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

Regeneration - Rated Ponystar



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

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Regeneration Part 13

“We’re capable of the most incredible change. We can evolve while still staying true to who we are. We can honor who we’ve been and choose who we want to be next. Now’s your chance.”

-The Thirteenth Doctor

“You may disguise your features but you can never disguise your intent.”

-The Fifth Doctor

+}{+

The knowledge that the Wendigos had returned had nearly sent the palace into a panic until Princess Celestia and Cadence called for order.

Even though Cadence had all but officially declared secession from Equestria, even she knew that she needed Twilight and Celestia’s help in dealing with Equestria’s oldest enemies. They were just as much a threat to her subjects as they were to theirs, and so a truce was called between their arguments to focus on dealing with the wind demons.

Everypony thought the Wendios died out long ago since nopony had seen them since the Foundation of Equestria. There were rumors that they never really died, only hiding away and waiting for the right time to strike again.

Well, they couldn’t have picked a better time.

Equestria had never been more divided than it was now, and the Fires of Friendship that had driven them back would not save them this time. Not when so many ponies hated each other and blamed each other for either being traitors or zealots in a war already tearing them apart. And with the Elements of Harmony either turncoat, dead, or divided, they couldn’t use them to help protect them from the Wendigos. The Crystal Heart would do its job, but Cadence wouldn’t take any chances.

The three alicorns were all armored up, and Cadence ordered the army to prepare for defense while a division followed her to see the Wendigos firsthoof to assess their actions. Civilians were to be put into bunkers, and the emergency heating generator crystals were to stand by if their icy cold weather passed the shielding. Canterlot was already being warned, but Cadence practically had to force Celestia to issue a warning to all ponies regardless of their loyalty.

Teleporting to the third line of defense and observation for Fort Obsidian as they could, Cadence winced as the blistering wind and snow nearly flooded her vision. The shrieking cries of spirits were everywhere, she looked up to see the ghastly horses flying around. “Damn, they really have returned.”

“We cannot let them go further than this! Everypony, prepare for battle! Use fire spells and heat crystals to give fire elements to your weapons! Let us go!” Princess Celestia ordered as she lit up her horn and unleashed a massive burst of sunlight from her horn. The Wendigos shrieked, but it seemed to do little to stop them save for scattering them.

Archers aimed their arrows and lit them with their magic before firing them at the spirits. They went through the astral creatures, who only responded by blowing them with more wind and cold.

Cadence crafted a shield around her as Twilight replied with a powerful tornado that sucked up the current and blew it back at them. The spirits temporarily disappeared before reappearing and started scattering around, causing a thick misty hail.

Summoning her two blades, Cadence charged at one and tried slicing it, but it went right through them as well as her body which made her shiver at the touch. “Damn it, how are we supposed to fight ghosts?!”

“Just keep them distracted! We’ll think of something!” Twilight shouted by her side as she unleashed fire spell after fire spell. Celestia was already shining like a miniature sun and unleashing waves of solar energy at the creatures who would disappear before reappearing again.

“Hope you think of something fast, Twilight, or we’ll be popsicles out here!”

+}{+

Lyra had to admit, getting the crystals and chemicals The Doctor needed was a lot easier now that most of the guards were called out of the fort to deal with the situation outside.

Once the call went out for most of the guards to head out and assist with the defenses, it was just a matter of dressing up as staff members and walking around with their heads down. Thankfully, a lot of the staff was hiding or running around panicking so they could roam around without being noticed too much.

Derpy said she would find the chemicals leaving Lyra and Carrot Top to get the crystals. Their room was almost like an ammo supply deposit with numerous crystals labeled, stored, and sealed in proper containers with a number counter for how many. Some ranged from tiny crystals the size of thumbtacks to ones the size of Princess Celestia.

There were six that The Doctor required, and all of them were about the size of a full-grown unicorn horn. Carrot Top found a large empty box that Lyra levitated with her horn and started to carry it around as they searched the containers for the right crystals based on the list The Doctor gave them.

"So, what are you going to do after this?" Carrot Top asked as Lyra put in a swirling purple crystal while the former looked through a section of ones the size of her head.

"What do you mean?" Lyra asked the carrot farmer, who shrugged.

"After the war? I mean, the way things are going, it looks like the war will end soon with how bad things have become for Equestria. I can't see it holding or even existing in the next few months whether the Doctor does something or not," Carrot Top said with a sigh. "What do you think happens next after that? Obviously, the U.N. will occupy Equestria for several years, and a new government will be built, but what about us?"

"...I haven't thought about that," Lyra admitted as she lowered her head. "Honestly, I don't know. I can't go back to Equestria. I got nothing left there."

"Same," Carrot Top muttered as she picked up a sparkling blue crystal and put it in the box. "My parents were outside of Equestria when we teleported her. Meaning they're....d-d-dead...all I got is Derpy and Dinky, so I'm with them in whatever they want to do."

"Yeah, my parents made it clear they never wanted to see me again the last time we spoke. I don't even know if they're still alive at this point," Lyra admitted but shrugged. Truth be told, she never really was close to her parents. They were always so busy with work that they never really had a close bond. "My old friendships are gone too. Bon-Bon... she hates me, so that's out."

"Were you two a couple?" Carrot Top asked, which made Lyra blush and nearly lose mental control over her magic. "Sorry, but there was always a bet in Ponyville on whether or not you two were together or had feelings for each other. I mean, it was kind of obvious that Bon-Bon liked you-"

"Wait, really?" Lyra asked in shock.

