Twilight Sparkle had been very eager to get started following her hunch. So it wasn't a surprise when the princesses invited her to the castle. The surprise, however, lay in the fact that they were so secretive about it: everything was obscured in shadows. From what looked like Celestia's shopping list fading to the real note about three minutes after Spike belched it out, to the strict order to tell nopony, not even Spike about the contents or her destination. This was, of course, encoded with the keyword from the shopping list banana, such that to anypony else trying to read it, it looked like gibberish. Even the way Twilight was to travel was secretive: Two Night Guards were going to show up tomorrow morning at exactly 5:37 AM, knock twice, and only twice, then depart one minute later, with or without Twilight in tow.
The whole thing made Twilight nervous, real nervous; stumbling into a Level 7 security clearance area nervous. She knew that while she was Celestia's favorite, that can only get you so far with the safety of the nation at stake. She didn't want to die just yet. No story was worth chasing for that to happen.
So she was completely bewildered when she found, at 5:48 AM the next day, she was in the air, en route to Canterlot, on Luna's private chariot, no less. The cool rushing air had awakened her, both from the physical component and the haze that had been her dread. Now that she was thinking clearly, she reviewed the facts from both the book and history class. First and foremost, it had always bothered her that the Hearth's Warming Eve pageant seemed vague in time frame, but she had always assumed that that was just because the message was the important part, not the details.
That said, she was suddenly curious why she herself hadn't scrutinized over the details before; it would have been easy enough to do, after all. Oh, well, she decidedly thought. At least I'll be able to ask the princesses about it, after the whole "Sun Swirl" and "Moon Swirl" thing, that is.
It was just after sunrise when they approached the normal dock for Canterlot Castle. The night guards picked Dock Eight and gave a yawn before starting their approach. Twilight didn't think anything about it, until they were decidedly not slowing down. As soon as she was certain of this, Twilight's mind went into panic mode, adrenaline making everything seem to slow down. She wanted to cry. So this is how it ends? Crashing into a dock on my way to the princesses? I bet they didn't even put this flight in record, so it'll look like an unsanctioned flight, too; the night guards were obviously fatigued and unfit to fly such an arduous journey–it's the perfect way to kill somepony who knew too much. Oh, there's the ground; I can't watch!
The impact never came, though. Instead, a strange sound rang on the ground in front of them, and when she ventured to open her eyes, she saw black nothingness ahead. Craning her neck toward the last source of light she was certain she'd ever see, she was startled when the bright red-orange ring around it suddenly vanished, leaving her and her flight crew in abyss.
As they leveled out, lights came on overhead with large metallic sounds. Twilight marveled at the sights that came with them: things she had never seen before; things the likes of which Pinkie Pie had only described. Suddenly, Pinkie didn't seem so crazy when, right in front of her face, were things Twilight would only describe as indescribable. There were things she thought forbidden being practiced here, such as necromancy and transmutation on live ponies. Things that, she knew, were to never see the light of day. There were technological marvels, stuff she theorized should be pony lifetimes away, being treated as though they were fifty-year-old technology, strewn about as though they were commonplace and ubiquitous around here.
Maybe they were, for all she knew.
At the end of the makeshift runway they found themselves on, Twilight noted there were two high-backed chairs facing away, one light, one dark. However, the Sun was on the dark one and the Moon the light one. The chairs also had two halves of a strange black-and-white circle, with a swirling, teardrop-like pattern contained therein. On the chair with the Moon, the black half was present; the Sun chair held the white half.
Upon reaching their destination, the two guards unhooked themselves from the chariot. They got no further than five paces away when that red ring opened up beneath them. This time, however, was different. There were flames shooting up from the ring. To Twilight, it looked like the very definition of Hell. The pegasi hadn't had time to react as their wings caught on fire. They whinnied in primal, abject fear, but the ring only increased in size in response. One more terrified look in their eyes, then they and the red ring were gone.
Twilight sat there, stunned. Just what had she gotten herself into? It was too late to turn back now; that much was certain. She wanted to, though. She wanted to run home and cry, now more than ever. She'd just sat by while two ponies were murdered. For her sake. She felt worse than if she had actually done the deed herself. All she could do, though, was look at those otherworldly chairs.
"You're 4.4 kilometers below ground, you should know. That game, Portal 2, all over the Ponynet? VALVe is run by operatives from here," an all-too-familiar voice stated, albeit without her usual warm, instructional, or motherly tones. Celestia continued, "We allowed them to release some of the technology early in a sci-fi fantasy setting. Still, the tech displayed in the game won't be available to the military for some two hundred years, so don't expect to go pick up a portal spell tome any time soon."
"Princess Celestia?" Twilight asked with a little more shock in her voice than she anticipated.
"And yet," the seemingly radically changed princess continued, as though she hadn't heard her favorite student at all, "none of this compares to the biggest secret of all of Equestria. The only Level 10 secret we have. The secret you uncovered." She and Luna turned around.
Twilight had to catch her gasp. The princesses were still princess sized, but gone were their pristine coats and blemish-less complexions. Replacing them were battle scars of various sizes, lazy eyes, and missing chunks of flesh that had been poorly hidden by bad comb-overs. What made it all the more unsettling is that their manes were the exact same as when they had their respective illusory spells applied.
"For you, Dearest Twilight, are the first pony to see us like this in over four hundred years. And, might I add, if you want to be the first to keep breathing in eight hundred, I suggest you tell us everything you know about Sun Swirl and Moon Swirl. Now."