• Published 8th Jan 2023
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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 7

Everything’s got to end sometime. Otherwise, nothing would ever get started.

- The 11th Doctor

+}{+

It had been two weeks since the Defeat At Osaka as many were calling it.

All of Equestria had been horrified and in mourning over the loss of so many of her brave soldiers that perished or were captured by the humans.

Cities and towns held vigils at their local Churches of Harmony as masses went on for hours in prayer to the holy alicorns to deliver the souls of the lost to Elyisum, and avenge those that had died. The families of those who had lost relatives to the battle were cared for both by their government and their local communities, but nothing would bring back their lost loved ones.

The survivors of the battle told their stories with bitter tears and hatred in their tones.

They talked about how the humans brutally destroyed their lines, rushed them without mercy, and saw their comrades die in horrible ways from being shot to death to one J.S.D.F. commander using a sword to slice a unicorn’s head off.

Many couldn’t sleep as they kept fearing the explosions of the artiliary or bombs of the human army coming to get them at any time. Others suffered mental and emotional breakdowns and had to be committed. One or two just killed themselves with notes stating how they couldn’t take the nightmares anymore.

Outside of the grieving, there was disbelief.

Never before had any Equestrian thought that their mighty forces would suffer a defeat so badly. The last time they had ever lost such a battle with high casualties had been the Battle of Westbeak in the griffin lands during the Fourth Pony-Griffin War three hundred years ago. It was often said that the battle had been what caused the war to become a stalemate slightly in Equestira’s favor rather than a full on victory. Not that it meant much to the griffins as their kingdom at the time fell twenty years later due to rebellion before falling into another warring states period.

While there had been rough battles in the Conversion War, most of them had been victories or stalemates.

This was the first full on defeat and many couldn’t wrap their heads around that. Even the fact the Osaka invasion force had Commander-General Shining Armor and two alicorn princesses and still lost was mind blowing.

It made ponies fear that the war wasn’t going to be as quick as they thought as they knew the humans would use this victory as a means to continue fighting with renewed vigor. All future invasions were put on hold for the time being and all Equestrian owned territory was put on full alert.

Rumors that traitors had been behind the downfall spread and the E.S.S. was working over time as ponies started accusing anypony around them of being spies or harboring traitorous thoughts.

It didn’t help that it finally became publicly known that Fluttershy and Discord had become traitors.

It broke the hearts of many, including foals, that one of their heroes had betrayed them to the point that any memories of her that old friends and family had were thrown out.

The Church of Harmony even declared her soul was doomed to Tartarus upon her inevitable death at the hands of the Princesses who would avenge their fallen.

There were also rumors of someone called “The Doctor”, but the E.S.S. stated that such a being wasn’t real and nothing but false propaganda.

Most had to agree with that. A time traveling alien in a blue box? Absurd.

If there was one positive thing that the defeat had done it was drive up recruitment. Seeing their brave fathers, mothers, sons, and daughters buried to sleep forever more, had invigorated many to join up to avenge them. Their pride was on the line and the safety of Equestria was paramount with many hoping the Princesses would have plans for a counter attack to see justice was done.

However, the Royal Family was more concerned about the wake and funeral of Commander-General Shining Armor.

It had been agreed upon, by both the crown and family, to have the wake and viewing ceremony in Canterlot before having the body taken to the Crystal Empire for the official funeral and burial into the catacombs of the past rulers of the nation. For as much as he was the Prince-Consort of the Crystal Empire, Shining Armor had been born and raised in Canterlot.

The least the city he loved so much could do was say farewell to him.

The third day of the five day viewing wake had been the same as the other two days. Prince-Consort Shining Armor had been placed on a purple pillowed silver-white casket, decorated in the finest of jewelry and cloths, in the middle of the Grand Cathedral of The Sun and Moon, the holiest place in the Church of Harmony faith.

He lay inside the lidless casket, void of any and all wounds to the point that it would appear he had been undamaged at all. Yet the shrapnel in his chest had done him in from the bombing. In his will, he asked to be buried in his Grandfather’s uniform and wore it with pride even in death with his hooves gently placed above his stomach as his expression was one of utter peace. It had been Cadence's request that he was smiling in death because it was his smile that she and Flurry Heart loved so much about him.