"Seriously? Girl, that mare was so into you that it was as obvious as Spike's crush on Rarity," Carrot Top laughed, which made Lyra cover her face in embarrassment. "But seriously, did you feel the same?”

"I...I admit I found Bon-Bon attractive, but I was more into guys than girls. It never became anything more than friendship between us," Lyra admitted while rubbing the back of her neck. "Maybe if things were different, I would have fallen in love with her, but I only saw her as a close friend."

Bon-Bon had been Lyra's first true friend in quite a while. As she got older, she grew apart from her old friends like Twilight, Moon Dancer, Minuette, and so forth. When Lyra decided to move to Ponyville, she found Bon-Bon as a roommate, and something clicked between them that made her want to stay. It was like finding the other half of her that she could do other things with, and Lyra always assumed they were just best friends.

But what if it was more?

What if she fell in love with Bon-Bon?

If so, when could it have happened?

What would their future have been like?

"What about The Doctor?" Carrot Top asked with a grin. "You two are close. I mean, you've known him for a while now. Any interest in him?"

Sticking out her tongue, Lyra said, "Ugh, no! If you ignore how he looks, he's way too old and weird to be a boyfriend. He's just my friend. I care about him and all, but not like that. We're close, but not that close."

When those who had supported Lyra's views about humanity started getting arrested, she felt like she was all alone in the universe. There were no friends or family besides her, and she was hated by many while being a wanted criminal on the run. Then The Doctor saved her, showed her so much, and helped her achieve her desire to save humanity.

The moment she met him and he offered his hoof to her on that day they met, something inside Lyra knew that she could trust him.

It was always like that around The Doctor.

Even now, after all their time together, that trust was still there. You could look at The Doctor and believe him when he says he'll carry you back to the ends of time and space.

He wanted to save the world, and Lyra thought he could do it. He really was amazing in what he did, and all his actions were so noble and brave that he was like those fabled heroes she used to read about as a filly. Yes, he made mistakes and occasionally showed a dark side that frightened her, but Lyra knew The Doctor would never hurt her or anyone close to him. He was a great stallion, and she would always trust him no matter what.

"Yeah, same here," Carrot Top said before chuckling. "It's funny. We've only been together briefly, but it feels like a lifetime already. I know he said we're free to leave whenever we want, but honestly? I kinda like traveling with him. He's got this... energy..."

"That makes you want to follow him, knowing everything will be okay? Yeah, I get it," Lyra said with a sigh. She smiled warmly and thought about her beginning days with the strange pony in a blue box. "To be honest, I think I want to travel with him forever. Or at least for a very long time. I've always wanted to be an adventurer. I moved out of Canterlot because I wanted to be a traveling minstrel on the road. Seeing new places and meeting new folks. I only stayed in Ponyville because of Bon-Bon."

"Well, we do have a new universe to explore. Maybe we'll find more interesting adventures along the way," Carrot Top suggested as they got the last of the crystals and left the room. "What do you think of his theory of the Princess being mind controlled?"

“I don’t know. But if she is being mind controlled what does that mean overall?” Lyra asked as she scrunched her face in thought. “Is Princess Celestia really in control of her own actions? Or was she just pushed and always had this darkness inside of her? Is she even working with this person controlling her? I don’t know but it doesn’t matter. What matters is that we stop this war no matter what regardless of who really is pulling the strings.”

BOOM!

The girls yelped as they turned down the hall where the room of chemicals that Derpy went into suddenly exploded, and smoke was coming out of it along with fire alarms. Whistling to herself, Derpy walked out with a number of vials in her saddlebags while covered in soot. Looking at both girls with her crossed eyes, she smiled at them. "Hi, girls. I got everything."

"...Derpy, what happened in there?" Carrot Top asked, pointing to the burning room.

Turning around, Derpy looked at the room she came out of before turning back to the others and giving a sheepish smile. "Oh, that. I accidentally knocked this glowing red thing into this glowing blue thing, and it made this glowing purple thing, and then there was a big explosion. My bad."

"...I would say that I'm surprised, but I'm not," Lyra sighed as Carrot Top facehoofed.

***

Applejack had always held a belief that if you worked hard and stayed true to a good cause that you believed in, you would get good things in return.

Applejack worked hard to keep her farm afloat with the rest of her family after her parents died. There were some rough months here and there, but overall her dedication to keeping her family farm and their legacy going was rewarded with prosperity. She performed the same thing when she did her duty as an Element of Harmony for the betterment of her nation and believed in the cause of the war when they came to Earth to help humanity find a better path.

And now that hard work and devotion were bucked right back into her face.

Applejack was stubborn to ever admit she was wrong. Everypony knew it, including herself. Laying on a prison bed as a prisoner was her reward for making the bad choices in her life recently. Karma had come, and it was making it clear to Applejack that she bucked up.

The worst part of all this was that her imprisonment was done by a former friend that Applejack had greatly respected and the very Princess she worshiped and trusted her entire life.

Well, that proved that all the hard work and faith in the world was worth nothing if it was all going to crap in your face by those who abused it. Applejack sacrificed everything for Equestria because she believed in its leaders, and the leaders betrayed her at the end of the day.

The Princesses betrayed her.

Her goddesses betrayed her.

A lot of rage was going through Applejack despite her cold, stoic expression. Anger at the fact that she wasted everything on a cause that ultimately didn't care about her and ruined her family.

Big Macintosh, Apple Bloom, and Sugar Belle were safe, at least, but they could never come to Equestria again. Mostly because Applejack doubted there were no more Sweet Apple Acres to go home to.

