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

Regeneration - Rated Ponystar

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

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Regeneration Part 3

"I do what I do because it's right! Because it's decent! And above all, it's kind! It's just that. Just kind."

- The 12th Doctor

"The very powerful and the very stupid have one thing in common. They don't alter their views to fit the facts. They alter the facts to fit their views."

- The 4th Doctor.


Princess Celestia could remember when she first had visions about the sun dying.

It was around four hundred or so years ago before her sister returned to her. In her nightmares, the sun was burning red hot like the fires of the underworld. Then it burst into an explosion never seen before in the history of their world.

A sea of hellish flames engulfed the planet as mountains fell, oceans evaporated, buildings crumbled, and ponies screamed in agony before turning to ash. No matter how fast the earth ponies ran, how strong the unicorn cast their shields, or how high the pegasi flew, all succumbed to a fiery death. The flames would spread throughout the world and leave nothing more than a dead husk floating in space forevermore.

When it was over, Celestia woke up screaming in horror, and it took hours to get her guards to stand down upon thinking she had been attacked in her sleep.

At first, she had thought it was simply a bad dream. But then she kept having the same one, again and again, each and every night to the point where she suffered from lack of sleep for hundreds of years.

The power of dreams was something that Celestia was no expert in. That was her sister's department of arcane knowledge, but she did know that "a recurring nightmare could be perceived as an ill-omen. A vision was all too clear to her: The sun would die and take all life with it.

Knowing that time was against them, Princess Celestia spent hundreds of years trying to save their world, but all she could do was protect her ponies.

Equestria would avoid the doomed fate of all the other nations even if, deep down, Celestia felt utterly guilty for doing so.

Princess Celestia was no fan of outsiders, pony or non-pony. The years of having to defend her home from countless invasions were enough to make her distrustful of them unless they fully embraced Equestrian society and their way of life. She had hoped to change the world with the powers of Friendship and Harmony so that all embraced their culture.

Alas, it was not meant to be.

She asked no forgiveness for what she had done because she knew there would be none to give.

The night they arrived on Earth for the first time, she drank herself to a stupor and cried all night in private with silencing spells around her. If she believed in such things as afterlives, Celestia would have declared herself doomed to Tartarus upon her death. But she had to be strong for her ponies and the future she hoped to bring to them.

Celestia sacrificed her soul and morality to save them from utter destruction. The least she could do for her subjects was give them a golden future where there would be no threats, no evil, and no sin. They would build a new one from the ashes of the old world that would achieve great wonders long after Celestia passed on.

The only problem was humanity.

A race of nothing but savages who embodied the worst of cultures and beliefs centered around hatred, selfishness, and bigotry. Princess Celestia quickly developed a mix of pity, loathing, and disgust for this species that should have destroyed itself long ago.

Still, they survived regardless while learning nothing in her eyes. Losing her adopted daughter, her beloved Sunset Shimmer, to them only worsened her opinion of them.

Soon her nightmares were filled with images of humans coming into Equestria, taking it over, raping her lands and her people, and treating them like animals while Celestia wept at the graves of those she loved. She would not let her subjects suffer at the hands of these monkeys. She would die first.

The visions had to be correct, after all. They were right about the sun. Why not be right about humanity? And so she did what she could to save them, even if they didn't want it, but in the end, the war had come. But she believed they could win. Even if it took time, the humans would submit to them thanks to the potion, the barrier, and their way of life.

And then she learned about The Doctor.

And her nightmares soon had his face in them.

Princess Celestia called for an emergency war council meeting as soon as Discord was done talking and told them of their new enemy. Of course, she had to say a few lies, but they believed he was a threat in the end.

Even if some were skeptical, an alien who had caused massive suffering and death in Equestrian history was enough to frighten them. Naturally, they had to keep a lid on his true identity to prevent an outright panic and simply said he was a terrorist in league with Equestria's Most Wanted Pony: Lyra Heartstrings, which wasn't far from the truth.