Numerous flowers surrounded the casket to the point that they made a near field of themselves save for a small circle for walking around the casket to pay respects. The lines of which extended so far out they went down to the lower levels of the city.

Guards wore black armor with purple and white sashes in honor of their beloved Commander, with many unable to keep themselves from crying even as they stood vigil over his body. Near the altar of the Church was the family, dressed in mourning, who stood there watching the lines of mourners move as funeral music played constantly around them.

Princess Celestia had seen friends die before, but that didn’t make it easier when it happened.

Shining Armor had been more than just a friend, he had been family.

Loyal. Protective. And brave.

Equestria was a darker place without him.

She glanced at Luna whose expression was one of anger and rage. It had taken all of Celestia’s willpower to force her younger sister to hold back on unleashing everything she had upon Osaka herself to the point where she wanted to make the atomic bombings Japan had gone through look tame in comparison.

Celestia was able to get her to calm down by pointing out that not only was humanity riding high and confident with their latest win, but they still had no means of defeating The Doctor. Plus, this was a time when family needed to come together. Luna conceded this but demanded that, come the next invasion, she would personally lead it herself.

Twilight Velvet and Nightlight were still in tears upon losing their son. Princess Celestia swore that she would take care of them for the rest of their lives. Anything they wanted was hers to give. She even made it so they never needed to pay for anything, yet that would be of no comfort for the fact they lost their son.

Meanwhile, Twilight, her beloved student, was standing there with a cold and stoic expression while her one eye was focused on her brother’s corpse while the other was behind a black eye-patch.

Something had changed inside Twilight after the battle. She had become colder, methodical, and spoke less to anyone save except for important factors like the war or planning her brother’s funeral. None of her friends, or even Spike, could get her to talk much. Princess Celestia even tried to get her to talk but she said that she couldn’t think of anything except one thing: Destroy The Doctor.

The fact that The Doctor had played a role in killing her brother and crippling her to using only one wing and eye for the rest of her life was bad, but reversing the Conversion Potion? The most prized alchemical achievement in modern history that took Twilight, Celestia, and dozens of other scientists to make? That was just applying oil to the burn.

Princess Celestia still couldn’t believe such a thing had been done, but it was true. Humanity had applied the cure The Doctor had created (without mentioning him personally for some reason) to all the newfoals that they had in their borders. Princess Celestia personally saw over a hundred videos of newfoals turning into humans again before she was forced to accept that this was the truth. One of their greatest weapons was now null and void.

The newfoals in their borders were restless when this was revealed. They claimed they didn’t want to be humans again and even started asking their fellow ponies to kill them if this happened. Another headache that Celestia had to deal with.

The other person who had been in complete despair was Shining’s wife, Cadence.

Although she was not crying, her eyes told a different story. When Celestia agreed to take Cadence in as part of her family by formally adopting her, she had always been so full of love and life in her expression that she was her own ray of sunshine. Cadence had quickly worked her way into Celestia’s heart and she showed herself to be wise, talented, and caring. A perfect ruler to work with Twilight when she and Luna passed the crown to them one day.

Now, that once happy alicorn that could brighten any room was in utter despair. Cadence had cried non-stop for days to the point that she couldn’t do anything with helping with the funeral save for one or two things.

She just didn’t have the energy in her to do anything as any time she looked at Shining she looked ready to collapse in grief. She couldn’t even make the opening speech on the first day of the wake.

The only time she ever snapped out of her funk was when she had to take care of Flurry Heart, who was a mess in herself. She only looked at her father for a few minutes on the first day of the wake before teleporting away in sorrow. Locking herself inside her room, she refused to come out and only let Cadence, Twilight, and Spike inside to talk or comfort her.

Currently, she was still inside her room sobbing her eyes out while Spike was with her to be there.

And all of it was his fault.

The Doctor.