She had no doubt the farm was already being occupied and nationalized by the crown. Even after all the money, donations, taxes, and food the Apple family had donated to it, that wasn't enough, and they would bleed it dry. The legacy of four generations of Apples was all but gone.

All that effort, time, sweat, and hard work was wasted.

And the worst of it all was part of it was thanks to Twilight Sparkle. Twilight was once a friend. Buck, she was somepony Applejack considered part of the family and treated her like a sister. And Twilight just stabbed her in the back like this.

If Applejack knew that this was how it would end, she would have snapped that bucking unicorn's neck with a buck to the face the first day they met. Even if it would mean eternal night forever by Nightmare Moon.

Of course, all that anger was pointless. She was trapped here with Rainbow Dash and Rarity and would be used against her will to cause more death and destruction.

‘Is this my punishment? Everythin' Ah did comin' back to bite mah flank?’ She thought glumly to herself.

She didn't know. And deep down, Applejack didn't care. She was just tired of everything. The fighting, the war, the chaos, the death, and so forth. She just wished she could just run away from it all.

Applejack heard the prison doors open and sighed while wondering if it was their new jailors or their meal being served. Then, she heard a voice she hadn't heard in years.

"Girls?"

Applejack's eyes snapped open, and she ran to the cell barrier as fast as her hooves could carry. She wasn't the only one, as Rainbow Dash and Rarity were doing the same thing, only with tears in their eyes. Applejack was too shocked to do the same thing, but her mouth dropped all the way down, and her heart beat rapidly in her chest. “F-F-Fluttershy?”

It was her. It really was her. Nearly a year since she left, and suddenly their friend, who they once cursed as a traitor, was there smiling at them with warm eyes. Beside her were Dinky Hooves and Flash Sentry, who stood there stoic and unmoving.

"F-F-Fluttershy, is that really you, Darling?!" Rarity almost asked in desperation.

"Yes, girls. It's me. We've come to get you out of here and sabotage the Harmony Cannon," Fluttershy said as she nodded. Flash Sentry walked over to the lever holding their barriers up before pushing it down. In a split second, Applejack found herself outside her prison, free as a bird.

Rainbow Dash was the first to rush out and wrapped her hooves around Fluttershy's neck, sobbing into her shoulder as the yellow pegasus wrapped her wings around her fillyhood friend and nuzzled her cheeks. Rainbow Dash was muttering between the gasps and the sobs, "I'm... I'm...so-s-sorry... I'm so...s-s-sorry!"

"Rainbow, it's okay," Fluttershy whispered, stroking her mane.

"No it's not! You were right! Lyra was right! I can't believe I was so stupid! I don't deserve to be a hero! Or your friend or anything! I'm... I'm..." Rainbow Dash weakly gasped before sobbing again, which made Applejack just lower her head in shame upon hearing Dash's words. Words she wanted to say but found it too painful to mutter. All she could do was let a tear drip down her cheek.

"What Dash means to say is...we were wrong...all of us..." Rarity said as she wiped her eyes. "I know this doesn't mean much, but we're so sorry, Fluttershy."

"You think that's enough?" Dinky said, glaring at them. "You realize that even if you are sorry, it will take more than that to compensate for what you've done."

"We know," Applejack said, narrowing her eyes at the younger mare. "But we'll do whatever it takes. The alicorns are the baddies here, and we're willin' to fight them now."

"Are you sure? You would be working with humans to do this," Flash Sentry pointed out. "Humans that you helped kill in the millions with the Elements."

The three winced at this and lowered their heads in shame. However, Fluttershy turned to the two and glared at them, "Flash. Dinky. Enough. This isn't the time nor the place for this. We need to get back to The Doctor."

"Are you seriously going to forgive them for everything they played a part in?" Flash Sentry asked in disbelief and anger as he glared again at them. "Even if they are sorry for it, and even if they regret it, they played a role in the deaths of millions of innocent lives thanks to giving Twilight their Elements for the Harmony Cannon and causing so much destruction."

"...We know," Applejack said as she looked up and stared back at Flash. "Yer right. We are murderers. Even if none of us wanted it as bad as it was, it doesn't change the fact we willingly gave our Elements to Twilight after she told us what the cannon was. To be honest, Ah didn't think much of it. It was just humans. Our enemies. The bad guys that Ah hated and feared. What wrong could it be?"

Applejack then sighed heavily and shook her head, looking ten years older. "Then, when Ah heard the death count, Ah suddenly felt the weighted burden of taking lives on mah back. Then Ah looked up all the deaths in the war, human and pony, which only doubled it. Ah never played any role in the war other than keepin' spirits up and feedin' the troops, but when Ah finally took action and took human lives...buck Ah couldn't look at the mirror and see who Ah was. A murderer. A damn bucking murderer. It only took Pinkie's death for me to see just how far Ah'd fallen. How we all had fallen."

She really wished Pinkie Pie was here. Heaven knows Applejack would do anything to hear the party pony just say something positive to make her have some hope for them all.

"However, that doesn't mean Ah won't make things right," Applejack said as she took a deep breath and glared at Flash and Dinky. "We bucked up. None of us will deny that. But Ah want to make it right or at least try. Even if Ah never succeed. Even if Ah'm never forgiven. Even if Ah'm going to Hell when Ah die, I still want to make it right. I want to stop this war. Ah want to do the right thing just once. Even if there is no reward for it, Ah can at least die knowin' that Ah tried in the end."

