New End 2: The War on the Impossible! (Part 1)
This new end occurs after Fluttershy asks, “What do we do, then?”
“We've got to go to the Princesses!” Applejack said.
“But if they see those notes about the planet going around the sun, they might punish Twilight!” Fluttershy reminded her.
“Not if they think Twilight's studies kin be put t'good use,” Applejack replied.
“But how? All she does is disprove stuff. How would that be valuable?” Rarity asked.
“I've got 'n idea. But we'll need t'act fast. Let's put Twi in a cart and get to Canterlot pronto!”
***
Twilight woke up from one of the best dreams she had ever had. She'd been working on the theorems in her head; with her perfect memory, she'd have no trouble finalizing the details on paper. When she woke up, however, she realized that she was not at home at all. Instead, she was in some kind of conference room. She sat up, rubbed her eyes, and tried to figure out what was going on.
“Ah, you're awake.” Twilight recognized the voice of Princess Celestia nearby. “We've brought you in for a very special mission.”
“I don't mean to be rude, Princess, but can it wait?” Twilight asked. “I need my tea before I can wake up. Oh, and is there some paper around? I really need to work on my theory about pony hair color—”
“No!” Celestia's voice shouted. “I mean, at the moment, you will not be supplied paper until we deem your research under control. But your tea and other breakfast foods are all here. We will let you have a short break while you eat. Once you are done, we will continue with the briefing.”
Twilight quickly complied. As she ate, she noticed that Celestia wasn't actually anywhere in the room. She determined that the voice must be coming from the speakers boxes in each corner. “Why aren't you here with me?” Twilight began to panic. “Did I catch some sort of disease? Is this a prison cell? I want to call my lawyer!”
“No, no, everything is fine. Your parents approved of this measure.” As an aside, Celestia added, “Although unspecified confinement is technically legal by executive decree.” But she quickly returned to her previous attitude. “In any case! Have you finished eating?”
Twilight drank the last of her tea, then nodded. “Yes.”
“Then we can begin,” Celestia said. “Now, your friends have been telling us about the... unusual effects your studies have had on the world.”
“I don't know what you mean by that,” Twilight said. “I've just been explaining how the world works. Sure, I've been claiming that things like flight and magic are impossible, but that's because they've always been!”
“I see. So it is worse than I thought.” There was a short pause over the intercom, then Celestia continued. “We'll get a team of archmagi to confirm your theories. In any case, we believe this work can be useful to us. Before you begin, however, you will need to make the following oaths: Do you swear to perform any and all research as specified by myself, Luna, Cadance, or another high-ranking official?”
“Sure,” Twilight replied.
“Do you swear to do no other research of any topic of any kind unless specifically given permission from Luna, Cadance, or another high-ranking official?”
“...Yes?”
“Do you swear to never consider the terrible ramifications of what you may be asked to do, to never go mad at the truth of your sins?”
“Hold on, I'm not so sure about that one--”
“Do you swear never to mention this project to anypony, through speech or body language, directly or indirectly, through statement or omission, under penalty of death?”
“Yes, I swear! I swear to everything! Can we move on now?”
“Very well. Then we may begin.” A panel of the wall opened up, revealing a dark tunnel. Twilight went through it and found another room. This one only had a single desk, a quill and ink, and a single sheet of paper. She sat down and picked up the quill with her hoof. “What do you want me to write?”
A photograph came out of a slot in the wall. It depicted an angry-looking griffon chieftain, one talon pointed at the camera. “The détente between the griffons and the nation of Equestria has been faltering the past few days. Without a strong bargaining chip, we may be doomed to war.”
“Where do I come in to this, Princess?” Twilight asked.
“We would like you to complete most of a theorem that proves that griffons cannot exist. Do not write the final line, and do not make any other conclusions.”
“That's it? Oh, okay.” She began to write, slowly at first, then more quickly as her ideas began to take hold. At one point, she got stuck in a rut. “Could I get some books on the mating habits of Panthera leo and Haliaeetus albicilla, please? Oh, and another sheet of paper?”
After a few seconds, a servant entered the room with the books and paper on a tray. Twilight took them and continued her work. As she came down the home stretch, Celestia yelled, “Stop!” Twilight set the pen down immediately. “That should be enough,” Celestia continued. “Thank you for your work, Twilight.”
“Does that mean I can go home now?” Twilight asked.
“For now, yes. Remember, no other research, and you cannot tell anypony about what you've been doing.”
“And no going mad, either, right?” Twilight added sarcastically.
“That too!” Another panel opened in the room she was in, leading outside to an empty hall in the castle. Twilight stepped outside, and the panel closed again, leaving no trace of the room she had been locked inside. Though she was confused, she shrugged it off and went to catch a train back home. Maybe she'd never be called back to do that again.