Ţ̸̡̩̰̙͎̬̱̼̺͂̐̿͘͜ḩ̵̛̫̤͔̱̼̤͍̳̰̘̰͆̓̽̊̄̀̓͊͜ë̵̪̰̗̰̗͓̰̝͕͍͍̺̭́̉̿̿ ̴̙̂̓̌̏̌͝D̸̨̀̀̄͌͂̉̿̈́͌̈́̇͒̈́͜ơ̴̲̲̗͚͙̳̑͆̾͂̀̿̽̌̓͂̌́̀͊c̷̭̬̖̺̠̠͍̖̀̍̄́͊͊̇̍͝t̸̡̜͖͚̲̯̤̙̤̜͉̖̗̍̍́̌̓͋̄͋͊̌̀͜͝͝o̶̧̦̘͈̩͎̮̥̣͍̲̥̖͌̆̂̏́̊̃̚̕r̸͕̪͓̺̮̜̯̺̖̬̟̋͌̅̿̌̾͑̾ ̷̧̢̥͔̩̫͚̹̬̲̣̄̊̊̿̆͗͘͠î̸̦͉̲̙͐̈̏̚ŝ̸͔̻͈̓̄͊͝͝͠ ̴͉̫͊͊ǫ̴̺͊ū̵̡̮̋ṙ̵͇̙͔͚̅̿̓̓ ̴̙̻̯̝̯̮͙͍̐̓̿̑̽͒̓̾͜͜ͅè̴̥͕̮͇̎n̸̨͔̰̐͂̆͆̇͗͊͐̍̇̆́̈́̇̊e̶̺͖͕̘̦̱̓̋̅̅̀͛̌̉̐͊̃͒̎̚m̸̢̢̯͉̳͎̘͍͍̈̑̐͊̀̉͋͌̍͘͜ͅÿ̶̧̛̖̤̲̱͕́̉͊͛̐̌̔̈͠͝ ̵̹̄̎̈́̃̆͠a̸̧̦̝̮͆͊͂̒̈͒̓̏̚n̸͓̥̠̬̠͚̉͂̈̈d̸̳͔̩̩̮̤͔̻̟͙̻̀͗̍̓͌̆̊̂̇̊͜ ̵̡͖̯̰̮̮͎̙̹͙̠̥͎̅͑̚ḩ̶̯̪̞͇͔̼̄̒̈́̇͂̅́̂̉̓͑̀͠͝ę̴͇̠̰̩͙̼̟̠͒͒͐̄̇͝ ̵̧̺̣͇̬̣͙̲̦̄̅̇͘m̸̢̬͓̘͔͉͔͓̜̳̪̝̣̮̺̄͒̐͋̾͛͑̂̄̕͠͝ṷ̷̧͓̩͖͗̈́̃̔̂̃̔̅̓̄̌͘̚͜͜͝s̶͈̜̭̖̩̲̦̫̔͑̓t̴̡̰͈̱͎̀̈́̄͆̓̽ ̴͎̪̠̥̳̙̠̝̘̱͔͎͕̺̉̉̒́̓̆̀̀̌͋̈́̈̂̔b̵̛̩̄̌̐̃͗́̈́̓͠͝e̸̛͖̞͎̬̝̗̔̏͆̀̉̓͌̒̿̎̈̽̕̚ ̵̢̮͇͚͉͕̤͍͔̠̫̳͕̈́͊̊͒d̷͍͓̗̮͚͕̮̅̎̏̽̎̌͛̓̽͆͊́ę̴̡̼̗͖̦̤̬͖̰̼̿̆͌͆̑̔͑̓̍̍͊͘͠͝͝s̷̢͉̗̪̮̪̲̻̟̞̙̋͐͝ͅṱ̶̱̳̫͚͎̞̪̇r̸̲̞̦̙̈́̓̌̋̆o̵̦̹̻̞̬̲͓͐̌̇̓͝y̶̛͙̘̙̙̐̒͑̽̎̀͘e̵̻̗͓̬͚̎͆͛̓̐̏̽͒̆̒d̶͍̺͓̦̖̦͌͑͛̔͛͛͛̂͆̈́̐̐̕.̴̡͍͎͚͈̼̤̖̰͔̗̪̊̈́͊ͅͅ

“The Doctor is our enemy and must be destroyed...” Celestia whispered.

