Well, whether or not there’s anything we can do on the solving-things front (I’m not entirely convinced either way), we always have the option of looking closer at the story part of the ARG. I’ll throw out some of my thoughts regarding it, in no particular order. Hopefully it makes sense, hah.
We know for sure that Welsh and Stone were stealing pizzas from Horn, and Sisk was eating them. Dr Montero might also be involved in some way (he was mentioned in Welsh’s diary to have complained about Lab D’s budget being disproportionate, and “thinks Dr Horn has been misappropriating funds from the lab budget to buy pizzas with, and fund some secret project”), but it’s not really clear either way. Meanwhile, Horn, Bottomley, and maybe Junek are all in on the conspiracy. Interesting to note that one of the whiteboards has Montero telling a Paul (possibly Dr Bottomley, but there is another Paul on the BMS team who’s in-game alias appears to work in Sector C, so it’s unclear) to call JD Marcel, who’s been associated with the ARG in general for quite a while. I know next to nothing about Bugs, so I can’t really say what that means.
Welsh is actively working against Horn, and appears to have gone into hiding, possibly with Stone (“Dr H–N #~~ Don__### LET HIM __ fi#d…us”). Horn knows about all this, is pissed (but apparently doesn’t care at this point: “They stole the lie, as if that matters to me, HALOS is far too complete to stop now.”), and is trying to hunt them down and get revenge (“I’ll find them though and they will pay, they will definitely pay.”).
What’s interesting to me, and I’m not sure it’s been really brought up, is the way that Horn segues immediately from “revenge” to the Bugs quote, then back to revenge. (“Dr Marcel was right when he said, “When you’re building a cage for Satan, you don’t ask him to wait around whilst you put the doors on.” Welsh is probably behind this, but he won’t get away with it.”) From what I recall from my skimming through the early thread, people figured ‘Satan’ referred to Halos itself, but what if instead refers to the other personnel at the Biodome complex? What if Halos was meant to be the ‘cage’ and keep an eye on all of them in some way, but Welsh/‘Satan’ figured it out too quickly, before the ‘doors’ were put on/Halos was finished? Considering the devil horns scribbled on Lies.jpg on the wiki, maybe this isn’t too unreasonable a jump. And if Halos was, indeed, intended to observe the other science personnel and keep tabs on them, it would fit with the references to being watched, and could explain Horn’s certainty that Welsh and co. couldn’t hide “not now, not now I have this, this holds the key to all things…”.
On a different note, I remembered hearing something about Sisk in the AM announcements on one playthrough, so I went through the VOX announcements on the mod version (don’t know where they’re kept in the Steam release, and I don’t think I have the tools to look at them anyway, but I’ll give it a shot later on anyway). There were only a few of interest, and I’m pretty sure most of them were mentioned already, but just for posterity’s sake here they are:
C1A0_18: “Security officer Sisk reports medical emergency in Administration Center.” (This one is repeated in C1A0_41, but with another security officer whose name I can’t make out.)
C1A0_23: “Doctor Stone, Doctor ???, Doctor Junek, please report to Plant Processing for unscheduled emergency shutdown procedural test review.” (Again, couldn’t make out the middle name. Nobody else involved with the ARG, though.)
C1A0_29: “Doctor Horn, please call Residue Observation Tank 4.” (This one I know’s been mentioned, but here it is anyway.)
The only ones that seem particularly relevant are 18/41, especially since it’s repeated the way it is. As I recall, the leading theory on the pizza-niobium connection was that niobium was being smuggled in on the pizzas, and we know that Sisk has been stealing and eating Horn’s pizzas. Niobium salts are very toxic, so eating a pizza seasoned with niobium would cause a medical emergency for sure, so this could back up that theory (if it wasn’t part of what inspired it in the first place). Of course, for Sisk to be doing the reporting, he’d have to have shared it with someone else (not inconceivable), but the bigger problem is that Administration Center, from what I gather, refers to the Office Complex, which is… an unknown distance from the Biodome Complex. That would be quite a way to travel with stolen pizza. (Also, they’d be eating pizza at 9 in the morning, but cold pizza is a great breakfast so it wouldn’t surprise me.) This would also mean that this is presumably the first time Sisk took one of the niobium pizzas, otherwise he would have gotten poisoned before; but the whiteboard note complaining about him would probably have been written recently, too, so it’s not too far a jump.
Finally, the room under the stairs in QE. Someone (Horn, possibly, though the pizza-lie graffiti suggests otherwise) was presumably using it to hide out after the Resonance Cascade, maybe beforehand. Last time I checked it out on the Steam version, there was no escape hatch, but it was otherwise pretty much the same. This is interesting; it suggests to me that whoever was hiding out in there wanted to make their escape inconspicuous. That might also be the purpose of the cube-man: if any of the military managed to get into that room (in spite of the complete lack of entrances, beyond the now-missing hatch), they’d see what looks like a dead scientist, and if they didn’t think to investigate closer they’d just assume someone else got to him first and leave it be.
The thing about that room that I’m not sure anyone’s brought up is how the ‘Die Freeman’ graffiti relates to the story. My theory was that Horn was keeping tabs on Freeman (possibly via Halos), and either A: saw that he was headed for the Biodome complex and was worried he would do something to Halos when he got there, or more likely B: Horn knew that he caused the Resonance Cascade, and was very pissed off about that (for both the obvious caused-the-end-of-the-world part, and for screwing up all his plans as a result). Remembering ‘21 goes into 1’ and the fact that sample EP-0021 was originally supposed to be used, it might be that Horn also wanted it for Halos for some reason or other, and was just mad that it got used (even though it didn’t, but he wouldn’t necessarily know that), but that wouldn’t be enough to warrant scribbling ‘die Freeman’ in multiple places around the room. Even if the person in the room wasn’t Horn but Welsh/Stone, B is still a possibility. Either way, the 247 graffiti still seems out of place, but I wouldn’t write off the whole room as just being there to catch our attention and get us looking for things.
So now there’s the problem of what Benaloh-Paillier refers to, when it apparently isn’t the key to the 752 hex, and it’s unlikely to be the series of encryptions used to get it either. We know from IRC clue 4 that halos is a username for something related to BMRF, and twice now Benaloh-Paillier has been referred to as a password related to Halos (either the password to the Halos files, or to ‘its area’). Plus, we have a mention by Horn on Stormseeker’s website about hiding something on ‘the secure site’, which I’d guess is either Stormseeker’s site again (in which case it’s probably a reference to HALOS.txt), or else terminal.bmrf.us.
My theory is that, whenever terminal.bmrf.us goes back up again, we’ll get to log in, and it’ll be username halos, password benalohpaillier.