For over two months, Celestia and her allies waited to hear any sign or appearance of The Doctor or Lyra, but there was nothing. This only unnerved her even more. That didn't mean she wasn't facing problems, however.

The non-ponies in Equestria had gotten more riled up. They were nearly revolting out of fear of being made into ponies against their will like the humans. Something that Celestia was uncertain about doing or not since the non-ponies in her land always assimilated very well, but apparently, there was a limit.

Seeing them perform acts of riots and violence had made up her mind, and she forced them into internment camps for now. The Conversion Potion was only capable of turning humans into ponies, but with some tweaks, perhaps it could affect other races as well.

This move caused groups of ponies, especially friends and spouses, to speak out against this action. Luna then thought of creating a task force to prevent further uprisings or discontent, so they started the Equestrian Secret Services.

They were authorized to ensure that Harmony was kept in place and that citizens were devoted to their noble cause. To make sure that there were no rebels or traitors who were thinking of causing problems or escaping to the human side. However, this didn't seem to fully work as there were reports of numerous ponies attempting to leave Equestria to the point that an "Underground Railroad" had been established to help them escape. She quickly made it law that anyone trying to use this "railroad" or being part of it would face prison.

Second, the U.N. had accused Princess Celestia and Luna of genocide against the species back home by accusing them of letting the sun and moon motionless in the air. According to anonymous sources, they stated that their home dimension was dead due to nobody being able to move the sun and moon without the princesses there.

Naturally, Equestria was divided about whether or not this was true, but Princess Celestia had reacted as fast as possible to hide the truth. Princess Celestia quickly put out a public statement across the nation saying that it was a lie and that she had left a plan for their allies in Saddle Arabia.

Long ago, Celestia and Luna created an amulet that was designed to hold both their powers and could be used to make sure the day and night cycle continued. It was this object she left behind for the Arabian royals to use to make sure the world continued its celestial process.

Of course, this wasn't the truth. It had never been completed due to Luna being on the moon before it was fixed, and she had lied, saying she had finished it in the thousand years she had been gone.

Regardless, most of the population, including her own sister, Twilight, Cadence, and their friends, accepted this, but ponies still doubted it. And doubt was enough to unravel things, so she quickly began making harsher rules in censorship and quickly centralized all news media to the crown. She had no idea who was behind figuring out the truth and leaking it to the world, but Celestia was willing to be The Doctor, or Discord was behind it.

Which led to the worst problem of them all. Like Discord promised, he had gone to Fluttershy and gotten her out. He went to all of the Elements, and even Spike himself, to convince them to leave in fear of The Doctor. They all refused for various reasons, but Fluttershy went with him. The others had been horrified and thought maybe she was brainwashed, discorded, or taken against her will. Nopony had seen them or the Element of Kindness since those two months...until now.

"Are you sure of this?" Princess Celestia asked, doing her best to hide her tone of disappointment and anger. Princess Luna, on her throne, looked both shocked and livid as Agent Bon-Bon of the ESS bowed before them.

"I'm sorry, your majesties, but the prisoner confirmed it," Bon-Bon said stoically, yet her stance was filled with anger. "Fluttershy and Discord are part of the Underground Railroad to get ponies who want out of Equestria and into the human lands. They've been working together with the U.N. in doing so."

Celestia tore the paper in two with her magic. How dare she?!How dare Fluttershy do this to them? To work with the enemy? The humans? Discord wasn't a surprise due to his chaotic spirit, and he had betrayed them already with the whole Tirek debacle. She really wished she had just turned him to stone or executed him after that, but the girls had insisted on giving him another chance. But Fluttershy?! Why?! I know she didn't like this war, but to outright defy us and work with the enemy?

"Have Princess Twilight, Princess Cadence, and the others been informed?" Luna asked sternly.

"They have...they didn't take it well," Agent Bon-Bon replied with a heavy sigh. "Our information says they're making their way with another group of escapees to Osaka, Japan. Princess Twilight is very determined to stop them and has decided to go through with the attack earlier than planned with Commander-General Shining Armor and Princess Cadence. They should be starting tomorrow."