“Did you say something, Sister?” Luna asked.

“Hmm?” Celestia blinked before shaking her head while wondering what she just felt, but dismissed it. “No, sorry. I was thinking.”

The wake continued as Princess Celestia slowly closed her eyes to calm herself and let the funeral music playing on the speakers continue. That was until they suddenly stopped and static began playing instead. Opening her eyes, Princess Celestia glanced at the speakers as the nearby technician crews tried to quickly fix what was going on much to their embarrassment as everypony stared at them awkwardly.

However, they all soon froze when the static ended and there was silence to replace it before...

“Citizens of Equestria. This is Lyra Heartstrings talking to you from Geneva in Switzerland.”

Princess Celestia felt her jaw drop and she was sure she wasn’t the only one. Everypony had frozen in place as the words of the infamous traitorous pony that had been wanted for months were now speaking to them. Before anypony could even begin to question how, Lyra continued.

“If you are wondering how I am speaking to you on your radios, speakers, magic mirrors, telecommunication crystals, and what few human electronic devices I know some of you are keeping in secret, this broadcast has been designed to hack into every form of communication in Equestria so that everypony can listen. So you can hear something that neither the Equestrian Secret Service or Princess Celestia and her cronies want you to hear. And that is the truth.

The truth about this war. Why we came to this world. And the horrors that we have partaken unknowingly thanks to the actions of a madmare. I know that most of you are going to be told this is a lie and that you should stop listening to me. That you should continue to listen to your precious ‘goddesses’ and ignore my heretical words. But you will listen because it's time you open your eyes.”

Twelve years ago, we were told we were coming to this world to save it from destruction. That the human race needed guidance to save them from extinction.

This was a lie.

The intention of Equestria was always to convert humanity into ponies, even before we knew of the barrier and its deadileness.

Princess Celestia had already given up on humanity even before we came here and assumed they were beyond saving so she decided on two options: Assimilation or Annihilation.

She chose to play god to a race that she had no right to control or decide for. A race that, while guilty of many faults, has achieved much in their time here on this planet. A race that is not too different from us and our past. We ignored most of our history before the unification of the tribes and the building of Equestria, but did you know that this is not the first time in our history that our tribes have been united?”

Whispers were uttered in confusion as Princess Celestia’s eyes widened. How...how does she...of course, The Doctor.

“The Empire of Ponita.

The Empire of Alicornia.

The Confederacy of Coltabana.

The Union of United Equines.

These were all nations that once held multiple pony races—some that no longer exist—that worked together in harmony for years before their downfall through war, hatred, and mutual destruction.

The Great Ancient War, which we only know very little about, turned out to be the one that divided us and set us back on a technological scale beyond counting. The three tribes blamed each other and set aside the hatred that lasted for three hundred years until we were united again.

Why is this not known?

Because Princess Celestia and Luna deemed it better that we remain ignorant of our past in fear of repeating it.

If so, they did a poor job. Because one of the things the Empire of Alicornia did was try to take over other races to enslave them until they revolted. The Union of United Equines made super powered magical weapons against the Holy Dragon Empire and ultimately they destroyed each other with them. Sound familiar? Because it’s very similar to human history. The history of many other species back home. The truth is that all life follows a similar history and that no race is an exception from the other. Not even us.”

“How does she know of this? We made sure to burn all the records!” Luna hissed to Celestia in secret.

“The Doctor must have known. Remember, he can apparently travel through time itself. I wouldn’t be surprised if he was there,” Celestia hissed back.

“We always were taught that Equestria was the first time we were all united together, but this was a lie. We’ve united, fallen, and repeated this process many times over. Does that sound like some chosen race to you? Or every other race in our world? Or even humanity?

In the end, our history is no different from their own. Only they choose to embrace their mistakes, learn from them and try to do better even if they don’t succeed. We just cover our ears, eyes, and repeat to ourselves ‘it's not real’ out of forced ignorance.”

There was a brief silence as everyone waited for Lyra to continue.