"Me too," Rarity said while nodding her head. "It's not about our reputations. It's about fixing our mistakes. Even if we can't succeed, we want to try."

"We want to be heroes again... even if we're cursed as villains for the rest of our lives," Rainbow Dash whispered as she separated from Fluttershy and smiled softly at her. "We want to be the ponies we once were before we got twisted. I want to be the Rainbow Dash that fought beside her best friends to save the day. Especially with you, Fluttershy. I...I missed you..."

"...I missed you too," Fluttershy whispered as she hugged Rainbow Dash, and the other Elements soon joined in the hug. "I missed you all."

Dinky and Flash looked at each other, their expression softening somewhat before the former sighed. "Alright, we get it. But let's deal with this after we escape from this place. Let's meet up with The Doctor and go from there."

"Yeah, he's probably already in the room of the Harmony Cannon preparing to destroy it right now," Flash Sentry said with a grin.

"Wait, how could he get in there just like that?" Rarity asked in confusion.

"The Doctor said he had a plan. Something about a paper?"

+}{+

"As you can see by my credentials, I am more than qualified for the job," The Doctor said as he held out his paper to the guard in the main room where the Harmony Cannon was being worked on by engineers and scientists.

The unicorn guard stared at it with confusion before asking, "I still didn't get any notice that you were coming. Why does Princess Twilight need an electrician again? A Royal Electrician? For that matter?"

"Well, with the Harmony Cannon being so powerful, it's quite draining for the current geo-crystalic generators that are powering the fort, and we want to make sure that constant testing and use of it will not overpower them and cause them to shut down permanently," The Doctor lied as he put his paper down and smiled. "Therefore, we're going to be preparing to hook up the Harmony Cannon to an electrical power system that will see to it that the power is not only used from an alternate source without risk to the fort's energy systems but possibly make it stronger."

"And you need us all out because?"

"I'll be working with wires and electrical currents. Don't want to shock anyone by accident. My assistants will help me shortly after they get my tools. Don't worry. It's all with Princess Twilight's permission."

The guard shrugged and nodded. "Well, your papers looked legit. So who am I to argue? I'll get everypony moving in a few minutes."

The Doctor nodded as the guard went about rounding everypony up to explain the situation. Once they all exited from the various doorways, he kissed the folded paper wallet in his hooves. "Psychic paper. Always useful."

"Hey, Doctor!" Turning around, The Doctor saw Lyra, Carrot Top, and Derpy Hooves entering the room with the crystals he requested in a box they were carrying while Derpy took off her saddlebags and presented them to the stallion. "We got everything you wanted!"

"Fantastic," The Doctor said as he took the crystals and placed them on a large steel table before getting the vials of chemicals. "This shouldn't take too long. Just gotta make these crystals soaked in the right chemicals, do a little mixing, and make some adjustments with the sonic screwdriver. Once all that's done, we should be ready to sabotage the cannon."

"How long will it take? I mean, I can't imagine Discord can keep distracting the others forever," Lyra pointed out.

"Oh, we got time. So long as nopony figures out what is really going on."

+}{+

“Just how many are there?!” Twilight shouted as she kept firing fire blast after fire blast. It had to have been nearly thirty minutes now, and the Wendigos were still flying around and giving them cold blasts.

“I don’t know, but I’m surprised we lasted this long!” Cadence pointed out as she used her magic to shield her, Twilight, and a few guards from a passing Wendigo. “How many on our side have been frozen?!”

“...None,” Twilight said but with a concerned tone. “Wait a minute. Cadence, do you remember how fast Wendigos can freeze a pony?”

“Um, no. Not really,” Cadence said with confusion.

“The fastest record of a Wendigo freezing a pony, according to the books about their abilities, is 0.7 seconds, while the longest it ever took was 1.96 seconds,” Twilight said as realization began to sink in. “We’ve been fighting these Wendigos for at least twenty or twenty-five minutes, but nopony has been frozen. In fact, the air is mostly just frigid but not chill to the freezing point needed to solidify a living body into ice.”

“...Wait a minute, if they aren’t freezing us, then that means-”

They aren’t real!” Twilight shouted in frustration as she started building up her magic. “This is all an illusion!”

Twilight began to harness as much energy as possible around her like a glowing star. Her eye began to glow white as she flew into the air before scrunching up her body.

With a loud cry of rage, she unleashed her magic in a giant purple shockwave that spread across the entire area. Her dispelling spell instantly made every Wendigo disappear as if they were wiped from existence, and the weather immediately changed from a bad snowstorm into a calm, cloudy one with a minimum amount of snowfall. Soldiers looked around in confusion as their enemies vanished into thin air, and Princess Celestia, panting from the energy she had already used, flew down to Twilight and Cadence.

“W-What happened?! Where are the Wendigos?!” Princess Celestia demanded in confusion.

“There were never any here! This was all an illusion! We’ve been distracted!” Twilight shouted as she began looking around.

“By who?” Cadence asked.

“...Him!” Twilight shouted as she fired a magical bolt straight into a nearby rock which soon warped away and shape changed into a certain draconequus who waved his hand in greeting. “Discord!”

“Hi, Twilight! Sorry, I didn’t phone ahead. My phone bill hasn’t been paid off for the year,” Discord said with a chuckle. “You know how it is with Verizon these days.”

“Wait, if Discord is here, then that means...” Celestia realized in horror.

“It’s The Doctor! He’s here for the Harmony Cannon!” Twilight shouted. “We have to get there!”

“Yeah, not happening. See ya!” Discord said as he snapped his fingers and was gone in a flash.