"What are we going to do, Sister?" Princess Luna asked.

Princess Celestia sighed and closed her eyes. Much as she was angry, she needed Fluttershy alive. She was the wielder of the Element of Harmony, and she needed every weapon Equestria had not just for humanity but for whatever The Doctor was planning. Besides, there are memory spells we can use to make her forget her rebellion. We can always just say Discord manipulated her.

"Fluttershy is to be captured at all costs. Discord is to be eliminated. Tell Twilight she has full permission to use whatever means she wishes in the attack," Princess Celestia ordered as she held her hoof out. "Make an example of this one. I want as many newfoals filling up Osaka that they'll be swimming in it."

"Yes, your majesty!"


It would shock anyone who knew the Spirit of Chaos to learn that he hated war. Having seen his planet's entire population reduced to just himself would be enough to drive anyone to hate killing.

In all honesty, the death of his entire race had affected Discord more than he liked to admit, but could anyone blame him? Seeing your entire culture, planet, family, and friends "exterminated" by cold and vicious machine-like abominations that had developed the means to negate your reality-warping powers would change anyone.

It didn't help that the natives of this world rejected and feared him because of his alien appearance. So yes, he went mad. He went crazy. But deep inside, he was just hurting and crying because he was still processing it all.

He wanted to just let it all out and rage against this perfect planet that had never known true horror and destruction like he did. A place that was supposed to be a new home his parents sacrificed everything to send him to but rejected him out of fear. Even after holding the entire world at his mercy, Discord did not feel any satisfaction deep inside. Only a hole that couldn't heal and a wish that he never left home in the first place.

Even if it meant joining his people in utter destruction.

After meeting Fluttershy, Discord finally began to wake up from his inner nightmare. She was the first, the very first, pony to get him to open up, but he was hesitant. A trick. Deep down, he believed they would reject him again because of who he was and that he would never be one of them.

He joined Tirek because he thought it was inevitable, but it hurt doing so, and he didn't know why. Only after he lost his powers and was at Tirek's mercy did he understand how low he had fallen and what he lost a second time. Twilight sacrificing her magic for even him had opened his eyes and accepted the truth. He had to change. Be better. And opened up again to others. Because there was no other way to heal what he had lost.

The day after nearly losing everything a second time with his betrayal to Tirek, he confessed everything to Fluttershy. Losing himself in tears and anger, he told her his true story: where he had come from, what he had seen that day, and what he wished deep down. At the end of it all, Fluttershy wrapped her arms and wings around him and let him sob endlessly on her shoulder while crying beside him.

She told him that he wasn't alone anymore and that she would always be there beside him. He promised to be good this time. Not just for his sake but for Fluttershy, who had put so much faith and determination to help him. All he really needed to help wound his damaged heart was just a little kindness.

This is why he got Fluttershy out of Equestria as fast as possible, despite her hesitation. He had begged her to trust him, just this one time to believe him when he said that danger was coming. He knew of The Doctor.

The whole universe knew of him.

The Time Pony who was like fire and ice. The storm that knew no end. A being that made angels cry with joy and demons shiver in fear. If he was facing Princess Celestia as an enemy, she must have done something terrible. Fluttershy listened, thought long and hard, and agreed to go with him in the end. The same couldn't be said for her friends.

Discord tried really hard to get them to understand. He begged, pleaded, and promised as well as he could that he was trying to help him, but the results were poor.

Twilight believed too much in her mentor to think she had done something terrible. Rainbow Dash and Applejack were full-on believers of the war, and they accused him of being a traitor quickly. Rarity didn't like the war, despite her husband fighting in it, but she didn't trust Discord and probably never had. Pinkie Pie refused to leave because she didn't want to leave behind her friends and family but secretly wished him good luck. He tried his hardest with Spike, who admitted he hated the war and everything going on but wouldn't abandon Twilight.

