• 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 12

“What’s the point in two hearts if you can’t be a bit forgiving now and then?”

-The Eleventh Doctor


Corporal Diamond Watch didn't know what to feel about his position at Fort Obsidian. As a Crystal Pony who grew up during the reign of Sombra, the thousand years in suspended animation exile, and witnessed the destruction of the monster once and for all, he had hoped to never again have to deal with anything associated with the tyrant ever again.

Yet, here he was as a member of security for not only one of the former king's top hidden fortresses but also part of a project based on one of his worst weapon designs. Which was approved of by the princesses he had pledged his loyalty to, but it was getting to the point where the pledge felt like ashes in his mouth.

Diamond Watch didn't particularly have an opinion on the war. He had read about some of the worst humans in history before such books became outlawed. A number of them made King Sombra look like a puppy in comparison, and he agreed, to an extent, that the humans were a threat to ponykind.

Somewhere down the line, a human with great power would try to rule or exterminate them, and if they could prevent that, Diamond was all for it. However, as the war continued, more extreme measures were being taken to achieve victory. Measures that reminded him of the dark days during the reign of his former king. Diamond couldn't help but wonder if he was destined to constantly live under the throne of some tyrant one way or another.

The ban on certain goods, silencing foreign viewpoints and opinions, arresting those who spoke out against the crown, the war, the jailing of non-ponies, the ESS, and the Harmony Cannon.

If there was an afterlife, King Sombra must have laughed at the irony of what had become of them after his death.

He was not blind, like the non-Crystal Ponies, about what a tyrant was like, and the Princesses of Equestria were becoming more and more like that every day.

Diamond Watch sighed as he looked at the crystal screens from the "Beholder Eyes." The Beholder Eyes were based on the now-extinct demons who could cast dangerous spells with their eyes to the point that gazing upon them could kill you with fear instantly.

Thankfully, these devices were just stone eye-like objects that could move left to right with a giant crystal that could capture the visualization of everything in front of it with sight-based magic and feed that image back to the crystalized screens in front of him and his partner. Say what you will about Sombra, but he was a genius when inventing security.

Said partner was a female unicorn pony from Canterlot who, sadly, supported everything going on. Naturally, Diamond had to pretend to be one because, deep down, he was a coward. After all, if he didn't speak up against Sombra, how would he speak out against Princess Celestia?

"So where do you think the Princesses will target the Harmony Cannon next?" Long Lilly, pink mane flowing past her right eye, asked as he sighed and gazed at her. "Personally, I'm hoping for Amsterdam. I lost a good friend in that battle, and I've been hoping for a chance to go back and raze it more to the ground than we did."

"I don't know. Does it even matter? Even after the first use of it, the humans refused to surrender or do anything," Diamond Watch pointed out.

"Hey, if they want to all die in futility, I'm not going to cry tears for them," Lone Lilly snorted.
Before Diamond could say anything, there was a knock on the door.

"Muffin Delivery!"

This made the two guards pause and tilt their heads at each other.

"I didn't order muffins. Did you?"

"No, but we'll see what this is about."

Diamond Watch got up from his seat and walked over to the door. He pressed the button to open, only to see a purple hoof come right for his face and knock him off his hooves to the ground, where he was stone-cold knocked out. Lone Lilly got up in shock and readied her horn, but Dinky was faster and hit her with a powerful blast of magic that also knocked her back and sent her into unconsciousness.

Lyra and Carrot Top were already getting the bodies and placing them into the nearby closet as The Doctor, Derpy, Fluttershy, and Flash Sentry walked over to the screens the two guards were previously looking at.

"Muffin delivery? Really?" Flash Sentry asked with a deadpan expression.

"What? It worked, right?" Derpy pointed out with a smile.

"I'm still surprised the TARDIS didn't get picked up by the Beholder Eyes," Fluttershy said with surprise as she looked at the crystal screen where they had landed in the blue box, only to not see it there.

"Yes, well, after getting constantly watched on by UNIT, Torchwood, and so many other agencies in the past, I finally put in a little gizmo that lets the TARDIS get ignored in any sort of visualized medium including those around it in a thirty feet radius," The Doctor said as he took his Sonic Screwdriver and started waving it around the crystal screens. After a few seconds, they all went static before returning to their proper settings. Looking at the glowing end, The Doctor nodded. "Excellent. I have control of all the Beholder Eyes."

