This alternate end takes place just after horse-Twilight thinks her last thought.
So this was it. Twilight had finally bitten off more than she could chew. The universe was crumbling like a poorly-made cookie, and there was nothing she could do. Thankfully, there was one thing she couldn't have calculated that finally saved her (hay) bacon.
The universe had finally had enough of her crap.
In most universes, you don't get so lucky. Most universes are content to let you sit back and let you entropy it to death, nuke yourself into oblivion, or accidentally build a device that denatures bosons or something. But this universe was special, and it decided to fight back. It didn't care if Twilight could see through the cave gas, or whether she bore the Element of Magic and had control over all magic, or whatever the case was. It wanted to live, dang it! It was like a rubber band on the verge of breaking, but instead of snapping in two, it was going to bounce back. And like all rubber bands bouncing back, this was going to sting a little.
Only this rubber band was a universe. Or something. ...So it was probably going to sting a lot.
The universe put itself back into the videotape rewinder, running itself back until it heard the click. Then it went back into the VCR and played on fast-forward until it caught back up to when Twilight was disproving magic. Of course, it got there a little late, so it had to rewind itself a bit. But then it went too far again, so it fast-forwarded again. This went back and forth about 8 times, until finally it found just where it wanted to be.
Twilight wrote her simple proof. “Assume magic. However, everything disproves that assumption. Therefore, not magic.” Once again, she began to laugh. “Haha. Hahaha! HAHAHAHA!”
Suddenly, she felt a massive migraine well up in her brain. It was something like déjà vu mixed with an incredible magical sense of wrongness. After a few seconds, it wore off, but she was still oddly perplexed by such a strange sensation. Was this what Pinkie Sense was like? She looked back at the paper. “That's odd,” she said. “There's some writing here that I didn't put.”
There, at the very bottom, was a note:
Twilight,
Saying that something's impossible doesn't make it so.
The headache was payback. Trust me, you deserved it.
Signed,
U.
“What in Equestria are you doing? What's so funny?” Spike asked.
“...I think I just got poked in the brain by the universe,” she replied.
“Uhh... have you been taking lessons from Pinkie Pie again?”
“I guess... I have, Spike.” She shut her books one by one. Looking back at Spike, she gave him a cheerful grin. “You know what I've learned? I've learned to take each day at a time, and to cut back and have fun now and then. Now, I think there's a party waiting for me, isn't there?”
“Yeah! Come on!” Spike led her out the door. Twilight looked back into the room, but it wasn't a sense of longing or regret. If she wanted to learn about the secrets of magic, she'd wait until the universe was good and ready to tell her.