In the end, he only took Fluttershy, her animals, and her cottage and teleported them to an isolated place in Yellowstone Park with a spell or two to hide them from everyone. And then, two weeks later, the U.N. put up their statement about what had happened to Equus. Discord knew what Celestia had done in that instant, and Fluttershy cried for five days straight.

Once again, Discord had lost a home.

When they arrived on Earth, Discord knew that there was something else planned besides trying to help humanity. He knew Princess Celestia better than she knew herself. She was not the perfect goddess she portrayed herself to be, but bitter and racked with inner rage, much like himself.

He wondered what she experienced as a child to make her who she was but decided it was probably useless to figure it out. Especially when it was all clear when the statement about what had happened in their old world came to light. Naturally, Princess Celestia denied it, and most of Equestria believed her, but some figured out the truth and rejected her.

Fluttershy demanded they help them. If only to give them a chance for a new life. Discord hesitated until Fluttershy pointed out that what was happening to humanity was what happened to Discord's people. They were not just being exterminated. They were being converted and dying inside while living as nothing more than automatic dolls. Soulless machines who did whatever Celestia programmed them to do.

That had won Discord over in an instant.

He would not allow what happened between his people and the Daleks to happen again. Even if it was not his people, his home, or even the same enemy, he wouldn't let this happen again. Which was why he was doing everything he could to protect Osaka from Equestrian forces.

They were really going all out on this one. Firing magical-based artillery and mega spells from the unicorn lines while protected by a giant magical shield protecting their central teleporting zone and any territory they picked up.

Pegasi were dive-bombing in the air and taking out any high-ranking targets with strategical strikes or unleashing bombardments of the potion to cause confusion in the ranks. And every street had armies of earth ponies charging forward with magical armor and gear, stomping on any threat against them.

Already they had all of the southern sides of Osaka from Nishiyodogawa to Higashisumiyoshi, while the humans were holding out on the northern side from Yodogawa to Hirano, with some of the fiercest fighting being in Kita, Chūō, and Tennōji. The last one was where Discord was personally.

It was a clever move as well.

Most of the U.N. forces worldwide were spread thin, trying to save what lives they could from the growing barrier while dealing with multiple attacks in Europe and South-East Asia. While the JSDF was doing what they could with what the U.N could spare, most of their best forces were in Kyoto and Tokyo at the moment and would take hours to arrive.

He knew why they were here. Fluttershy and Discord had arrived with their latest group of escaped ponies with a few other members of the Underground Railroad. Osaka was their last checkpoint before crossing over to the United States. Then the attack came, and Discord had to put his energy into protecting Osaka as much as possible while Fluttershy fled with their group.

Already their numbers had dwindled in the opening attack, and he was doing what he could to give Fluttershy enough time to get to the U.N. forces.

Snapping his fingers left and right, Discord unleashed as much chaos as he could: storms sending down lighting that turned ponies into chickens, giant samurai statues coming to life to hold off the enemy, summoning living anime characters to fight against their invaders, and turning weapons into sashimi. All while teleporting ammunition, soldiers, and wounded humans in and out of the battle whenever he could.

But Equestria kept coming, and Discord was spread thin. His powers were weaker in this dimension, and he couldn't do as much as he used to back home.

Discord was about to fly a bit higher when he felt a blast of magical energy nearly rip his horn off. He ducked down and flew close to the ground. Preparing himself, he grumbled upon seeing two familiar figures fly down while another rushed towards him with a squad of Crystal Pony Soldiers in their best diamond armor and weaponry.

Seeing Twilight Sparkle, the ever-living bookworm, dressed in gold and purple armor while holding a long amethyst glowing crystal sword was still amusing. While Princess Cadence wearing platinum armor mixed with different crystals was also funny to see due to being the princess of "love" and all. Especially since she had two bloody crystal axes in her magical aura. Prince-Consort Shining Armor, dressed in his usual purple armor, was the only one who looked the part of all three members of the Sparkle family.

Holding the Commander's Sword given to him by Princess Celestia at the start of the war, Shining Armor shouted, "Discord! In the name of the Princesses of Equestria, you are to surrender for your treason! Again!"

