This Alternate End takes place after Twilight has explained everything she's figured out, but before Celestia asks sarcastically for more and Twilight removes their speech.
“Okay, so maybe you are disproving the nature of reality,” Celestia responded.
“No, you think?” said Rainbow Dash.
“Very well then. It seems I'll have to explain the correct answer to your dilemma.”
Twilight gasped, and her eyes lit up like fireworks. “You mean you'll tell me how magic works?”
Celestia nodded. “That's right. In fact, it's very simple.” She moved close to Twilight and whispered, “There are only three ponies in the universe that know this secret: myself, Pinkie Pie, and Lyra Heartstrings. Among the three of us, we know that learning this secret would drive a lesser pony mad. This is not something that can be simply accepted and moved on with. This will change you. Permanently and utterly. It is earthshattering, mindblowing, and in a word, unbelievable. But I, Pinkie, and Lyra promise you, it is 100%, absolutely true. Are you prepared for such a discovery?”
Twilight paused for a moment. “It's thaumic particles, isn't it?” she asked.
“...No, Twilight, it is not thaumic particles.”
“All right then, I'm willing to find out. What is it?”
Celestia drew in a deep breath, then said simply, “This world is a Fiction.”
“A... a what?” Twilight asked.
“A Fiction,” Lyra said. “It's created from the minds of Authors and Writers.”
“Drawn into being by the hands of Storyboarders and Animators,” said Pinkie Pie.
“Voiced and brought to life by Voice Actors and Actresses,” said Celestia.
“Our rules are their ultimate decision. Our lives are their playthings,” said Lyra.
“To bend or to break. To exist or to cease to be,” said Pinkie Pie.
“They are Omnipotent, and their Word is Law,” said Celestia.
“They're also really annoying,” Lyra added with a huff.
“And they let me do whatever I want!” said Pinkie.
“And I watch over it all, guiding them with inspiration and maintaining the Canon,” Celestia added with a tone of finality. “Do you understand?”
“Uhh... I think I lost you. What's a Storyboarder, exactly?” Twilight asked.
“Ugh...” Lyra and Pinkie slapped their foreheads.
“The point is, the laws of this universe do not necessarily conform to the normal rules of physics, chemistry, or common sense,” Celestia said.
“If the Author says you can walk on air, you can,” Lyra said.
“Or if the Animators want, you can be in two places at once!” Pinkie added.
“And they can also bend Luck and Fate to suit their Story,” Celestia concluded.
“So let me get this straight...” Twilight said. “Magic works because... the Authors say so?”
“Yes!” Lyra replied. She grinned widely. “Now you get it!”
“But that doesn't make any sense! I want to speak to this Author person. They should make the universe logically consistent!”
“Okay,” said the Author. “Here's your new explanation: Magic works because shut up, it just does. Do I make myself clear?”
“Yes, sir,” Twilight replied meekly.
“Good,” He replied. Then He stitched back together the Fourth Wall and went back to His normal writing.
“Are you all right, then, Twilight?” Pinkie asked.
“I guess so.”
“Don't worry, I hate interacting with the Author too,” Lyra replied. “He's kind of a jerk.”
“I heard that,” He said back.
“I thought you said you had fixed the Fourth Wall,” Lyra said,
“Oops, you're right,” He replied. So He stopped butting in again (I promise!) and let the story continue.
“Aren't you forgetting something, Twilight?” Celestia asked her.
“Oh yeah,” Twilight said. She nodded her head, and everything went back to normal.
“Well, that was kind of convenient,” Pinkie noticed. “I guess the Author is kind of a hack, huh?”
“Wait a second. One more thing,” Twilight asked. “Did an Author write this whole situation, too?”
“Yes, he did,” said Celestia.
“In fact, that guy you just talked to? That was Him,” Lyra added.
“So if he hadn't written this story, we could have avoided this whole thing?”
“Uh-huh.”
“Yup.”
“Yes.”
“Oh, that is it!” Twilight yelled. “Now I'm really going to give that guy a piece of my mind! I'm gonna find a way to his world, find where he lives, and then I'm gonna--”
And Twilight never found a way to the real world and she lived the rest of her pony life without punching me in the face or whatever her plan was THE END.