade to fix as they had become like family to him, but he had them swear to never reveal what they had done with him to their friends and families or to the Princesses.

The Doctor personally was never a fan of Princess Celestia most of all. She looked every bit of the regal and loving princess that was worshiped by her people, and there was no doubt she was a powerful ruler. But The Doctor knew there was a darkness in her that few could see in the rare times he saw her in passing. One didn't live as long as he did without seeing such things.

Still, nothing she did ever amounted to anything that would overall harm Equestria in the long run save for her death which caused the Crisis of Faith in the Church of Harmony until Princess Twilight dismantled the religion shortly after. Ironically, the atheist herself would convert to the old Fausticorn religion a few years later after her own religious experience.

That is if any of this was going to happen now.

The entire timestream had been completely altered. No, it had been destroyed. Whatever future their old dimension had was no more. That meant anything could have changed. The Doctor's thoughts turned to many companions and friends he knew in the future. We're they lost? Gone forever? Sunny, Izzy, Hitch, Zipp, and Pipp...were they all gone? It was too heartbreaking to even think about.

Yet he knew what happened if timestreams were interrupted, especially at this magnitude.

Had the Princesses been brainwashed into doing this? Forced? Did Discord teleport them? No, even with his power, he was not capable of this. Putting himself into an alternate dimension and maybe an entire town if he tried, but a whole nation of millions? Not possible.

The story, at least to the public, was that Equestria had come over here to teach humanity the magic of friendship, but the consequences led to a powerful energy shield growing from Equestria that was spreading throughout the world. One that was dangerous and deadly for humans to touch.

To spare them from a total wipeout, the Princesses created what was known as the Conversion Potion that would turn humans into ponies. Only after getting his hooves on one of them did The Doctor, and later humanity, realize it did much more.

The potion completely changed not just the DNA of the human, but their mental state, morals, mindset, and even programmed any human touched with it new obedient personalities that were boiled down to "hate everything human" and "love everything pony."

If there was one thing that The Doctor hated, it was when science was used for evil, and this was one of the evilest things he had ever seen to the point that he compared it to a combination of The Master's mind control and The Cyberponies conversion. It was even equivalent to Sutekh’s abilities in some ways. They even sterilize the poor souls, which only made The Doctor vow even harder to find a cure as soon as possible.

It was clear humanity was very reluctant to do this transformation and that their suspicions paid off as it turned out they discovered the same thing the Doctor did. This led to the war. Princess Celestia declared the humans to be unfit for anything but either assimilation or destruction. Calling them pretty much evil but with prettier and sympathetic words as if she had the right to play god over them.

The Doctor had snorted upon that. There were hundreds of more races and creatures far eviler than humanity. Many of which The Doctor had personally dealt with.

He also found out how Equestria managed to get to Earth. They had solved Starswirl the Bearded's Theory of Dimensional Travel and combined it with the power of the Elements of Harmony. The only good thing was they only took Equestria with them. If they had taken the whole planet, the two massive worlds would have collided and destroyed each other.

Which led him to another realization. If Equestria was here...who was raising the sun and moon?

And it was at that moment that The Doctor screamed in his TARDIS so loud that she wept for him.

They were gone.

All of them were gone.

There was nothing left of Equus now but a burned and frozen planet with no life.

That meant that all of his Non-Equestrian friends of the current time and beyond were dead.

Rose. Fizzle The Dragon. Sarah Dane Smith. The Ponds. Gallus. Silverstream.

And so many more.

At that moment, The Doctor would show Equestria why he was known as "The Oncoming Storm."

Because a good stallion was going to war.


Lyra cursed as she ducked into an alley to escape her pursuers. Ever since she started her public denouncements of Equestria's actions against humanity, her life was in constant danger with little to no aid. Her family had disowned her. Her oldest friends had deserted her. And Bon-Bon? No, it was clear where her views were, even if it hurt to break their friendship.

Worst of all, the Princesses had sent their goon squads to try and capture her. What for, she didn't know, but it couldn't have been anything good. Lyra thought Appleloosa would be a safe place to lie low, but she forgot that "Wanted" posters were a thing, and now she had the local sheriff and his two deputies after him. Plus, it didn't help that she was the only unicorn in an all-earth pony town so she stuck out like a sore hoof. Blasting open the doors of a local barn with her magic, Lyra went inside only to curse upon seeing no back exit.

"There's no point in running anymore, missy!" Lyra turned around as the sheriff and his two goons walked inside with narrow eyes. "Just give up, and we won't have to hog tie ya."

Lyra lit up her horn and gritted her teeth. She wasn't going to get captured here. Not without a fight. I swore to stop this war even if it takes everything from me!

Suddenly, there was a strange buzzing noise followed by a loud snap. Everypony looked up and gasped as a large pile of hay bales fell from the ceiling and landed on Lyra's pursuers. The three were still conscious, but barely as their groans moaned through the pile of hay that had just fallen on them, the rope holding it snapped suspiciously.

Lyra wondered what happened when she felt somepony take her hoof and turn her around. She gasped upon meeting the firm, young-looking (yet his piercing green eyes held such age) mysterious brown-maned and ash gray earth pony as he said only one word. "Run."

Without even thinking, she ran with him outside the barn, past the stunned sheriff and his posse. She then followed her mysterious rescuer out into another alley. He was wearing, of all things, a dark blue admiral trench coat with white lining and buttons while a dark undershirt lay underneath. He looked adventurous in a classic navy commander sort of way but without the fancy medals and decor. They continued to run until they came to the edge of town where awaiting them was some kind of blue box that had "Police" on it. This made her skirt to a halt. "Wait a minute, you're police?!"

"No, I'm The Doctor," He said, reaching the police box and opening it.

"Doctor who?"

"Just The Doctor," He replied. "I think you better get in before they reach us."

Lyra turned around and saw that the sheriff and his deputies had recovered quickly and rushed towards them. She looked back at The Doctor. "How do I know you're not working for them?! Or the Princesses?!"

"Because I'm going to stop them and save the billions of lives on this planet, both human and Equestrian. Before their madness destroys everything good about both races that will last for generations," The Doctor said firmly with such power behind those words that Lyra couldn't help but tremble in fear. "So you have to trust me if you want to save everyone. Because that's what I am offering. A way to stop this."

The Doctor offered his hoof, and Lyra looked at it for two seconds before grabbing it. "Lyra Heartstrings."

"Welcome to TARDIS, Lyra Heartstrings," The Doctor said as he pulled her inside. "And before you ask, yes, it's bigger on the inside than it is on the outside."

Lyra barely had any time to ask what that meant before being dragged into the police box. Almost immediately, it started to make a strange "wooing" sound as it began to slowly dematerialize before the shocked earth ponies eyes. They watched in both fascination and confusion as to the blue box that held the criminal disappeared slowly before any of them could do anything. A minute later and it was gone entirely. Vanished into thin air.

"What...what was that?" One of the deputies asked.

"Some fancy new Canterlot traveling device?" The other said.

"Well, whatever it is, it's gone now. Better send a message to Canterlot about this blue box thing. The Princesses can figure it out, I'm sure."

Little did the sheriff know that the blue box would soon become a nightmare for all four Princesses in the very near future.