"Funny," Discord said with an amused smirk. "It's ironic that I'm being declared a traitor when your own Princess Fatsun is the one who betrayed our world."

"Those are just lies, Discord! Lies that you no doubt spread to cause chaos in Equestria!" Twilight shouted as she landed on the ground next to her brother, seething with rage.

"Believe it or not, Twilight, I didn't do such a thing, but I really should have realized it when I learned that The Doctor is here," Discord said with a shiver. "No wonder he's fighting against Celestia. To have her ruin the world that he once cared for so much and saved multiple times? Quite frankly, I hate to see what he has planned."

"Again with this "Doctor" pony," Cadence said with an eye-roll. "I am willing to believe my aunt's statement's about him being dangerous, but since we haven't seen him in two months, I'm willing to believe he doesn't even exist. Just another lie by you to scare us."

"Trust me, Cadence. I am a liar, I will admit that, but when it comes to The Doctor? I tell nothing but the truth," Discord stated as he glared at them. "And the truth is you are all being played by Celestia, who doomed everyone else back home. You've been manipulated into thinking you are doing a great crusade to save an entire race when you are practically genociding them and their culture. I always knew you ponies were selfish, arrogant, and self-righteous to the point of narrow-mindedness, but I never believed you were also stupid. Especially you, Twilight!"

He pointed at her and glared. "I respected you greatly for beating me. You were smart and clever to outwit me, and I saw you as a worthy adversary and later a friend. I practically thought of you as one of my closest friends after you saved me from Tirek despite all I had done. But what I admired most was that you were so faithful to the ideals you preached throughout all the time I got to know you about friendship. Well, I guess the truth is you're nothing but a hypocrite along with the rest of your friends except for Fluttershy. What makes you different from the rest of the ponies of Ponyville, who feared and hated Zecora when she came to town? What makes you different from Starlight Glimmer, who forced ponies to give up their cutie mark for equality and greater good? How are you different from Queen Chrysalis taking over Equestria against their will?"

Twilight was about to say something, but Discord wouldn't let her do so and instead turned to Cadence and Shining Armor with a snort. "And you two? Princess of Love, my scaly butt. You outright condemned the romantic relationships between humans and ponies. Do you know how many ponies I've helped leave Equestria so they could find the humans they loved? How happy are they together? And those you deny and capture suffer heartache while between bars. Did you once tell me that not all nobility accepted your relationship with Shining Armor? Well, I guess now you know how they felt about you two."

He then turned to a snarling Commander-General. "Meanwhile, Shining Armor here is being used as his tool. Instead of thinking for himself and fighting for justice, he's being used to promote a hostile takeover of a nation and eliminating the people on it like a good little soldier. You know that feeling you had when you were brainwashed by Chystalis during your wedding, Shiny? That's what the newfoals deal with every day, thanks to your potion. Your daughter should be ashamed of you!"

"That's enough!" Shining Armor shouted as he stomped his hoof so hard on the concrete street that it cracked. "What right do you have to preach about anything?! You're chaos incarnate! You drove ponies insane in some twisted sense of humor! You took over our land! Corrupted our subjects! Turned us against one another! And betrayed us to an enemy who nearly destroyed everything we built only to do it again even after giving you another chance! You are a selfish, immature monster who should have been smashed as a statue or dropped into a volcano!"

Discord stared at the ponies, who glared at him with utter hatred and sighed. "You are right. I am a monster. I never realized it until after Tirek, but I was no different from those that ruined my life, so I ruined others to deal with that pain. I went through a tragic moment in my life when I lost my people, but it doesn't excuse the actions I took to deal with it. Discording ponies really is no different from turning humans into newfoals." He narrowed his eyes and pointed to them. "Yet, you ponies showed me there was another way. Another means to help me. Friendship was what saved me, and Fluttershy is everything to me because she taught me to really laugh, smile, and love. I took it all for granted until I was betrayed by Tirek. I swore to use it well when you all gave me another chance. Believe it or not, I saw you as my friends despite everything we went through."