+}{+

Listening in from their shared radio, Vinyl Scratch and Octavia Melody, roommates and best friends, were listening to the broadcast as well. While Vinyl had always been against the war herself, being a mare of peace, she and Octavia, who disagreed with her, never let their feelings come between their friendship. Vinyl looked at Octavia who was looking at the radio with interest and wondered if she was going to finally convince her friend that she was right.

“We are repeating the mistakes of our past. We are letting hatred and fear guide us. We are taking over a world that not only doesn’t belong to us, but killing a race.

Yes, killing them.

Converting them into mindless drones who just do nothing but love Equestrian society and hate everything else.

Have you ever talked to the newfoals? Listen to them speak? They are like robots that are programmed to obey us like slaves. They cannot refuse to deny any service asked by any Equestrian because they are brainwashed to do so. They will not even refuse sex because they cannot mentally say no. What does that sound like to you?”

“Oh my gosh...” Octavia whispered in horror as she covered her mouth while Vinyl just stared at her in confusion. Swallowing what was in her throat, Octavia said, “One of my fellow cello players...he told him his cousin has been sleeping with this newfoal and...one time when he joked about having sex in public, she thought he was serious. What if...what if...”

Vinyl grit her teeth and turned back to the radio.

“We don’t let the newfoals keep their culture because we are determined to wipe it out. All the art, statues, books, music, theaters, movies, and more. All the creative works of humanity are being destroyed. Its wonders burned. Its soul is being sucked dry until nothing remains. We are killing them in every manner possible. Not just through physical violence and forced conversion, but by erasing their very spirit.”

At that moment, Vinyl made up her mind. To hell with Equestria. To hell with the princesses. How could she call herself a musician if she was going to let this happen? She glanced at Octavia’s firm expression and Vinyl realized she wouldn’t be fighting alone. She would be fighting with her best friend at this too.

+}{+

“This war we are fighting is a needless war.

We attacked first because it was our holy duty to force humanity to convert to us.

That they were beyond saving.

The Princesses are not gods. I don’t know if there is a god or not, but I know that any loving god would not want their followers to kill others just for disagreeing with them. And if his followers did, that god would never accept them into whatever afterlife awaits them.

We believe the Princesses to be gods only because we were taught that our entire lives, but if they are real goddesses then why do they always need other ponies to fix their messes like Discord, Nightmare Moon, Tirek and so forth?

Why not revive the dead such as those who have fallen?

How can they bless those entering the afterlife if they are here with us on the mortal plane?

Moving the sun and the moon is the only reason we use as an excuse for their so-called ‘divinity’ but unicorns were doing this before them.

And before them the sun and moon were moved by the kitsune and lycans respectively.

Before them were the dragons.

And even before that they moved on their own.

If they really are a duo of powerful sun and moon goddesses, why not use this universe’s moon and sun as weapons to manipulate the weather to wipe out humanity? They cannot. Because they aren’t as powerful as you might think. Especially if they can easily fall to a Changeling Queen, an evil centaur, a Spirit of Chaos, or even a bunch of sharp thorny vines while letting a bunch of non-divine ponies stop them.”

“Father, are you sure we should be listening to such heresy?!”

“...Just be quiet, Halberd. I want to hear this.”

“Because of our full devotion and blind loyalty to the Princesses, or alicorns in general, we have forgotten to think for ourselves.

Think about the humans you interacted with, the technology they showed, the wonders you saw, and what you learned from them.

Was all of it really evil?

Wasn’t some of it good?

Did you not enjoy the feeling of riding an airplane?

Taking in the wonders of their national parks?

Love their shows and movies?

Listened to their music?

Get healed by their advanced medicine and healthcare?

They were able to connect with each other with information free for everyone to share.

They can go to space. They can create alternate forms of energy we never dreamed of. All without magic!

They have advanced factories, inventions, methods of distribution, philosophies we never thought of, and more.

The only reason they sound like a barbaric nation is because of how they wage war. Yet look at what we’ve done in this war? Aren’t we barbaric then? Or is it because of the so called “Elements” that we value so much that make us different?

Well, I’ll tell you right now. Equestria failed to live up to those Elements.”