"So where is the Harmony Canon?" Lyra asked, looking at them intently.

"It should still be in the same place that Twilight showed it to us last time," Spike said with a growl. Sure enough, the Doctor made it appear on one of the screens. Naturally, there were a lot of guards and scientists working around it.

"Look at the size of that thing," Carrot Top whispered in awe. "Are you sure this plan is going to work, Doctor?"

"Please, I've taken down bigger weapons of mass destruction than this," The Doctor scoffed as he changed a few screens with his screwdriver, and various rooms appeared until he found what he was looking for. One was a potion lab filled with elixirs and ingredients, and the other was what appeared to be a storage for various magical crystals from the Empire in multiple quantities.

"Alright, found what we are looking for," The Doctor said as he turned to the group. "For this sabotage to work, we will need the chemicals and crystals I told you about. You have the notes?"

Lyra and Flash Sentry nodded and showed their lists from their saddle bags.

"Alright, then, we stick with the plan. Discord's diversion is going to occur soon. I'll be here monitoring everypony and giving instructions. You all have your communicators?" The group all pointed to their ears where electronic ear pieces were placed, modified for their ear shapes, with small mikes that could be used for communication. "Excellent. Then our first group shall consist of."

"Applejack, Rainbow Dash, and Rarity?!" Spike shouted in surprise, which made everyone stare at him.

"Um, I don't think the former Elements of Harmony are in our group, Spike," Dinky pointed out but soon turned to where Spike was staring and gasped. "What the hay?!"

The entire group stared as one of the screens showed the prison section containing the said three Elements of Harmony as prisoners. Rainbow Dash was doing push-ups with fury on her face while Rarity was sitting on her bed, looking almost in tears, as Applejack was staring up at the ceiling while lying on her bed.

"What are they doing there?" Fluttershy asked with worry.

"...Whatever it is, I doubt it's good," The Doctor said with a sigh. "Alright, side plan. We also have to save them."

"What?!" Lyra shouted in disbelief. "Are you kidding me?! No offense, Doctor, but why should we save them after everything they've done?!"

"And what have they done, Lyra?" The Doctor asked calmly.

"They teleported us from our world and doomed our home-"

"Celestia tricked everypony into doing that. If they are to blame for being allowed for that to happen, Fluttershy should also be condemned," The Doctor said, making the shy pegasus wince and hide behind her mane.

"They supported the war. Isn't that bad enough?" Dinky asked as she also looked furious about the idea of saving them.

"So did Big Macintosh, but we changed his mind, didn't we?" The Doctor said as he shook his head. "Many who supported the war are now against it because they've finally had their eyes opened. Princess Celestia created an entire cult of personality. She has manipulated everypony into living in a world of fear of anything outside of Equestrian culture because she is afraid of being unable to control things she cannot understand or order around.

Yes, they supported the war, but how much was based on lies and manipulation rather than thinking for themselves? Sometimes the villains need to see how they are villains in the first place to earn their redemption."

"They let their Elements be used for the Harmony Cannon," Flash Sentry said with a snarl. "Millions are dead because of them. They have blood on their hooves."

"So do I," The Doctor said coldly, making the others stare at him. "Do you really think I am a saint? For every world that praises me, some curse me. Most live in fear of me because of what I am capable of. Believe me, if I really, really, really wanted to, I could destroy the entire nation of Equestria or even this entire planet in several ways. I have burned empires, destroyed planets, ended the existence of numerous aliens, and been in wars that make this pale in comparison. One that nearly ended the existence of all reality and time itself.

I have so many sins that I'll never be able to wash my hands clean of them, but I still do it not for redemption but to make sure nobody else has to go through what I do to make the galaxy safe. I will seek to end things with as little loss as possible. Always. But if the chips are down, and mercy is not an option, then you best hope the damage is as minimal as possible."

Nopony said a word. And honestly, they couldn't.

A few of them even stepped back in shock. They saw the Doctor as a paragon of virtue for so long, but if what he was saying was true. It only made them more confused. This stallion had done so much good in his efforts to save the lives of so many, both human, pony, and others. And yet, he here was confessing to having done more genocide than even the worst of humanity and Equestria's monsters.

