I was typing this just as a quick reply but it got really long and complicated, so I'm organizing it. These are just my thoughts/theories on the current story and what I think is coming in the future. Worth noting that I haven't done all of the content and the wiki isn't entirely comprehensive, so there's some gaps here and some clues I'm not taking into consideration, particularly anything from the dungeon that Bailey sends you to or the things that doctor harper does with you, because I haven't played either of those things.
The old town
The history teacher, Winter, talks a lot about how the town is built on an old fortress, and that there's secret passages connecting everything. We find this and make use of it as the player, too. Particularly, the sewer is filled with relics of the old town and seemingly even whatever was before the old town.
The old town seems to have been wealthy and important people that had all kinds of magical sex voodoo shit. We find an old horn in the sewers that's on an altar surrounded by a pit. When you give it to Winter (this is just from memory, the quote isn't repeatable and it's not on the wiki) they say it was an actual horn from an animal turned into an instrument, but that's not what they would have done with it. Interacting with the horn makes your arousal go way up, and I think even just being near it does the same.
You also find some other remnants of people who used to live in the town, most of which indicate that they were rich and important. There's a fancy candlestick, a fancy watch, rich people shit. There's also a 'cucumber statue', likely a dildo, but notably Winter seems unimpressed by it, like it's poor quality. Not something rich, important, sex crazed people would have.
Most importantly, you find a 'rough crystal' paired with a canister of pepper spray. The crystal isn't described by color and it has no effect on you, it says it's just washed up on the shore where you find it. I'll talk about the crystal more in a different section. It's also worth noting that the pepper spray is described as being the same as what you have, except it has a microchip on the bottom of it.
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The other part of the old town is the forest/lake. This area seems more ancient, not like it was inhabited by the rich people, but by whoever was before them. You can find arrowheads, ancient daggers, and (according to the wiki, haven't seen it myself) a translucent green stone on the floor of the forest.
In the lake you find the ancient ruins underwater, which is filled with glowing purple lichen. When you search the pots, there's also a chance of them being filled with purple dust that increases your arousal when you touch it, similar to other lichens we find. You can also find various pieces of jewelery, but as far as I remember, none of the man-made things in the forest make you horny, only the natural things.
The corporations
When you sell the rough crystal you find in the sewers to Winter, they tell you that they don't know what it is, but a corporation who seemed to know what it was showed up and bought it.
When you get into the compound on Elk street, you can break into various buildings there.
The first building has storage tanks around it. When you go inside, there's a pink crystal surrounded by a pool of pink liquid. There's also a chance of tentacles coming out of the liquid and attacking you
The second building has smoke stacks. The inside is filled with a dense, sweet smelling smoke that gives you a hallucinogenic affect. In the center you find a purple crystal, which also gives you a hallucinogenic affect when you touch it.
The third building has a laptop and a canister of pepper spray, again, described as being the same as yours but with a microchip on it.
When you're working at the docks, you can find a shipping crate with a similar sweet smelling, hallucinogenic smoke coming out of it, one that you're instructed to ignore.
You're also told to ignore a crate that contains a human trafficking victim that's being shipped into the town and doesn't seem to speak english.
The crystals
The crystals obviously contain some form of power that the corporations are interested in. The (probably) first one you find is in the sewers, along with all of the discarded, but definitely not trash, things from the old town. It isn't described by color and it has no affect on you, so it seems like it's 'empty'
The other two have strong, obvious effects. One being purple and hallucinogenic, very similar to the glowing purple lichen in the lake ruins.
The other is pink and tied to the pool of tentacles, and there's a pink lichen at the temple for the science fair. The lichen doesn't have any tentacles, but you are threatened with rape when you collect it, similar to when you collect the pink crystal.
There's also a white lichen, where you meet Avery and get harassed by a cop, and a violet lichen in the drains, but I don't remember the effect it had.
So there's two logical reasons that one would be empty. Either the power in it has been used up, or it hasn't been filled with a power yet. Considering the immediate interest the corporations have in buying it, I would assume it's the latter and they want to fill it up with something for themselves. Maybe avoid letting them get their hands on this crystal in future updates when it becomes relevant.
The darkness
The affects of the town seem to be stronger in the dark. I would just pass this off as a trope, but there's a couple things that make me think it's significant.
Everyone in town gets more aggressive at night. This can easily be explained by it being easier to attack people at night and get away with it.
There's one place in town that's described as being very dark, though. "The sewers are very dark, encounters aren't affected by allure." Encounters not being affected by allure because of how dark it is makes it sound like it's too dark for anything to see what you actually look like.
Coincidentally, the craziest person we know lives in the darkest place we know. Morgan has been down here for a long time and is essentially insane with rape energy.
An interesting thing about Morgan is how we know their name, they wear a uniform with a name tag on it. To me that indicates that they were still doing work when they lost their mind. Now what do we know about a place of work that has a heavy interest in mind altering affects and places like the sewers, that are filled with old town artifacts and crystals? I think Morgan worked for the corporation that bought the crystal from Winter.
Morgan was most likely sent down into the sewers to search for the crystals that you find down there. But, the sewers are a dangerous place, and it's easy to have your control meter drop to 0 down there. Unfortunately for Morgan, though, there's no extortionists or doctors to rescue them when they start to lose it, so they were left in the darkness to go insane. Morgan also suffers from the strongest hallucinations of anyone else, describing rats and other culinary horrors as "crumpets and tea," and mistaking the player for their own child.
