Okay, this is far from your first time around the block. You know it's awesome. I won't belabor you with compliments. Until it's on the mainsite.
The biggest issues I see are that the deeper you get into the story, the more that clinical tone starts to slip away, or the more that the loving descriptions of what's happening get too lovely and don't quite feel appropriate for what the document is.
PoI-5963 ascends a raised edifice overlooking the basin and begins to chant unintelligible words that no human could possibly reproduce.
You're pointing to the lampshade. The Karcist is a person, but not a human. We get it. It's a little strong. That last phrase just feels unnecessary.
This torturous method of sacrifice continues for over 2 hours, bathing the chrysalis in blood, organs, and general viscera.
I'm all in with the body horror generally, but this is now an engineering problem in my mind. What kind of saw takes two hours to cut through a person? I'm imagining the triceps you have to have to even hold the damn thing up that long. Two hours is a long time. Is every victim being sawed by one "hooded servant"? There's a plurality of servants but it's not specified. Is everyone just quietly listening to the sound of tooth-on-viscera that whole time? You might consider toning this little bit down just to avoid silliness. Or don't. Again, you don't really need much critique on this.
She tear off a portion of her dress and uses it to cover her face before entering the courtyard.
tears
she suddenly peers down and finds her bare feet (high heel shoes were not conducive to her survival) on top of what appears to be the first step of a stairwell.
That's just a weird aside. It's correct, but why does it need to be mentioned? If you need her to have bare feet for later plot purposes, she can just lose or abandon the heels earlier before this point. It's a jarring addendum.
Agent Kennedy looks to a nearby building, which is so close that it nearly touches the structure where she presently resides. She notices an opening in the building, left behind by a collapsed wall, which she proceeds to jump through, tumbling among the wreckage. Standing up, she takes a moment to observe her new environment. Though just as ruined as the last, its architecture implies a drastically different culture or time period
This whole paragraph is very Tomb Raider-y. It's hard to pinpoint what parts of it feel nonclinical to me. I think a lot of it is phrases like "the structure where she presently resides", which just feel too circuitous and not direct enough. "Though just as ruined as the last, its architecture" has the same feel. Starting that sentence with "its architecture" gives it more of a feeling of someone passively describing a video they're watching, rather than someone lovingly narrating visual scenery that they're attached to because it's a universe they're trying to depict for a reader.
Also, you missed a period there.
She entered the room, discovering a number of personal objects more suggestive of an apartment.
I mean, the things about the room that appear to suggest that it's an apartment are more like appliances than "personal objects", but I guess I'm getting technical here.
The black effluvium dissipates after the passing of several minutes, revealing little more than fresh blood and viscera
That purple prose again. Not the effluvium; that sounds clinical enough. The "little more than" adds nothing to the clause it's a part of, and including that phrase makes it sound very "telling a scary story by the campfire" vibe to it. "And when the werewolves were done with the cheerleader, the police found little more than scraps of pom-poms littering the forest! And she was never seen ag-ayn! Bwa-ha-ha!"
She pauses in front of a mirror, revealing the gross extent of her skin damage.
"Gross" doesn't help you here. We can guess that it's probably not cute. Unless you meant "gross" in the sense of "large or expansive", in which case we still don't need the word. We can guess that it's probably not small, or you wouldn't have commented on it.
She encounters a Brazilian newspaper dated 04/09/1977, though its faded words are illegible.
I mean, it can't be that illegible if you could tell that it was Brazilian, right? There must have been some words. I would resolve that inconsistency.
Do the rest of you hear the whispers? I've hear them in the howling wind. Heard them spill from the wound of a dying beast. Spoken from the motionless jaws of a hundred thousand skulls.
This whole segment has the super purple vibe going on. Don't get me wrong, I understand that a transition has happened by now from "she's a tired refugee trying to survive to make it back to the baseline world that we, the reader, are familiar with" to "she's some kind of prophet trying to work her way towards whoever the master of this world is to elucidate the plot of this story". I get that the writing style should change to reflect that. But it doesn't change the fact that this whole thing has a "responding-to-a-high-school-creative-writing-prompt" feel to it. I don't know how to suggest you fix that. Maybe you don't need to. I'm just kvetching.
She approaches the edge of a cliff, the video feed revealing a landscape of tormented faces and malformed fetuses the size of mountains. She sits down, dangling her legs over the edge, and stares at the colossal aberrations for hours.
Again, it feels like the Foundation employee who's transcribing this video went a little rogue on the description. The video reveals pixels. The pixels suggest shapes. The transcriber has to choose how to describe this for scientists and archivists to record and analyze later. And the transcriber chose to describe "an landscape of tormented faces". It's a little Slipknot.
Maybe one day we'll meet again beneath rose colored skies.
Tsk. Not feeling it for a last line. I know that's what you're going for, the stinger, the little line that makes the whole piece memorable. The line that people will quote in conversation with others and the others will know exactly what they're referencing. I dunno if this is it. And no, I can't suggest a better one. I would just suggest brainstorming different options. This one feels too long, and at the same time both too specific (wait, why is the sky rose-colored? is it red for good reasons or bad reasons?) and too vague (wait, that's all you have to say about the circumstances that would cause you and me to be in the same place? Because I really want some assurances that if we ever meet, there aren't going to be a big collection of flesh monsters roaming the landscape eating my cats).
Okay, that's all I have. Mostly nitpicking. You could probably post the whole thing as is and be fine. But these are thoughts. Do with them as you will. Good luck!