Well...That Explains It.
It was a peaceful night in Ponyville. After the chaos of Tirek's rampage, things were finally starting to go back to normal. Unfortunately, the peace was interrupted by a particularly loud scream of frustration that could only have come from a lavender unicorn named Twilight Sparkle.
"Twilight, you've been at this for hours, and you know trying to understand Pinkie Pie is just about impossible anyway." Spike said as he descended the steps to the castle basement. He found Twilight in the same spot he had left her hours before, after she had decided it was time to finally make sense of Pinkie's nonsense, a task widely viewed as impossible.
"I know, Spike, but this is something that must be done!" Twilight replied. "I was willing to let it slide the first time, but then we found out there are others with the same crazy abilities. First Pinkie, then Discord, then Cheese. There must be a connection,"
"It's probably just a coincidence. It's not like half of Equestria is as strange as them," Spike said, heading towards the freezer for some ice cream. Before he could open it, however, the freezer door slammed open, smashing Spike against the wall.
"Pinkie! What are you doing in there?!" asked a very surprised Twilight.
"Pretending to be ice cream," Pinkie literally bounced out of the freezer. "Have you seen Spike?"
"Right..Here..." came a muffled groan from behind the door. Pinkie closed the freezer, revealing a flat, purple and green mass.
"So that's why my Pinkie Sense was telling me to watch out for opening doors," Pinkie said as she attempted to unflatten the dragon. At that exact moment, her tail started twitching. Pinkie got out of the way just in time. Spike was not so lucky, and any attempt to make him 3D again were quickly undone, as a random flowerpot fell out of thin air.
Twilight looked up to see the grinning face of Discord.
"Discord!" she screamed.
"That was priceless! Simply priceless!" he said between fits of uncontrollable laughter. Seconds later, Discord's tail started twitching and another flowerpot came down on his head, putting an end to his laughter.
Noticing this, an idea came to Twilight's mind. "Discord, does your tail always twitch just before something falls?" she asked.
"It does, actually," Discord's reply was all the evidence Twilight needed. She whispered something in Pinkie's ear.
"I have a surprise for you, Discord. Follow me," Pinkie said. Discord took the bait. As Discord entered the doorway, Twilight used her magic to slam the door on his face, knocking him back. Just before the impact, Twilight noticed Discord's body perform the same combo as Pinkie and a look of shock appearing on his face.
"How rude," Discord muttered as he tried to fix his now flat face.
"Discord, I notice that you and Pinkie seem to share some abilities. Do you know how this could have happened?" Twilight turned to Pinkie "You can answer too if you know anything."
When both Discord and Pinkie said they had no clue why they had the same powers, Twilight decided it was time to do some research. The next day, she invited Discord and Pinkie to her castle, claiming that she had found something.
"Good morning, both of you. Now, I bet you're wondering why I called you here today. Well it's because, after some research-" Twilight was interrupted as a pink blur shot past her, slamming her against the wall.
"You found out that the Pie family was descended from a pony named Cheesecake, and he was the first known pony to have these kind of powers?" Pinkie asked, speaking so fast that most of her words seemed to blend together into one very long word.
"How did you know?" Twilight lifted herself off the ground.
"Just a hunch," Pinkie grinned.
Twilight was speechless for almost a full minute. When she was finally able to speak, she said "Pinkie is right. Cheesecake was the first known pony to exhibit these powers. Even better, we've solved Cheese Sandwich. Cheesecake has two foals, Cheeseburger and Cheese Pie. Cheese Sandwich is descended from Cheeseburger, while Cheese Pie had a daughter named Apple Pie, and Apple Pie's children formed the Apple family and the Pie family."
Pinkie was so excited she started bouncing around the room, crashing into just about everything before landing on Twilight. Neither of them noticed that Discord had been unusually quiet this whole time, until Pinkie asked "Wait, so what does this have to do with Discord?" As they both turned towards him, they realized he looked very sheepish.
"Tell us what you know, Discord," said Twilight.
"Ah, well you see...Cheesecakewasmedisguisedasapony!" He blurted out.
"What!?"
"Well...The Draconequus king sent me to spy on Equestria and... My disguise was a pony name Cheesecake,"
"You... Were Cheesecake..." Twilight's eye twitched. "You! Were Cheesecake! And you didn't think to mention it sooner!?" She shouted as her eyes twitched uncontrollably.
"Slipped my mind."
That was the last straw. There was an extremely loud scream of "Discord!" coming straight from the Castle of Friendship, just before all of Ponyville was obliterated by a massive wall of purple magic.
o0 Five Hours Later 0o
Princess Celestia looked upon the ruins of Ponyville from her balcony in Canterot. "Good thing we were able to evacuate the entire town before it met its unfortunate end," came the voice of Princess Luna.
Celestia only nodded before replying "Indeed. Twilight can overreact to just about anything."
"Well, learning that one of your best friends is the descendant of one of the most tyrannical rulers of all time can have that effect."
"True... But it was still rather amusing,"
With a smile, Princess Luna replied "Agreed."