“Come on! We have to teleport!” Twilight shouted as she and Celestia focused their horns on sending everypony in the vicinity to Fort Obsidian.

However, a split second later, their horns let out a burst of magical backlash that knocked them off their hooves and onto their flanks. Shaking their heads, the two winced upon feeling the whiplash of their magic being blocked against their skulls. “What happened?”

+}{+ Ten Seconds Ago +}{+

Discord appeared back in the security room where Spike was waiting for him. He sighed out of tiredness and said, "Jig is up. They figured it out."

"Good thing we got a backup plan to give us more time," Spike said as he walked to the security station they had arrived in earlier.

The Doctor said there was a chance that the plan would distract most of the guards and any reinforcements would be figured out. Not to mention there was also the chance that Discord would run out of energy before they could destroy the cannon. As such, he made a backup plan to give them more time by hacking the defenses of the Fort through the crystal's complex magical nexus network and activating a specific shield that Twilight had installed.

Twilight was extremely paranoid about anyone coming in and ruining her hard work, and The Doctor was one of them. It reasoned she would create some kind of anti-teleportation shield to prevent him from arriving, but Twilight failed to understand that the TARDIS was more advanced than just simple teleporting. It was far beyond even her brilliant mind's magical and scientific understanding. However, just because it didn't work for the TARDIS doesn't mean it couldn't work for anypony else.

Especially alicorns.

Spike pressed the right crystal button, and it started to glow green to indicate the defenses were up. Turning to Discord, he said, "Come on. We better meet up with the others."

+}{+

"No! No! No!" Twilight screamed in frustration as her hooves pounded the snow. "That bastard! He must have activated Fort Obsidian's Anti-Teleportation Shield! How?! I wrote that complex system myself!"

"Considering he was able to easily hack our communications back in Osaka, I'm honestly not surprised to hear this," Cadence said rather calmly despite her worries. She didn't care if The Doctor was here to destroy the cannon. Honestly, she'd be happy to see it turned to rubble. What Cadence did care about was if Flurry Heart was with him and the rest of his companions.

And no matter what happened, Cadance would not let Twilight or Celestia hurt her daughter if this was true.

"Doesn't matter! We're flying to the Fort now and gathering every bodied soldier we can!" Celestia shouted before her voice suddenly turned into a dark and sickening tone that made everypony freeze up in fear upon hearing it. "THE DOCTOR WILL NOT ESCAPE AND RUIN EVERYTHING!"

“C-C-Celestia?” Cadence whispered in fear as her aunt's tone was unlike anything she had ever heard. It was like hearing nails against a chalkboard while distorted in unholy words. However, Celestia didn't answer and just flew as fast as possible toward the direction of the Fort as if she were a white and yellow comet.

Cadence slowly turned to Twilight and asked, "Y-You h-heard that, right?"

"Y-Y-Yeah," Twilight answered, looking as disturbed and scared as Cadence. "I-I-I've never heard her speak like that before."

"...Something is wrong," Cadence said, an awful feeling growing in her gut. "We have to catch up to her. Can you teleport us as close to the Fort as possible?"

"I can try," Twilight said as she closed her eyes and concentrated before there was a large blink, and both she and Cadence teleported along with the troops.

+}{+

The Doctor used his Sonic Screwdriver one last time before pressing a few buttons on the computer connected to the Harmony Cannon. He was glad that Spike and Discord came when they did, as he needed their help to load the chemical-soaked crystals into the cylinder container used to house the regular Elements of Harmony. The real ones were not going to waste, however, as The Doctor happily asked Derpy to hold them in her saddlebags as they would be safer in their hooves.

It wasn't long after that Dinky, Flash Sentry, and Fluttershy arrived with the formerly imprisoned Rarity, Rainbow Dash, and Applejack, who were soon enveloped by Spike. The five friends all hugged each other with tears in their eyes before noticing the others staring at them. There was a bit of awkward and intense staring for a few minutes until The Doctor coughed into his hoof.

"Well, glad to see we're all caught up and back together again," The Doctor said as he smiled at everyone. "I must say this is a large group, but the TARDIS should be able to hold us all together once we're out of here."

"I take it that you're The Doctor?" Rarity said as she looked at him. "Hmm, not a bad outfit. But it could do with some work."

"You should have seen what he wore in the past," Lyra giggled. "He actually looked like a clown in his sixth outfit."

"Ugh, please don't remind me. I don't know what I was thinking. I blame the suffering from Regeneration effects for that one," The Doctor grumbled as he facehoofed.

"At least it's better than that eleventh outfit you wore. You looked like a geek," Carrot Top said with a snicker.

"Oi, bowties are cool," The Doctor pouted.

"Okay, can we focus here?" Applejack said, getting everyone's attention. "We already know yer here to sabotage the Harmony Cannon. What can we do to help?"

"Oh, there is no need for that!" The Doctor chirped as he pointed at the giant weapon. "Everything's set and ready. Just a few more things to do, and we'll be set."

"You sure that this is going to work, Doctor?" Dinky asked, looking up at the giant monstrosity.

"Positive! I did a similar thing with Gallus and Silverstream on a Rutan ship when they created that giant world-destroying mega railgun that nearly destroyed Equus in the year 4012," The Doctor claimed as he got out his Sonic Screwdriver. "Just need to-"

SMASH!

Everyone turned around to see the front doors get blasted open to pieces as Twilight and Cadence rushed out with armed guards.

"Doctor!" Twilight shouted with rage. "Stop right there!"