***
“This is insane!” the griffon chieftain shouted. There were four creatures in the conference room: Celestia, Luna, the chieftain (whose name was Gregory), and his right-hand griffon, Gadsden. “What you are suggesting is impossible!”
“Not at all,” Celestia replied, her voice as cool as ice. “You've threatened the death of all of my little ponies if we do not comply to your ridiculous demands. So we have turned it around on you. Accept our treaty, or we will have Agent Logos complete this theorem and disprove you out of existence.”
“Why would we think that finishing a theorem like that would cause us to cease to exist?” Gadsden asked.
“I'm sure your spies heard about the evacuation of Cloudsdale, yes?” At Gregory's nod, Celestia told him, “That was Agent Logos' doing.”
Gregory stared wide at the two princesses. “Your Agent Logos can disprove cloudwalking?”
“Agent Logos can disprove quite a lot of things,” Celestia answered him.
The two griffons huddled together in discussion. After a few seconds, they broke apart. Gregory grabbed the treaty and signed it with an angry flourish. Luna took the treaty, rolled it up, and put it into a safe container. “It's been a pleasure doing business with you,” she told them.
After the meeting was over, the two princesses met in Celestia's bedroom. “Was that right?” Luna asked.
Celestia shrugged. “It was the best for our ponies, and it worked. Who is to say whether it was right or not?”
“Still, it almost seems unfair.”
“When the minotaurs developed steel before us, was that unfair? When the Homin developed the atomic bomb, was that unfair? Twilight's theories are weapons. That is all.” Celestia returned to her desk, where another document lay waiting. “Now, help me with this treaty for the dragons.”
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And now we go full on evil
4222708 Oh, believe me, I have plans for this New End. Terrible plans.
4222902 Yup, only instead of physical movement, it's logical leaps. Believe me, it was way too much fun coming up with all of those goofy points.
Well then... I don't think I've ever seen this many alternate endings. Quite entertaining. Also, I'm pretty
4222708 I see you all the time here on fimfiction.
4760591
) I don't know what the Veil is, I don't know why AJ wants to take it down, and I don't know why Rarity put her mother behind it. But... since I wrote it, I have been more and more sold on the idea. So, to answer the question, there might be something coming up. Stay tuned... 
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Thanks for reading, everyone! I'm glad you like it.
Sometimes ideas just spiral out of control like this. Really, all this started with was the idea that Fluttershy got her "freaky knowledge of sewing" in "Suited for Success" from a deal with a demon. I came up with the idea of each character getting a question, but I couldn't figure out what question I wanted to stump Kalos with. Then I noticed Rarity was all calm and collected, so I decided to make her "The Lady of the Veil." Then I had her counsel each of the other ponies, but nothing seemed to stick for AJ. "You'd never make a deal with a demon" seemed obvious, and it led straight into the ending with Tovaris.
Anyways, I have no idea if this is going into another story or not. (I just like ending these with cliffhanger hooks. [See: Alternate End 4.]
I like your version of Celestia. Very evil, but incredibly intriguing and quite frankly hilarious at the same time.
Please take this moustache as incentive to never disprove humanity.
Cupcake to the power of light, dived by watermelon, taking into account the theorems of water balloon and constantinopolis = there is a second chapter of this. And it's a good one.
4222723 Next I shall prove that you do not exist.
Flufflepuff said so.
*you cease to exist by the power of Puff!*
5391944 All hail Empress Flufflepuff, Alicorn of Taco!
This isn't evil at all. Her last line makes perfect sense. Every nation is in an arms' race. The griffons seem like if they won it they'd try to conquer Equestria. Seems like the Minotaur and Humans already tried it. Celestia seems to prefer diplomacy and HAVING the power without needing to use it. If anything that already makes her and Luna more virtuous. The goal of any true and proper leader is the prosperity and survival of their people. If others are hankering to gut your nation and eat your people and take your resources, you do whatever it takes to keep them back. And I can guarantee almost no one will listen to fancy talk or accept soothing tea when they've got their eyes on your riches and their hand on their gun.
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Technically, I never said Celestia was wrong, per se. But outside the text, yeah, I'm not a fan of Celestia's actions here. I suppose I'm a deontologist at heart. Yes, protecting your people is all well and good, but literally erasing people from existence? That's just sick. Whether or not you agree with that or not, I think what's important is how the characters feel about it and what they do as the result of their beliefs. In other words, justified beliefs or no, it makes for good storytelling.
HEY!
*Cackle.* This is amazing! And downright dirty!