+}{+

“WHAT?!” Rainbow Dash shouted as she listened in with her fellow Wonderbolts at their HQ. She was about to get out of her uniform and head to the wake to meet up with the others when Soarin came in with the radio playing Lyra’s speech. “What the buck does she know?! She’s a disloyal bitch!”

“We failed at Honestly because we’ve lied not just to the human race, but to ourselves why we are here. Not to mention the propaganda you hear is nothing but horse dung.

We failed at Generosity because instead of offering magical means of helping humanity we’re using our magic to hurt them and convert them. All without their free will.

We failed at Laughter because we’ve caused untold amounts of deaths, suffering, sorrow, sadness, and pain.

We failed at Kindness because we assume the worst of humanity and make them suffer at seeing their cities ruined, their people no longer who they are, and taking over their lands.

Even Fluttershy, the Element of Kindness, has rejected the way Equestria is going. By failing at all of these we’ve also falled at Loyalty because we failed to be true to ourselves.

Upon hearing this, Rainbow Dash smashed her locker so hard that it made a huge dent and she started cursing up a storm but none of the other Wonderbolts, even her captain, tried to calm her down.

+}{+

“And finally, we failed Friendship.

All of us know the lessons that Twilight Sparkle, the so-called Princess of Friendship, had learned in Ponyville.

I was there. I read her books. Attended her sermons.

And I once knew her personally growing up.

I can tell you right now that Twilight failed her own teachings. Because everything we are doing is proof that Twilight can preach all she wants, but she failed to put what she learned into practice.”

Everypony near Twilight backed away as her mane was lit aflame and she gritted her teeth with rage before teleporting away. A large explosion was soon heard nearby and from the windows one could see a towering inferno erupt into the sky.

“But this isn’t the worst of the lies. No, another lie that you have been told is that our world is fine. That Princess Celestia left behind the means to have the world’s sun and moon continue to move without us.

This is...this is a lie.

One of the worst lies of them all....”

+}{+

“Ask yourself this: who is controlling the sun and moon back home? The Princesses will tell you that it's Saddle Arabia, but this is a lie.

The sun and moon are not moving.

They are stuck and without them moving...all life back home is dead.

Every griffin, changeling, minotaur, dragon, donkey, cow, yak, diamond dog, kitsune, lycan, hippogriff, siren, wyvern, abyssinian, and other races, including ponies who didn’t live in Equestria?

They are all gone.

1.2 billion lives. Dead. Because of Equestria leaving the dimension.

That is 1.2 billion lives on Equestria’s bloody hooves.”

Around the various concentration cities where all non-pony residents had been living, a great sorrowful cry was heard across the fields and skies.

A cry of endless sorrow and grief.

+}{+

“You may say I am a liar. You may think I am joking. Or maybe you just don’t want to believe it. But this is the truth.

The truth is that Equestria is the monster in the dark.

The demons under the bed.

The bad guy that is trying to destroy this world.

I, and many others like me, have joined with humanity to stop this. I do this not because I hate Equestria, but because I love her. I love my country, but that means fighting her when she is doing something wrong.

And right now, you are in the wrong.

So I urge you all, citizens of Equestria, to remember who you are. To think for yourself. To stop and listen to what is inside your heart. Do not listen to the Princesses for they are lying to you. Listen to your own mind and soul. Rise up and reject this sick infection that has plagued our beloved home.

We will stop this war.

We will save humanity.

We will rebuild Equestria into a nation that she is supposed to be instead of a nation of insanity and bloodshed.

Join us as we fight on to tell Princess Celestia, Princess Luna, Princess Cadence, Princess Twilight, and all their allies two simple words...”

“NO MORE.”

And then the broadcast ended.

For a long time, the entire nation fell into silence as many stood or sat there in thought and many wondered what would happen not knowing that the dominos had started falling.

And there was no stopping them.

+}{+

Lyra took the big glass of water provided for her in the sound booth before exiting the room. The Doctor was waiting for her with a big smile on his face as she took a deep breath and asked, “So? Did I do well?”

The Doctor lifted his amulet and saw the orange gem glowing. He smiled and said, “You were fantastic.”

Author's Note:

What the Jumbled Text Says: "The Doctor is Our Enemy And Must Be Destroyed"


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