"Oh, hello, Princess Twilight. Princess Cadence," The Doctor said passively with a nod. "Was wondering if you were going to get here."

"Doctor! You will not destroy the Harmony Cannon! I will kill you if you try to stop the only weapon we have to survive against mankind!" Twilight cried out as she pointed her horn at The Doctor, who didn't look bothered by this.

Glaringly, Lyra marched in front of The Doctor and shouted back, "If you want to get to him, you have to go through me!"

"Fine! I can't even believe I was friends with you once!" Twilight shouted in disgust.

"And you'll have to go through me too!" Flash Sentry said, marching forward and standing beside Twilight, who winced upon seeing her old boyfriend. "I'm not afraid to stand against you, Twilight."

"Flash..."

"Twilight, I care about you. Even after all this and all you'd done, a part of me still loves and cares about you. And I care about what you have become," Flash Sentry said with a deep sigh. "But I cannot side with you. What you are doing is wrong; deep down, you know this. The mare I fell in love with was smart, brave, kind, and wise. This isn't you. Not at all."

"Y-You don't-"

"Twilight, enough," Spike said as he stepped forward to stand side-by-side with The Doctor. "Are you willing to go so far in your lust for revenge that you'll kill anyone? Even me?"

"S-S-Spike you don't..." Twilight shut her eyes and started to leak tears. "You don't have to...I...just come back and..."

"No, Twilight. I'm not coming back. Not until I have my sister and best friend again," Spike whispered as he solemnly looked at Twilight with pity. "I don't know what's become of you, Twilight, but this isn't you. This war has twisted you, and so has Celestia."

"No! That's a lie! Celestia-"

"Celestia is the liar!" Fluttershy screamed, which surprised all her friends as she huffed and put her hoof down. "Think, Twilight! Look around you! All of us are against you! The friends and family that love you! Do you really think we would betray you without a good reason?! Celestia used us to teleport Equestria all to this world and abandon our own to die! Every creature back home is dead because nopony is there to raise the sun and moon! We started a war of genocide, not peace! All because of her lies!"

"Equestria has always preached about peace and harmony, Twilight," Dinky pointed out as the purple alicorn began to tremble. "What kind of peace is there in invading a planet while causing its people to slowly die out from a giant deadly barrier and forcing them to convert to a form against their will or suffer an agonizing death? What harmony is there in starting a war just because they wanted to be left alone as their own selves and decide their own fate?"

"Why did we not try to find other peaceful ways of coexistence? Why go to the extreme?" Carrot Top said while shaking her head. "Celestia was always going to try to eliminate humanity, Twilight. Be it from the Conversion Bureaus or war itself, Celestia's ultimate goal has always been a world where ponies only exist. Not humans, griffins, dragons, diamond dogs, changelings, or any other creature. Just us."

"But...But..." Twilight was now openly crying as her hair was in a frizzle. Slowly the magic in her horn began to subside.

"Twilight," Applejack said, stepping forward. "We're your friends. We've been through so much, but look at what's happened to us. We're... we're not the same anymore."

"We committed a terrible crime, Twilight," Rarity whispered, closing her eyes in shame. "We've done things our old selves would be ashamed of."

"Pinkie Pie is dead, Twilight," Rainbow Dash pointed out with a heavy tone. "She couldn't accept what she did and ended her life. She knew what we did was wrong but couldn't live with it. The truth is, Twilight, we were all wrong. We're the bad guys. We're the Nightmare Moon, Tirek, Chrysalis, and so forth. We... we're the monsters this time."

"...My brother is dead," Twilight whimpered.

"And how many other brothers are dead from this war, Twilight?" Discord pointed out as he folded his arms. "How many fathers, mothers, sons, daughters, brothers, sisters, and more have died on both sides? A war that has seen nothing but utter hatred, death, and destruction on all sides. You have caused more chaos for one species than I ever did during my evil days. And I never killed anypony in all my years! Tell me, is this the Harmony and Friendship you have fought for all your life? Look around you. All of us, those you once trusted and loved, stand against you. Will you let your admiration of Celestia blind you from the truth until there is nothing left for you to hold onto?"

Twilight couldn't speak. She looked down so lost and conflicted that she looked ready to explode. With a heavy sigh, Cadence slowly walked over, put her wing on Twilight, and made her sister-in-law look up. "Twilight. Enough. It's over."

"...I...I...I..."

"Twilight?" The Doctor said as he stepped forward. "Do you know I was traveling with a mare named Sunny Starscout? She comes from far from your future. Long after you died. Equestria was separated and divided thanks to the manipulations of an evil alicorn named Queen Opaline Arcana. Earth Ponies, Unicorn Ponies, and Pegasus Ponies separated from each other, and all of them lost their magic."

Everyone was staring at The Doctor with wide eyes and shocked upon hearing about such a future. A divided Equestria? Ponies without magic? Did that mean that their efforts would ultimately be undone no matter what?

"But there was this one earth pony who believed in the tales of the old days. When all ponies worked together with Friendship and Harmony. She dreamed of being an alicorn like her precious hero from those days. A hero who stood for what was right by helping others and uniting not just ponies but all creatures with the magic of Friendship. Sunny's faith in her teachings led her to befriend unicorns and pegasi. Together they brought back the Magic of Friendship and made it even stronger."