He then snapped his fingers and found himself dressed in a familiar green tunic costume with a copy of The Master Sword and Hylian Shield from a game he played not long after their arrival here. "But you know what the difference between you and me is? I at least admit that I was wrong, and I'm willing to admit it now. You, however, are not. I'm protecting humanity not just because Fluttershy asked me to, but because it's right. I saw one world burn to ashes with a race of evil beings destroying everything good about it." He then pointed the sword at them all. "I will not allow it to happen again."

"...Tell us where Fluttershy is, Discord," Twilight said while raising her own weapon. "And we'll make sure you are put in stone instead of outright execution."

"You want her? You have to go through me," Discord said as there was a split second, and both sides charged at each other.


"You know, I never really understood Eco-terrorism," The Doctor said as he used his Sonic Screwdriver to work the controls of the nuclear power planet to cool it down. He had decided to make a new one after using the last of his old one to save Lyra, and the TARDIS was quick to give him a spare. The baseline was made out of a special near unbreakable crystal that allowed the glowing swirls of energy mechanics to be noticed. At the same time, the white orb on the top continued to glow in whatever color he needed. It had a black and white handle with white Gallopfrian language that had meant "The Doctor" on it so people would know who it belonged to if it was lost. Although, in hindsight, very few knew the language.

"I mean, I do understand the reasoning. Wanting to save the planet from utter pollution and ecological destruction is a nice thought, but the way so many races go about it is stupid. Blowing up buildings, killing people, setting fire to everything, and blowing up nuclear reactors?" He snorted. "You realize that radiation is deadly and spreads around, affecting flora and fauna, right? I mean, the city has a zoo and reservation section nearby. And you were talking about saving the plants and animals while doing this?"

A few humans in muffled voices said something in the back, but The Doctor shrugged. "Well, it wasn't a full-on stupid plan. Infiltrate the staff, find out the codes and details of the workings, bring in a few guns and open the door to storm the place. Then cause a meltdown to make it look like things went wrong instead of outright sabotage. The stupid part was bragging about it on that one site. Reddit, I believe?"

Another few muffles were heard as The Doctor finished shutting the power planet down and put his Sonic Screwdriver away. Walking over to the tied-up and gagged humans, he glared down at them. "Well, good thing that your little plan failed. I also managed to hack your computer systems at your base, found all the locations of your fellow terrorists, sent the data to the police, and they should be coming here in about ten minutes. Quite frankly, I should be shocked that there are radical humans like you who think that humanity needs to be turned into ponies out of your own personal misanthropy, so you decide to cause as much damage to your own people as possible. But I'm not. I think I'm just getting numb to things like this at my age."

The sound of feet rushing down the hall, followed by hooves, alerted The Doctor, who turned around and saw a lip bleeding and blackened eye human dressed in a tactical armor growl upon seeing The Doctor and charged at him. A few seconds later, a worried-looking Lyra followed and shouted, "Doctor! Look out!"

The Doctor calmly waited until the human was close enough to shift to the right to avoid his punch and swiftly brought his rear left leg to his gut. "HAI!" The blow to the solar plexus caused the terrorist to go down on their knees, where The Doctor cried out again and delivered a downward chop to the back of the neck. Dusting his hoof, The Doctor smiled. "Venusian Aikido. Good to see I still remember the basics."

Lyra rushed over and looked at the console. "The reactor?"

"Silent as a sleeping baby," The Doctor said as he took out a pocket watch from his coat. "Police should be here in two minutes. Tie him up, Lyra. Let's get going."

Lyra nodded and used her magic to tie up the unconscious terrorist before kicking him in the face for good measure. Following The Doctor, Lyra then asked, "Doctor, forgive me for saying this, but shouldn't we be doing more?"

"What do you mean?" The Doctor asked as he continued onward without looking back.

