Two hundred years ago, Luna disappeared, and a few hours later, so did Celestia. Twilight explains the real reason why, and what it had to do with what Celestia had discovered in the vast and brutal world of the humans a thousand years prior: a being far more ancient, powerful, and inscrutable than anything Celestia had ever known.
Princess Celestia I of Equestria was, or perhaps is, just as mighty, wise, and good as the legends say. But she was afraid, too, and with good reason. On the two hundredth anniversary of her and her sister Luna's disappearance, it's probably time that the whole story be told, or as much as we ponies know of it.
I write for the ages, so I should assume no familiarity with the present. I am Princess Celestia II, appointed successor to Celestia I, born under the name Twilight Sparkle 254 years ago. I rule Equestria, the ancient country of ponies, with Princess Luna II, born under the name Cadance 265 years ago. We are sisters by marriage, but Luna's husband (my brother) and their daughter were mortal, and died long ago. To today's mortals, Celestia I and Luna I are no more than historical characters, the half-mythical founders of our country. But I knew Celestia from when I was a filly, and what I didn't see of this story with my own eyes, I heard from the horse's mouth.
Celestia wore many hats in the first few centuries of her reign. She was busy trying to nourish the growth of a shared civilization that had abruptly formed, as a matter of necessity, from the remnants of three different tribes that were interdependent but all nursed ancient grudges against each other. At the same time, she had to protect the infant nation against warmongers and titanic monsters who didn't even feign interest in diplomacy. Like her sister, and her subjects collectively, she was frequently underestimated, and the Equestrian border turned out to be the last stop of many would-be world conquerors.
However, Celestia's power came from wisdom, and her wisdom told her that there were some fights she could never win—some foes who, were they to set sights on Equestria, would be totally unstoppable. At first she only suspected this out of humility; later, as her magic grew strong enough to let her peer across the gulfs between worlds, she found examples.
She found what she described as by far the most important and fearsome of these examples in the world of humans. Humans are a race of almost hairless apes who walk upright, towering over other animals. They have no magical ability whatsoever, but are probably the universe's greatest scientists, having built, with their thin, nimble fingers, powerful machines for every conceivable purpose. They have machines that can travel hundreds of miles an hour through the air, machines that allow them to hold a library's worth of books in a tiny piece of metal, machines that allow them to speak to other humans anywhere else in the world as if in the same room, even machines to use as weapons that can level a city in a moment, and machines to assist in sexual gratification. They are in a sense brutes, being endlessly preoccupied with sex and violence. But who can blame them? They have delicate constitutions and live in a brutal world, where the sun (which their planet rotates around) is a million miles wide and millions of miles away, where nature runs autonomously and ranges from indifferent to lethally hostile towards humans. Even the sights of the human world are harsh, being dully colored, and often either too dark to see or washed out in the intense glare of the sun. To humans, our world would seem gentle and forgiving.
The humans' harsh world is reflected in one of their most central scientific ideas. According to human scientists, the complexity of the natural world didn't come into being fully formed. It developed from extremely simple beginnings over an extremely long period of time, from countless iterations of simple processes of random change and elimination. In this worldview, morality and narrative are auxiliary, not causal. The world itself is a giant machine, grinding on with no regard for who might be caught between the gears. This is not a cheery way to think about things, but it provides a fitting founding myth for a race of creatures who have struggled so hard to eke out an existence. What's more, humans' painstaking scientific work has uncovered what appear to be the traces of eons of change in the earth, its flora, and its fauna.
Here is where things grow genuinely troubling. The reality is far worse than human scientists suspect, although most humans, who are not scientists, are at least partly aware of it. The human world, like the universe itself, is no more than 20,000 years old; the "traces" of earlier things, supposedly millions or billions of years old, were planted by a being whose power and machinations are beyond all other beings. For as with everything else, humans have an extreme and brutal notion of a god. To them, a god is not merely another human who has achieved immortality and great magical power and is now a head of state. A god is not even a living creature, or at least, not solely one. It is a being beyond space, perhaps beyond time, who was involved in the very creation of the universe. Its desires are what define morality, and it looks upon humans not as subjects but as servants or playthings. It doesn't bother using magic, because the world itself is an expression of its will. And of all the gods that humanity has hypothesized to exist, the mightiest and best-known among them is the one Celestia found, named Yahweh, whose supremacy is such that most humans simply call him "God".
Yahweh's nature is so extreme that it poses basic logical challenges, which humans have struggled with for so long that the nature of Yahweh is a central issue in their philosophy. First, Yahweh is omnipotent. Roughly, that means that he can do anything; more precisely, what he wills to be the case, is unerringly the case. Second, he is timeless and without an origin, having always existed, and never being less powerful than he is today. Third, he is omnibenevolent, meaning that all his actions and desires (which, it follows from omnipotence, invariably coincide anyway) are morally perfect. These principles can be a bitter pill to swallow even for humans, who have debated apparent paradoxes such as whether Yahweh can limit his own power and his failure to intervene against morally imperfect humans. Doubt that Yahweh exists at all has become increasingly common among humans, especially the scientists, who I suppose have enough to worry about already.
