I don't think that this is going to work. Not as an 001 proposal. Probably not as a mainlister. Sorry, I'm going to be pretty direct with this.
At it's heart, this is just too basic - all the bells and whistles, mystery and misdirection, can't hide the fact that there isn't enough substance at the core of the article. It feels like a bunch of literary devices (the "does not exist" stuff, "it listens", the expungement, the various epistolary sections) that aren't being coordinated towards a common purpose. If you've ever seen a bad fireworks display, you might get what I mean - none of the individual elements are bad, it's just they aren't deployed in an effective way. And I don't think that shuffling them around will help - you need to find a stronger story to anchor your writing.
A few specific thoughts:
- Starting with the physical description of the site would be better than what happened there.
- "supposedly", "appease", "fed", "hinted" - your description starts with a lot of non-clinical tone, which undermines it immediately.
- "despite the fact …" - there is nothing in the text to suggest that Darkbody scenarios can only be caused by sapient things, so this phrase was jarring.
- "Evidence recovered from…" - it's weird that the Foundation had no records of the site other than what was on the site itself. I can't think of any other example of this in any organisation. I also note that the Description is clear that Site-01 is a Foundation site, despite the Specialised Containment Procedures requiring otherwise.
- You have way too much redaction and expungement - it hits the stage of detracting from interest, rather than piquing it. That's particularly true where you say so little about the anomaly to begin with.
- The diary entry is unconvincing, I think. Why would anyone (especially anyone with knowledge of the anomalous) stay at a place described here, let alone keep a diary while they wait for their transfer?
- The HCML notes are also very heavy-handed and not terribly clinical - the exposition here is forced, rather than natural.
- The footage log has some decent motions towards nightmare surreality. I think it would be improved by lengthening it, and losing all the "does not exist" stuff, and the footnotes in particular. That phrase is not descriptive, meaning it is out of place in a log (the purpose of which is to describe).
- The first O5 note is again very unprofessional and exposition-y. No-one writes like this to fellow executives - it's too faux-poetic. The comparison to Site-13 is doing you no favours! I would lose it.
- The last bit, with O5-12 on a chat(?) and then switching to narrative description for four lines, is really jarring. If you want to get the stinger across, you should try to build it into diagetic documentation.
Your writing isn't bad. Clearly you can use writing elements to aim for particular effects, so you have the ability to use them more effectively than you do here. But this idea either needs a lot more work put into the core story and concept, or needs scrapping so that you can use your literary fireworks in a more fitting display.