Kuwaya wakes up on the Red Onyx Plateau

To learn how Kuwaya got here, read this

Kuwaya Wakes Up

Kuwaya's awareness emerges from nowhere and is filled with a sound, loud, hollow, and deep. Next, comes the pain, and the worst part it is the smell of burnt flesh. For a moment, he screams.
His first thoughts are questions, in no particular order: Where am I? What happened? Am I alive? Did it work? Why am I hurting? He waits, but no answers come.
Unsatisfied, he tries a different tactic. My back is colder than my front, he observes, my front is warmed by the surface on which I am lying. Impressed with himself for figuring out that much, he rolls over his right side and onto his back. His left hand flops onto the surface, and the pain intensifies. "I must have hurt my left hand. Well, that answers one question, at least," He says to no one.
His voice is carried away, and he realizes that the sound is wind, chilly, arid, and unchanging. He thinks he can open his eyes; so, he does. He stares at a pale golden sky without a sun.
He sits up and considers the warm glass-like surface. It constitutes thick and thin bands of reds, blacks, and whites. I'm sitting on a chalcedony plateau, a Red Onyx Plateau. Then he gazes outward and realizes that it is a plateau, one that stretches out as far as his eyes can see, an infinite flat surface. This gives him vertigo and he retches.
"Ok, enough of that. Focus. Collect data," he sets his shoulders and straightens his back. He observes the featureless sky, featureless landscape, infinite surface and raises his eyebrows, "Ok, data collected. That was quick."
"I must be dead," he theorizes, "well, I could be in a coma. And, since it's harder to come back from the dead, coma it is." He pushes himself up and winces, Oh, yeah, that. His hand is burnt - red, swollen fingers, a few blisters. He flexes just a bit. "Prognosis, Doctor?" he asks himself. "You'll live," he says, standing.
He gathers his long hair blowing in the wind and does his best to tie it in a knot. As he does so, he glimpses something black against the horizon. Shrugging, "good a direction as any," he says and starts walking.

Kuwaya starts walking

Kuwaya reconstructs his last moments. "Lmar at the console, server rack that I keep forgetting to install in the hallway, my favorite wool socks," he pauses to consider his bare feet, dammit, he sighs, "exposed pipe, capacitor, red wire, Russell." Kuwaya stops. "Shit, the Faraday cage. The detector wasn't designed to handle ambient electromagnetic fields. No wonder it went to crap."
Walking is a bore until he realizes the blackness on the horizon had morphed into a spire. It is a jagged soot-colored edifice. Its craggy surface is pocked with inky-black caves. Without any point of reference, Kuwaya is unable to determine the structure's size. However, he surmises that "it's fucking big." Kuwaya gestures with his hands as if announcing to an audience, "I dub thee, The Spire!"
At that point, one of the pocks begins to move. He slows to a stop and lowers his hands. The pock at first sprouts what reminds Kuwaya of filaments. Sensory organs? Is this thing alive? is his first thought. A cacophony of thoughts replaces that one as the filaments become worms, worms that begin to crawl down the side of the spire, leaving a wet-looking black smear on its surface.
Curiosity sinks into the part of his stomach where fear resides as the mass of black worms swarm over each other and move in his direction. Their bodies undulate rhythmically. As they approach, one or both ends of a worm will lift and vibrate. It's like Quantum Strings, he thinks before the vibrations resonate in Kuwaya's brain, causing pain. The pain can't be in my brain, is his last rational thought as fear, having consumed all curiosity, emerges triumphant from his stomach as terror. He turns and runs.
Better in brain than in brawn, Kuwaya's step falters. He tumbles a few feet. The pain in his brain explodes as blood from his nose, eyes, and ears. Can't be brain; doesn't make sense. He looks up through a red haze at an oncoming tide of inky wet streaks. As he does, a thick cloud of silver whistles over his head. The silver cloud hits the worms, riddling them with holes. The first worms collapse as more silver, spheres, it's a cloud of silver spheres, tear their way through the worms' flesh. The worms try to fan out in defense, screaming their pain into Kuwaya's brain, but they react too late. The stench of burn and blood and something else altogether fouler fills Kuwaya's mouth and nose.
Too frightened to look at what might be behind him, too disgusted to look at the smoking oily flesh before him, Kuwaya closes his eyes. He feels a cool liquid seep under his body. His breath quickens as it lifts and moves him away from the towering rock and its vile denizens. Kuwaya does not move. The only sound is his crying, and that is silenced by the howling of the wind.

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To learn what happens to Kuwaya, read this