The Doctor pointed to a stunned Twilight, who collapsed onto her haunches. "That alicorn who she loved, worshiped, and admired so much that she practically acted as her successor? That was you. But she doesn't exist anymore. She never will because Equus is gone. The future that could have been is gone. A future where the entire world united and set out to the stars. I've seen that future, but now it's gone forever. So let me ask you, Twilight. What future would you have preferred? This one? Or the one that never should have been lost in the first place? The future now where war and death linger in the air or the one where Friendship, even if it was lost for a while, never truly died?"

“....aaaaaaAAAAAAAAAAAAAAAAAAAAAHHHHHHHHH!!!!!

Twilight fell to the floor and wailed. She wailed and sobbed. Cried and screamed. Pounding her hooves into the ground repeatedly as her emotions flooded out. In an instant, her friends were all there for her, as were Spike and Cadence. Twilight continued to moan in sorrow and shame as they hugged her, crying beside her as the truth finally pierced through her heart.

"I'M SORRY! I'M SORRY!" Twilight screamed in the middle of her fit. "WHAT HAVE I DONE?!"
Lyra just watched as Twilight, guilt-ridden and full of pain, continued to cry, yet there was no satisfaction on her face. Nopony on the Doctor's side looked satisfied. If anything, it looked painful to watch because, to the surprise of all those inside who thought they hated her, they felt some sympathy deep down for her.

Lyra slowly walked over to The Doctor and whispered, "Do you always manage to get your enemies to give up by talking to them?"

"Not as much as you think. I wish it would happen more often," The Doctor sighed heavily.

"So, we're out of danger now, right?" Lyra asked.

"No, we still need to worry about-"

SMASH!

Everything suddenly went cold as the ceiling above crumbled, and out came a furious alicorn of the sun who screamed with hatred. "DOCTOR!!!"

Discord quickly snapped to The Doctor's side and summoned an energy shield to protect him and the Time Pony as a large blast from Celestia's horn was blocked by it. Princess Celestia soon landed on the ground, growling at The Doctor before turning into a shocked and teary-eyed Twilight. "What are you doing, Twilight?! We need to-"

"You will not speak to her!" Spike shouted as he stood in front of Twilight with a growl. "You will not speak to her or anyone ever again, you lying witch!"

"How dare you! I am-"

"A traitor to everything we stood for!" Lyra shouted with hatred in her tone. "You lied to us all! You manipulated us into leaving our home world and leaving everyone to die! Didn't you! Don't deny it anymore!"

"I did-"

"Celestia!" Cadence shouted as she stood tall and brave. "This is over! Everypony here stands against you! I am, at this moment I am relieving you of your crown! You are under arrest for treason, genocide, murder, lying to the Equestrian people, and many more crimes!"

Everypony was glaring at her, but The Doctor, who was just observing, and Twilight, who just looked away in despair. Even the guards, both Equestrian and Crystal Empire, had finally seemed to know where the wind was blowing and raised their weapons toward Princess Celestia a bit with some reluctance.

"...I can't believe this," Princess Celestia said in disbelief as she looked at them all. "After everything I did! All that I've done to save you?! You do this to me?! The one who saved us all from total destruction?! I prevented our entire race from being extinct! I sacrificed everything for us, and you turn against me?!"

"What are you talking about?! Just shut up and make sense already!" Rainbow Dash screamed.

"THE SUN WAS GOING TO DIE!"

There was a sudden wave of silence as the words that Celestia had said. Some were just confused, while others were just looking in disbelief at each other. Finally, Flash Sentry asked, "W-What are you talking about."

With a heavy sigh, as if a burden had been lifted off her shoulders, Celestia closed her eyes and lowered her head. "You want to know the truth? Fine. For hundreds of years, I have had visions of the sun dying. It was going to explode into one big bang and doom us all. Rivers would be set aflame like lava. Entire nations were wiped out. Our very forests turned to ash. All I saw was death, death, and more death for so many nights I feared I might go mad."

Raising her head up and glaring at everyone, Celestia continued to defend her actions. "I tried so many methods to save the sun! I did! You think I wanted to do this?! We only had a few more years until the sun would die! I didn't want to leave our home and come to this forsaken planet of destitution, but I had no choice! There was no choice but to leave! Yes, I sacrificed all the other life on the planet, but it was them or all of us! I never wanted to kill them all, but I had to do it for the sake of my ponies! That is the burden I carry every day with this crown! Everything I do is for our survival and way of life to flourish! Even if it means lying, manipulating, and even killing, it's worth it for every single foal in Equestria to sleep peacefully at night!"

She pointed her hoof at every single one of them. "Could any of you do what I had to do?! To make that choice?! To choose between annihilation or genocide?! I had to choose the lesser of two evils, so I chose to abandon Equus for our own survival! Call me a monster if you wish but do not call me a traitor! Not when everything I did was for Equestria!"

Nopony said anything for a long time.

Until...

"...So that's how they did." Everyone turned to The Doctor as he slowly stepped forward and stared at Celestia with narrow eyes. "That's how they manipulated you. Of course. Something so simple. Affecting the dreams of someone. Showing them the same images of disaster and destruction repeatedly. Such a thing would slowly corrupt your sanity and weaken your mental defenses so they could start influencing you. As your psyche began to fail, they started to get inside of you personally. I wonder how much of you they took control of and how much they have now?"

"Umm, Doctor? What are you talking about?" Derpy asked, with one eye focused on him and one eye focused on Celestia.

"...Everypony, I know this will be hard to believe, but I've been suspecting this ever since Spike and Flurry Heart told us about the black eyes. I have always wondered why Celestia would do something like this when it goes against all reason, but now I have it," The Doctor growled with such rage that it surprised a few of those who knew him. "We've all been deceived. All of us. Humanity. Equestria. Even myself. We've all been manipulated. This entire war? It was all for someone else's benefit!"