"Well, it's not that we haven't done a lot," Lyra said as she pointed out all the things she had done with The Doctor since her rescue. "Using the TARDIS to go back and forth to help ponies escape Equestria. Exposing the truth to everyone worldwide about what happened to Equus, even if Celestia did massive damage control. Using the TARDIS to warn areas of attacks ahead of time to better prepare the humans. Not to mention shutting down groups of fanatics like these who want to destroy humanity and turn themselves into ponies because they believe it is the best way to save their species and the planet."

"Don't forget how we prevented that crazy Turkish general from blowing up Istanbul with a nuclear weapon because three-fourths of the population got ponified," The Doctor pointed out as he used his key to open the TARDIS.

Even though she had been inside the strange blue box multiple times in the past two months, Lyra was still amazed by it every single time.

The main control center was sleekly clean, with numerous buttons, switches, and gizmos that she didn't know she could do. There were also giant blue screens with various symbols that she didn't recognize, but the Doctor did and only assumed they were in some kind of alien language. The center crystal tower was the most beautiful part as it glowed like a rainbow and with rings going up and down each time it was used, while computer screens attached to its base could be moved around for usage.

The interior was a mixture of white and tan with glowing white circle lights that she asked about, but The Doctor confessed he didn't know what those were for. The floor around the TARDIS was made of class with two sets of stairs leading to the control center's platform encased in steel golden with silver railings and comfy black leather seats for sitting down by the edges.

To the left of the TARDIS's mainframe was a giant computer with multiple screens recording information about the war from the U.N.'s HQ or showing various news reports of the war itself. There was even a tactical map in the center showing the entire world with positions of various military forces for both sides of the war. To the right, there was a set of Victorian-style oak chairs with a large tea table with warm tea prepared and biscuits, scones, and crumpets on a plate that read "To Doctor, From Yaz." A series of books were on the shelves around it, along with an old telephone that actually worked surprisingly.

The Doctor said one needed to rest and relax in times of war so that you didn't get burned out. Lyra still hadn't figured out it managed to automatically fill itself up with different tea each time or where the goodies came from. And finally, in the center was the giant hallway that led to other parts of the TARDIS, including the bedrooms, bathrooms, laundry room, clothing room, garden, pool, billiard room, weapons department, laboratories, and more. According to The Doctor, he had only explored fifty-nine percent of the TARDIS, and he didn't know what else was inside her.

The Doctor walked over to the console and activated the TARDIS, sending her off through the waves of time and space while he began to check something on one of the computer screens nearby. "I'm guessing you think we need to do something more? Don't worry. I have plans to do so. We're just waiting for the right moment."

"You have a time machine," Lyra pointed out, shaking her head in confusion. "Can't we just use that to go to the right moment in the future or go back to the past and prevent the war from happening at all?"

"Unfortunately, no," The Doctor explained with a heavy sigh. "Time travel is complicated. It would take three of your lifetimes to explain even the basics. For one, this dimension operates under a different set of laws regarding time, much like how physics is different here than back home. Second, going too far into the future could prevent us from missing something important. The most I'm using the TARDIS for is to go into the future for a few days here and there. And changing the past has consequences with only the most extreme reasoning needed to do it. I did go back to when Equestria first landed, only to find out that we're now a fixed time event. Meaning that we cannot change this or the entire history of his planet will alter, and what happens afterward could tear everything apart for the worse."

Lyra slowly nodded her head and decided to trust his reasoning. After all, he was the expert when it came to this. She decided to walk over and noticed he was concentrating on a set of numbers and chemical formulas that made her tilt her head. "What are you working on?"

"A cure for the Conversion Potion," The Doctor simply said.

"What?!" Lyra shouted in shock. "How long have you been working on a cure?!"

"Since I learned about it," The Doctor said before pausing and looking over the data while rubbing his hoof to his chin. "It's actually very advanced for the magic and technology Equestria has in its period. I've seen similar alchemic and mathematical formulas before, but Twilight really outdid herself this time. Too bad it's being made to be used for evil. There are numerous ways this can benefit physical and mental health."