"So why save them?" Derpy whispered, not out of anger but curiosity.

"...Because it's the kind thing to do," Fluttershy said with a heavy sigh as everypony looked at her. She gave a sad smile to the others. "I...I want to save them. I know they've done so many horrible things. I know they've made mistakes...but... they're my friends. Even if they curse, hate, or look at me with shame, deep down, I still love them. And even if I didn't, I'd still do it. Because it's the right thing to do."


"Look at them," The Doctor said as he pointed to them. "Do those faces look like the expression of heartless monsters? No, I see regret, sorrow, and shame. I see three mares who feel hopeless and lost. Awakened from their darkness and searching for light.

I'm not saying forgive them for what they have done. It takes more than regret to make things right again; it can be a starting point. One where they can start making that path to do the right thing again.

They were once good ponies. Heroes and saviors. They had been decent folk who would do anything to help others and were lost in darkness by the actions of a mare who twisted them. They're not just asking someone to help free them from their prisons. They are also asking for someone to help them free them from themselves. From the monsters they became. And I can't ignore anyone who needs that kind of help...

...Can you?"

Everypony stared at each other before Derpy smiled brightly and stepped forward. "Okay! Let's do it!"

"Wait, seriously, Mom?" Dinky asked in surprise.

"Yup! I trust the Doctor and Fluttershy! So let's do it!" Derpy said with a big smile to her daughter.

Dinky was quiet at first before shaking her head. "Sometimes, Mom, you are too nice for your own good. But that's what makes you the mother I love and respect. I'm in."

"...I guess we might as well," Lyra sighed heavily. "I don't like it, but I get it. Equestria was once about helping others when they needed it the most. We can't let them rot in prison as victims of Celestia's madness, even if they were once a part of it."

"Plus, it would deny the Princesses the other Elements, and if we get them to turn traitor, it will only look bad for them," Flash Sentry said with a shrug.

"...They're my friends too," Spike answered as he gripped his hand. "Those girls... they're my sisters in all but blood. We've been through too much for me to completely abandon them. If they really are sorry for what they've done... if they are the girls I grew to love for all those years, then we have to rescue them."

Carrot Top sighed. "For the record, I think this is a bad idea. But I guess I'll trust you, Doc."
Fluttershy's eyes turned to steel, and she nodded. "Let's do it."

"Right! Here's the plan!" The Doctor said as he gathered them around.


When Fort Obsidian was refurbished to suit the needs of Princess Twilight’s project of the Harmony Cannon, she wanted to guarantee that it had all the necessary protections.

To that end, she ensured that there were multiple watch stations around the fort. There were three rings of watch towers starting from three miles, seven miles, and ten miles. All were given top-of-the-line radio equipment to report any disturbance or attack that would alert all the other watch towers, the main base, and The Crystal Empire so that reinforcements could be sent.

Since they were formed, none of them had since reported anything suspicious or dangerous. However, today would be the day when all Hell broke loose. One of the far outer ring watch stations was huddling up and trying to stay warm as the winter weather was colder and more furious than usual.

Most of the group gathered for lunch save for one lone Earth Pony who was keeping watch in their station’s tower while wrapped in three blankets with frost on them. Shivering, he kept still a lookout at the snow field in the distance of nothing, only to notice that a large storm cloud was forming and heading straight for them.

At first, he grumbled at the prospect of it suddenly getting colder to the point that he was thinking of getting two more blankets, only to pause upon noticing a storm on the horizon in the distance.

Having been born into a half-pegasus and half-earth pony family living in Cloudsdale, he had known much about weather growing up. Curious, he grabbed his telescope and lifted it to his eyes only to see the storm approaching. The clouds looked a lot lower than usual. Clouds were not supposed to be that low, even during a snowstorm. Far closer than any typical storm could commonly do so. There was also an extensive line of wispy figures in front of it. Almost ghost-like.

Something inside his gut told him that this was not an ordinary storm at all, and as it got closer and closer, the figures leading it became more apparent. When he saw what they were with a clear eye, he felt the telescope drop out of his hooves in utter shock. What he was seeing was impossible. It had to be. They were extinct. They all died a thousand or so years ago. Even if they weren’t all dead, they couldn’t possibly be here on this planet.

