Dues Ex Regina
The universe was awfully quiet.
This was, of course, to be expected, as all baryonic matter had evaporated into radiation or been sucked into infinitely dense singularities. Things had been this way for a long time. The entire Stelliferous Era could've happened a trillion trillion times over, and it would all happen a vigintillion times again until the final heat death of the universe.
But it was far from dead.
Princess Twilight Sparkle wandered this dark, empty universe, no longer bound to any physical form, but instead existing as a quantum excitation of gravitationally bound photonic radiation - a fancy way of saying that she was a sentient ball of light. She was its caretaker and its sole occupant - so far as she could tell, anyway.
She had kept it all going for as long as physically possible. After the first Equestria had died, unable to survive once her star had cooled to a brown dwarf, she had been lost. She was an Alicorn who could not die, trapped in a universe that still obeyed the second law of thermodynamics. Her magic was unfathomably powerful, but nothing could reverse entropy. Eventually, she realized she didn't need to reverse it - she just needed to forestall it as long as possible.
And so she built a new Equestria, throwing together a sun from wisps of gas and crafting a suitable planet from interstellar dust. It took her a couple billion years to figure out how to create ponies from scratch, but eventually she managed it. She was filled with joy as her happy little ponies flourished on her new world, bringing joy to each other and making the universe a better place.
Then, over billions upon billions of years, its star began to cool, and eventually she was left with another barren wasteland. So she did it again, and again. She got clever with how she constructed her white dwarves, maximizing the amount of usable heat they would generate. She started building her own stellar neighborhoods, her own nebulas and binary systems. Eventually she was building entire galaxies, trying desperately to replace the dwindling number of twinkling dots in the night sky and crafting entire interstellar civilizations that ran on friendship and magic. She was determined to fill the universe with as much joy as she could possibly create, so that every imaginable creature could live and breathe and contemplate the joy of existence in the paradises that she wrought from dust and wishes.
Alas, conquering entropy proved to be beyond her grasp - It would always increase to a maximum. All her godlike powers could do nothing but carefully shepherd her existing matter until it finally all evaporated after a trillion, trillion, trillion years.
But Princess Twilight wouldn't give up. The same physical processes that were driving the slow heat death of the universe created more and more computational potential in the quantum foam of space-time. By extracting energy from rotating black holes as they dragged the fabric of reality around them, she could turn her entire universe into a giant computer, enough to simulate any other universe she wanted trillions of times. The lonely stretches of space and time that she watched over ticked away, tiny quantum gates making single-qubit calculations at a glacial pace.
She just needed something to simulate.
And so, she made Equestria whole again. Yet, by following the laws of physics she knew, she was introducing the very law that threatened to unravel her universe. In each and every one of her toy universes, entropy tends to a maximum. Eventually, everything died. They would always die in the end.
She, however, was Princess Twilight Sparkle, who had built her own reality out of the tattered remnants of her universe. It was time for some experiments. Her goal: to build a universe without entropy. She quickly discovered, however, that entropy was quite necessary for life to exist, because actions required some sort of thermal gradient to operate in, which itself implied entropy.
So she tried to be sneaky. She would instead create a universe where entropy existed, but was reversible. This seemed promising at first, but she couldn't get life as she knew it to evolve. Strange, possibly intelligent structures of some sort emerged from the primordial soup, but their actions seemed overly predictable and simplistic. It was like watching a bunch of self-replicating typewriters, and she deleted the whole thing in a bout of frustration.
She needed something more radical - like a universe that minimized entropy instead of getting rid of it entirely in a way that still allowed life to exist in all its wonderful forms and to spread friendship and magic, but on enormously extended time scales. This proved to be difficult, because magic kept getting in the way.
It seemed that magic had an intrinsic property of increasing entropy. This was frustrating because she didn't know how to build a harmonious planet, let alone an entire universe, without magic. It was dangerous and what life did manage to evolve was limited to violent predators that existed in a state of perpetual misery, fighting amongst themselves over bits of meat or golden trinkets. It was sickening, and she put those simulations out of their misery as quickly as she could.
Sometimes she felt guilty about creating such pitiful creatures. She never intended to, of course, but had they known their entire wretched existence was a goddess’ mistake, they likely wouldn't be too charitable about it. It got to the point where she developed several new theories of existence to help make better estimations. Now she could check if her initial conditions were worth simulating at all, and minimize the amount of misery she might inadvertently create.
Eventually, she ended up with a sort of meta-simulation, a gigantic program churning through trillions of possible initial values, searching an infinitely dimensional fractal solution space for hints of a universe that would result in Equestria, but with physics that did not allow magic.
Finally, it found one.
Twilight was so excited she didn't even check the parameters at first, she simply dove right in. The universe looked beautiful, but also seemed alarmingly devoid of life. However, this was simply a prototype, so she executed a short search routine to find the location of Equestria along the universe's 4-dimensional hypersurface. She found herself hovering above a large blue marble, and while it was teeming with life, she immediately realized she must have made a grave mistake.
Most of the planet was made of primitive creatures viciously hunting each other in a never ending fight for survival, and the only intelligent life was a bunch of violent predators, who had run out of meat to fight over and invented an alarming number of other things to fight over instead.
Princess Twilight Sparkle was absolutely baffled. Surely she had made a mistake in her calculations? Yet, the results were clear, pointing to a form of Equestria buried somewhere in this chaotic world. Part of her wanted to simply leave and try again, but she was drawn in by her insatiable curiosity. How could any form of Equestria exist here?
For months she scoured the planet's surface, trying to find where her ponies had buried themselves. Perhaps they needed to be rescued? Taken far away to a safe place filled with friendship and, well, safety, since this universe didn't have magic. But she found no ponies, and precious little friendship.
While meandering through one of the massive concrete jungles, she noticed something that looked incredibly familiar. It was a picture of one of her little ponies, drawn by one of the intelligent predators. Twilight's imagination was filled with visions of a dystopian zoo, where her little ponies were trapped. Immediately, she began executing a search routine for graphical depictions of her ponies, hoping she could at least find them, though they might be beyond saving.
She found many drawings, but no ponies. Despondent, she wandered through an enormous hall filled with pictures that all seemed to resemble her ponies. So close, yet always missing some crucial detail. Why was it all here? They even had animations, though thankfully they seemed entirely imaginary and not actual recordings.
Lost and confused, Twilight's disembodied mind floated around the city, looking at the strange behavior of the local population. It was while she was staring idly at a wailing child that she had an epiphany. An adult handed the child a small stuffed pony, and the child's wails were almost immediately silenced. It clutched the small pony and seemed calmed by it.
She had made a mistake. Equestria certainly existed in this universe, but not in any physical form. It existed only as a fantasy in the minds of these tortured creatures she had accidentally created. She had built an entire universe inhabited by miserable, violent predators whose only joy was found in the fantasies they shared with each other - yearning for impossible things that could never exist, and never knowing why they were so drawn to them.
Had she still been corporeal, she probably would have vomited, but instead she swore to end this universe's pain as quickly as possible. Next time, she needed to refine her equations to correctly differentiate mental constructs from physical ones, and probably inspect the initial conditions a bit more carefully before simulating an entire universe so carelessly.
Princess Twilight Sparkle floated beyond the 4-dimensional curvature of that doomed universe, back into her own, trying not to think about what she had done.
She turned off the universe, and you ceased to exist.