"How close are you to a cure?" Lyra asked, eager to see the look on Equestria's face when their prized newfoals turned back into humans.

"Oh, I created one about two weeks after I started," The Doctor said before shaking his head. "The problem is that it's designed for one specific newfoal and no other."

"What do you mean? A cure is a cure, right?" Lyra asked as The Doctor pressed a few buttons, and a hologram shot out of the TARDIS showing a pony, his DNA, and what looked like more chemical data.

"The problem is that the potion has a unique enzyme that comes from Celestia's own blood. It's been used to create the central chemical compound for the potion," The Doctor explained. "What the enzyme does is find a unique portion in the human DNA that allows it to modify the human into any of the three pony races based on the information it gathers from the strains. This unique base is always different for every human, but it forms the basic building block for the new DNA that replaces the old one. Because of this, every cure would either need to be different. That would take a long time. Fortunately, there is an alternate solution. I need a counter enzyme that is the opposite of Celestia's blood to neutralize this."

"Any idea where we can find that enzyme?" Lyra asked as many lights began blaring from the "War Computer" that made the Doctor rush towards with a smile on his face. Lyra soon followed and watched as he typed into the computer with haste. "What is it?"

"The enzyme," The Doctor said as he pulled up a screen that showed shaky footage of what appeared to be Discord dodging giant missile-like spells from Twilight and Cadence while summoning a big umbrella to bat them away. "Discord's blood is the key. If I can get a small sample of it, I can have a cure that will affect every newfoal regardless of their differences. Plus, where Discord is, Fluttershy is there to follow, and we need her for the next part of my plan."

Rushing back to the TARDIS main controls, The Doctor knelt down and opened a compartment with junk inside it. He started digging through it while licking his chops as Lyra walked over. "Let's see..." He popped up and held a recorder in his hooves before giving a nostalgic smile. "Huh, I was wondering where that was." He played it a few times before handing it over to Lyra. "Maybe in here?" Rising back up, he looked at a giant green crystal ball with screaming voices. "Nope. Not it." He handed it also to Lyra, who rolled her eyes before he dragged out a very long scarf, and raised his eyebrow. "Ugh, why does this always appear every time I regenerate? It was a fun time, but I've outgrown it." He tossed it over his shoulder, where it landed on Lyra's head. She puffed it out of her eyes just as The Doctor shouted in triumph and pulled out what he was looking for. "Eureka!"

Lyra, levitating the other stuff away, asked, "What is that?"

The Doctor presented it to her. It looked like an amulet of sorts with six jewels circling around what appeared to be miniature radar. The jewels were in the colors purple, green, blue, red, yellow, and pink.

"A surprise," The Doctor said as he rushed over to the TARDIS and started putting in controls. "Alright, the next stop is Osaka! We will find Discord, get Fluttershy, stop the battle, and save Japan! Next stop, the human base of operations in the city! Tally ho!"

Pulling the lever, the TARDIS moved and jerked around for a few seconds before stopping. Smirking, The Doctor put the amulet in his coat pocket and walked towards the entrance. "Well, let's go."

"Where are we? In the base?" Lyra asked.

"Don't be silly," The Doctor said with a smile as he put his hoof on the doorway entrance. "We'd freak everyone out if we did that. No, I landed us a few feet away so we could calmly walk over to the guards and explain that we are here to help. I've been traveling for about two thousand plus years in the TARDIS. I know how to manage her."

Opening the door, The Doctor soon found at least half a dozen barrels of assault rifles held by UN soldiers aiming at his face. He noticed that he was not outside the military base like he had planned but instead seemed to be in the center of communications, where everyone inside was staring at him with fear and confusion save for the guard holding him. The Doctor turned to Lyra and said, "Of course, sometimes, there are margins of error."

Lyra couldn't help but facehoof.

Author's Note:

And here we go with part 3. Be sure to help out at the TV Tropes Pages for the Negotations_verse series: https://tvtropes.org/pmwiki/pmwiki.php/Fanfic/TheNegotiationsVerse