Yet, upon grabbing his telescope and seeing them coming so close that they were now just a few feet away, he couldn’t deny it anymore. He rushed to the emergency radio and began screaming in it just as the first flurry of ice and snow began to freeze the borders of the station, and chaos erupted from it.

Along with the shilling spectral shrieks of a long-time enemy of ponykind...


"Absolutely not!" Cadence screamed as she threw her goblet of wine against the wall with her magic.

When she heard that Princess Celestia and Twilight were coming over, Cadence didn't even bother preparing herself for their visit. She didn't care much about anything since her daughter fled to the humans. That even extended to her fellow Princesses to the point where she barely wanted to deal with them.

They would like to talk about the war, but as far as Cadence was concerned, it was nothing compared to finding her daughter and bringing her home. She let them come into her home only because she had to play politely with them both, but now Cadence wished she tossed them out and let them land on their flanks.

"Cadence, please," Princess Celestia tried to speak, but Cadence glared at her and interrupted with bitterness in her tone.

"Don't Cadence me, Celestia! You actually want to use the Harmony Cannon again after what it did last time?! Especially since my daughter is now in the human lands and could potentially be killed by it?! Are you bucking insane?!" Cadence screamed with fury.

"Cadence, we aren't going to hurt Flurry Heart! We're not planning to target Geneva!" Celestia said in surprise.

"And what's to stop some grieving humans from taking their revenge on her? Even if Flurry Heart is a child, I cannot risk her life being in danger by our actions!" Cadence argued before grumbling. "Where do you plan on firing it anyway?"

"We're going to aim for Japan, where Shining Armor was killed, along with any other Asian nations like Korea, China, Mongolia, Vietnam, and so forth," Celestia explained. "They have some of the highest concentrations of populated masses. If we can use the Harmony Cannon there, then maybe-"

"Oh, don't you dare bring my husband into this! Let alone convince me that committing more mass murder will solve this stupid war! A war that has cost us everything because of your stupid pride!" Cadence yelled in disgust.

"Mi Amore Cadenza!" Celestia shouted sternly. "You are a princess of Equestria and my adopted niece! You are not supposed to act like this!"

"Do you really think I care anymore about what you think?" Cadence muttered as she shook her head and looked out the window of her room. "Celestia. We've been fighting this war for four years. I believed in it and thought we were doing the right thing. But ever since losing Shining... Ever since we used the Harmony Cannon... seeing so many of my own subjects turn against me, and everypony in Equestria so divided that we're on the cusp of civil war... The war against the humans seems so... pointless."

"It's not pointless, Cadence," Twilight stated as she softly walked over to her sister-in-law and put a wing around her back. "It's for our survival. The humans will never let us live in peace after everything that's happened. Even if they don't destroy Equestria, they will not see any of us alicorns live. Everything we treasure is at risk of being lost because, ever since Osaka, we have been losing this war. We only have two options left to win. Either we destroy them so much they give up and surrender, or we annihilate them all. The only thing that matters is our survival."

"So instead of saving them all like we originally intended, we're now killing them all," Cadence snorted as she glared at Twilight. "What makes us different from all the so-called villains we used to defeat, Twilight? Because I hear from my subjects that I have become just as bad or worse than King Sombra himself. And I can't help but think they are right after what we've done."

"Cadence, they are just-"

"My daughter has left because of what we have done," Cadence sobbed. She covered her eyes with her hooves in shame while weeping. "I'm such a horrible mother. I was so occupied with Shining's death that I didn't see how much pain she was in. I knew she hated the war and the use of the Harmony Cannon, but I still ignored her feelings. She left me because she believes we're in the wrong, and I know Flurry Heart. She would never have done this unless she was sure, especially since humanity killed her father."

Wiping the tears from her eyes, Cadence glared at the two. "How can I continue this war knowing that I will have to fight my own daughter?"

"Cadence-" Twilight tried to say something, but Cadence lifted her hoof and shook her head.

"No, Twilight. I love you. You are my sister in all but blood. And you, Auntie Celestia, are like a second mother to me, but I have to finally listen to my own heart instead of listening to you two for the sake of my daughter and my kingdom," Cadence muttered as she took a deep breath and stood tall. "I will do what I should have done long ago and listen to my subjects. As of this moment, I decree that the Crystal Empire will no longer have any part in the war against humanity, and we will seek a ceasefire if not a peaceful means of negotiations going forward."