"What are you talking about!" Celestia demanded.

"Celestia," The Doctor said. "You claimed that the sun was going to die. But I am a time traveler and can tell you now that never happens for millions of years! The sun was young and healthy! It doesn't die for a very long time!"

"L-Lies you are-"

"I'm a Time Lord!" The Doctor screamed as he slammed his hoof to the ground in such a loud and haunting tone it made everyone step back with their spines tingling in their backs. "I have seen the birth and death of the universe! I have crossed the boundaries of time and space! I have witnessed empires rise and fall! Watched as species of endless numbers live and die! I have been to countless realms and dimensions beyond the natural state of our own reality! Past, Present, and Future are all available to me! I ride the threads of Fate and turn the wheel of Destiny. I have been to Equus since the day it was first made to the day it breathed its last, and I tell you now, Celestia, that the vision you speak up never happens!"

Suddenly, Celestia went pale as a ghost. Her mouth dropped, and her eyes widened. A look of sudden realization hit not just her but also everyone in the room as they realized The Doctor was right. Everypony, even those who never joined him, learned and were told he was a time traveler. Those who were among his companions had seen it firsthand. If The Doctor was still visiting Equus long after the supposed date of the so-called destruction of the sun was to happen...

Her visions were a lie.

The entire war was a lie.

Everything Celestia had done was for nothing because what she feared would never come to pass.

Which meant that their entire involvement on Earth was never supposed to happen in the first place.

All of those deaths, all of those battles, the suffering and so forth.

It was all never supposed to happen.

"...I...I...What...I don't...the visions..." Celestia muttered in disbelief as she began to step back in shock. "No...no, I saw...I was told...he told me...wait...who...I...Ugh!" She started clutching her head and shaking. "Ugh! Ugh!"

"C-Celestia?" Twilight asked, slowly standing up.

"Wh-I...I..It hurts! It hurts!" Celestia started screaming as her eyes began to glow a sickly black, making everyone back away.

"There you are!" The Doctor shouted as he glared at Celestia. "No more lies! Stop hiding behind the curtain and reveal yourself! Who are you?!"

"....I suppose it's time we ended this charade, Doctor."

Suddenly, a wave of pure dark, and evil energy erupted from Celestia's body. That nearly wiped everyone off their hooves. Gasps were given as everybody, even The Doctor and Discord, felt their souls turn to ice from the sinister and depraved energy coming from Celestia's body. The power behind this force could only be described in one word.

Evil.

Pure evil.

The Doctor watched in horror and soon snarled as the energy began to form above Celestia, who went limp like a puppet without strings. "I should have known. You. Of course, it was you. Of all the beings twisted and dark in the galaxy, only you would want this sort of chaos and destruction. It suits you, doesn't it?"

"D-D-D-Doctor, what's going on?!" Lyra shouted in fear as she felt her entire body shiver at the pure dark being emitting out of Princess Celestia like a specter.

"The real villain behind all of this, Lyra! Princess Celestia was manipulated into thinking that the sun would die by this evil force that stands before us! Sending her false visions and preying on her fears, he slowly began to influence and control her!" The Doctor shouted in both fury and caution. "All the deaths, suffering, and pain both planets have felt are because of him! He's the real mastermind behind everything!"

"But who is he?!"

"One of my oldest enemies and one of the most dangerous. A god-like being of unimaginable evil power. The source of all darkness and chaos in our universe," The Doctor muttered as he narrowed his eyes. "The residents of E-Space call him the Night Hunter. The Draconequus called him the Soul Stealer. The Star Changelings call him the Great Demon of Darkness. And in Equestria's oldest tales, he is even called The Father of Shadows. But there is only one true name to his being..."

The concept then began to finalize its form in an astral project, taking that of a robed giant vulture of pure black wings and dark purple eyes of darkness. It loomed over them with its enormous wings and smiled sinisterly with its beak before letting out such bone-chilling laughter that fear engulfed all their hearts, and they stood in terror before what could be the human concept of the Devil in proper form.

And then the Doctor gave him his true name.

“The Black Guardian.”

Author's Note:

All non-old school Doctor Who fans go..."WHO?!"

Okay, so The Black Guardian is a villain the 4th and 5th Doctor faced during their years and hasn't appeared in the TV series ever since (though he has appeared in additional material like comics, short stories, and radio adventures.)

The Black Guardian, also known as the Guardian of Darkness and Chaos, is the anthropomorphic personification of the forces of evil in the universe with his brother, the White Guardian, being the one for Light, Order and Good. He was basically a powerful deity like God whose power was in check with the White Guardians as neither could be more powerful then the other as they were each their own antithesis not that the Black Guardian hasn't tried to become more powerful to rule or destroy the universe since its in his very nature to do so. There is a lot more backstory to him, but that's all you really need to know basic wise.

A lot of people believed it was going to be The Master, but I wanted to avoid using him since that was too obvious of a villain and wanted to use a classic one. I still am going to have the Daleks and Cybermen/Cyberponies as part of the villains, but The Black Guardian is our main one. As for the vulture appearance, that's based on his outfit where he wore a vulture's head https://doctorwhoworlduk.com/wp-content/uploads/2019/01/begene.jpg

Special thanks to zelkova48 for helping me edit this.

As always feel free to help at the NegotationsVerse TV Tropes Page were we do have a Regeneration folder that could use some tropes added in :)