In any case, human beliefs are beside the point. The point is that Yahweh exists—or at least some being with those three qualities exists, and we might as well call him "Yahweh"—and he has been particularly active in the human world. Celestia could sense him the moment she first gazed onto the human world. With her direction, I was able to sense him, too—an unimaginably vast and alien power whispering at the edge of reality. Perhaps he seems so quiet because he is so different from magic as we know it. Perhaps he is difficult to see because he is ubiquitous and we wizards have all taken him for granted as part of the psychic background, like air in the material realm. Or perhaps he stands outside the universe, like a flesh-and-blood pony looking down at a painting full of painted ponies. Think of this flesh-and-blood pony tearing up the painting on a whim and you will begin to understand why Celestia found Yahweh's existence so terrifying, even back then. Inspection of his magical traces suggested that he'd been much more active in the human world than our world, or any other world we know of, but there is no question that a being of this power could do whatever he wanted here. Indeed, he could cover his tracks, if it pleased him to.
There is no question of resisting an omnipotent being. Celestia spoke out to him many times, but he never answered. Could we at least understand him, and learn to cope with him? Celestia pored over human texts and tried, as many humans tried, to infer the nature of Yahweh from his interventions in the human world. She then realized that because he could have affected any other world, too, the entirety of the universe was a living statement as to what he wanted to see. It would not make sense to say that something was not to his liking, because to say that somepony "likes" or "wants" or "desires" something is to make a claim about what they would bring about were they able, and Yahweh is always able. What's more, because Yahweh is omnibenevolent, the universe as it is must be the most morally perfect of all universes that might be. Our own sense of what is moral says that the universe could be a lot better, but this only shows that we must have very inaccurate senses of morality. Humans have a depressing explanation for this, too, at least for humans: humans are forever tainted by the stain of an irredeemably evil act, an act of disobedience against Yahweh, that the first humans committed.
There are still many questions. Yahweh is effectively responsible for every detail of the universe, and hence every detail poses a new riddle about his motivations. What sort of being would want exactly this universe? For one thing, what sort of being would clearly state rules that he expected humans to follow, and then cause them to break the rules? Celestia eventually concluded that Yahweh is too far beyond the experience of ordinary gods such as herself, not to mention mortals, for her to understand his thinking in a meaningful sense. It would be like trying to understand the thinking of the humans' colossal autonomous sun. Yahweh is omnibenevolent, but beyond pony morality. Would it be any different to us if, rather than being perfectly good, he were perfectly evil?
Celestia wasn't sure what to do. Yahweh created a religion, Christianity, by which humans can to an extent benefit from Yahweh's moral perfection and curry his favor. But Christianity is human-centered and offers no hope to other peoples. And clearly Yahweh does not want ponies to worship him, because they do not. Celestia decided she could do nothing but take to heart the knowledge that much more powerful beings than she had ever dared imagine were out there, and Equestria only existed because Yahweh tolerated it, or had brought it about himself—they added up to the same thing.
Celestia first had all these thoughts more than a thousand years ago, before Luna's banishment, even before Tirek's first invasion of Equestria. To an extent, she allowed herself to forget. But she told it all to me that terrible night two hundred years ago, when all of us, Equestria collectively, had grossly underestimated something ourselves. The monster said that it was here to purge the diarchy, that Equestria was mired in sin and idoltary, and that if the princesses did not leave, it would remove them by force. It wasn't very large or threatening-looking. Luna attacked it. The monster raised a hand, and Luna was gone without a trace. Her empty armor clattered to the ground. The monster said that if Celestia did not leave, it would be back in twelve hours, and disappeared. Equestria had no time for national mourning; it was scrambling to come up with a way to protect its sole remaining diarch. And Celestia sent all her advisors away, brought me alone to the most secret room of the castle, and told me the story that, she said, she should have told me long ago.
Finally, after describing everything she knew about Yahweh, she said haltingly "The being that came here today is an angel of the Almighty." She had used a traditional human epithet for Yahweh. "I cannot doubt it now. Why did he send this angel? Why did he give us an ultimatum, instead of willing it so that we had never even existed to begin with? I do not know the Almighty's plan. Nopony can. But for the first time, he has given me an order, and I, like all the universe, am his slave. I must obey."
She was remarkably calm, as she had always been in the worst of times. She explained that I would need to take over tending the sun and ruling the country as Celestia II, as I had long been training to do, and Cadance would rule alongside me as Luna II. Celestia would leave for a distant world. We should explain to the citizenry of Equestria that Celestia had fled to make the monster forever chase her across the universe and away from Equestria; Equestrians were not ready to hear that their ruler had submitted to a foreign god. With any luck, the monster would not return.
"But I must not return." said Celestia. "The Almighty has spoken. Perhaps he will let me live, and perhaps we will meet again, my most faithful student. Perhaps I will see my sister again. The humans say that God works in mysterious ways. But I'm not optimistic."
In two hundred years, I have never seen the angel again, nor Luna, nor Celestia. I like to believe that Celestia and Luna still live, roaming the universe, righting wrongs and spreading peace and happiness among alien peoples. Yahweh is so inscrutable that he might, conceivably, someday allow them to return. Having to relinquish this throne would be a small price to pay to see them again.