There were surprised looks on both Celestia and Twilight as they stared at Cadence, who glared at them with such defiance that it made them wince. Both were struggling to come to the concept of what their fellow Princess just said.

After a long moment of silence, Princess Celestia just sighed and closed her eyes. "Cadence, we can't fight this war without the Crystal Empire. Half of our means of making war and living are due to the magical crystals your nation provides. Your subjects need our food and resources as well. If you do this-"

"We'll survive," Princess Cadence stated firmly. "The Crystal Empire will find a way to survive, but it will not do so by continuing to fight a war we have no hope of winning."

Twilight snarled and snapped at Cadence. "So that's it?! You want to give up?! Just like that?! Don't you see that we must stay together to win, Cadence?! Are you really going to let me and Princess Celestia, your family, fight this war on our own?! Let The Doctor win?! My brother's death go unavenged?! My friends have left me, Spike left me, Flash left me, and now you?! IS EVERYPONY I LOVE GOING TO KEEP BETRAYING ME?!"

Cadence just stared at Twilight and shook her head. "Twilight, the war is over. We lost. Even if you were to kill every human in the world, we would still lose because we would lose ourselves. We're no longer the harmonious ponies I once was proud to call myself as one. What we are...I don't even know, but the past me would have looked at us and seen us no different from Chrysalis and her changelings."

She then towered over a glaring Twilight and gritted her teeth. "And don't you bucking dare bring Shining Armor into this, Twilight. He's dead. Nothing you do will bring him back, and it's time we both recognized that. Shining died because of The Doctor and humanity, but in the end, we started this war, and he wouldn't be dead if we didn't do so in the first place. I don't know if we could have lived with humanity in peace, but at least we wouldn't be trying to obliterate each other out of pure hatred."

Then she pointed at Twilight. "And as for everypony betraying you? Who betrayed who, Twilight? Flash betrayed you because he stuck to his principles. Something we all forgot.

Your friends left you because you refused to take their feelings into account of what happened with the Harmony Cannon and Pinkie's death. And I overheard what you said to Spike in your argument. Quite frankly, I am ashamed of you for that one. You can hate me all you want, Twilight, but at the end of the day, I cannot do this anymore.

Call me a traitor.

Call me a coward.

Even refuse to call me a sister ever again. But I am done. I want an end to this war and my daughter to be safe and sound. Even if I must surrender my position or face humanity in whatever trial they want out of me, I don't care. So long as my daughter is safe and sound and my subjects have a future outside of war, I'll live with that."

"...You would really rather see Equestria fall than help us?" Twilight whispered with bitterness and spite.

"Equestria has already fallen, Twilight," Cadence whispered as she turned around to face the window of her kingdom. "If you cannot see it? Then I sadly have only one thing left to say to you.

She took a deep breath, turned to her sister-in-law, and said, "You have a lot to think about."

Twilight's eyes widened upon hearing this, and she began to shake. Her one good eye began to twitch, and flames began to emit from her mane. Twilight's horn started glowing with magic as Cadence bit her lip and slowly prepared herself for a fight until Princess Celestia spoke.

"Enough." The young alicorns stopped but continued to gaze at each other as Celestia stood between them. "If this is what you want, Cadence, then so be it. But as of this moment, you and the rest of the Crystal Empire are no longer recognized as part of the greater whole of Equestria. You are on your own as you wish, but I hope you know I am disappointed in you."

"Funny," Cadence growled. "I feel the same way with you both. Now get out of my kingdom."

Before any of the three could say anything else, the door was slammed open as a pale-faced and gasping Crystal Guard rushed inside as all three alicorns stared at him. He quickly straightened up and saluted, "Your majesties! Message from Fort Obsidian! It's under attack!"

"What?!" Twilight shouted with worry and rage. Wings flaring out, she demanded, "Who is it?! Humanity?! The Underground Railroad?! The Doctor?!"

"It's... It's..."


“Wendigos! The Wendigos have returned!”

Author's Note:

A lot of those who never changed sides before seem to be now huh? It's interesting to write.

Special thanks to zelkova48 for helping me edit this.

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