The player also suffers from hallucinations when they start to lose control.
But again, being insane in a dark place doesn't necessarily mean the darkness is the cause, especially with the other shit going on down there. The main reason I think darkness is a factor is the dark pendant we can buy in the forest shop. It has an effect on it called "Profane - Absorbs all light"
The forest shop
When you first visit the forest shop, Gwylan tells you that not even they know what's in stock, because the stock only shows itself to people it wants to be bought by (if my memory is correct, this line isn't repeatable or on the wiki). Gwylan is also depicted as kind of magical, being able to obtain these seemingly magical items that nobody else knows about. They also briefly mention but try to hide that it's their grandmother's shop, but I don't know the significance of that.
I think the forest shop is actually the least magical thing in the town, though. I think the items in the shop are things that the corporation wouldn't want you to have, so your hallucinations prevent you from seeing what they don't want you to. At least until you do something that 'breaks the spell' over that blockage in your mind and lets you see the things for what they are.
I don't know how much Gwylan is aware of, but I suspect the grandmother knows what's going on
The Orphanage
The orphans are different than the rest of the town. They're by far the least crazed group of people we meet, and the orphanage is nearly a safe haven from the dangers of the town, and I think that's deliberate.
I think Bailey is keeping us from suffering the effects that the town is having on everyone else. Not out of the kindness of their heart, but because that's what the corporation wants. We know Bailey will sell you into slavery if you don't cooperate, a concept we're familiar with from our above-the-law shipping container friends at the corporation.
I don't know the motivation behind it, though. The orphans could just be rape fodder for the rest of the town, like rabbits for dogs to hunt. It could also be an experiment to see how an unaffected group interacts with an affected group.
Another important thing about Bailey is that they won't rape you (in the content that I've seen). They'll be the shit out of you and sell your body to rapists, but they won't do it themselves. Every encounter in the game begins with "The plump ____ exposes their _____" but not encounters with Bailey. Bailey is also the only character in the game that loses encounters by orgasming. Everyone else defeats the player by orgasming, but if Bailey cums, the player wins.
I think Bailey is almost or entirely unaffected by what's going on in the town, which is likely related to being able to keep the orphans more or less unaffected.
Bailey does have one fear, which is the attic/loft in the orphanage. They're crippled with fear at the thought of going in there, and tells you to stay out. When we go in there, though, there's nothing. Just a bunch of empty rooms and dust. Discovering this fear allows you to see the dark pendant in the forest shop.
I think there is something in there, something our hallucinations prevent us from seeing, but Bailey sees it.
Kylar
Kylar is weird. We know Kylar is weird. Kylar is almost Morgan level crazy, but in a different way. Kylar doesn't want sex, Kylar wants you. Again, Kylar is absolutely batshit nuts, but in a violent and love-fueled way, rather than lust-fueled rape. Another thing that makes Kylar stand out is that they almost seem to have super powers, always knowing where the player is and being able to be anywhere the player is without being seen.
Kylar also isn't an orphan and doesn't live in the orphanage, they have parents. They also keep a really strict schedule, saying things like "I have to go, they're waiting for me" after looking at their watch. "They" could be referring to their parents, or it could be someone else.
I think Kylar's parents work for the corporation, and their relationship with Kylar is probably dictated by the corporation, very similar to Morgan and their kid. I think Kylar's parents keep them on that strict schedule to be able to do experiments or otherwise affect Kylar in a very deliberate way with the crystals or whatever else.
The reason I'm even mentioning Kylar might not actually be significant at all, but it might be. When you pay Kylar to set up the lab, they go into the loft and check all the different rooms before choosing one that's okay to set up in. All of the empty and likely identical rooms. That means either Kylar knows what was up there and chose the room carefully, or Kylar was unknowingly guided to a room carefully chosen by whatever is up there, or it was just meaningless flavor text.
Kylar also mentions that the ingredients used to make pepper spray take a while to grow, which means that they're using something found in nature to make it. That makes me think of the various lichens you find and their possible significance in relation to the crystals. (purple, glowing, hallucinogenic lichen and a purple, glowing, hallucinogenic crystal. Then the pink crystal with a threat of tentacle rape, and a pink lichen with a threat of nun rape.) So Kylar might know about the significance and effects of the lichens and possible even the crystals. There's also the fact that the pepper sprays you find in town have microchips and are vaguely connected to the corporation and old town might indicate something about Kylar, too.
On a sort of related note, we have one other peer that seems crazy but has different motivations than everyone else. Whitney doesn't live in the orphanage, but I can't recall any mention of their parents.
Tying everything together
The old town got fucked up in some way, leaving behind the crystals and other mind altering artifacts. The corporations moved in and started using that stuff for their own mysterious goals, causing the town to go nuts in the process. The crystals might be powered by the lichens around town, and the pepper spray we use might be the same except it causes pain instead of lust, since it comes from a different lichen. Bailey is in on it and knows what's going on, but isn't in charge, they're still scared of whoever or whatever really is in charge. We, the player, are always hallucinating to an extent, only seeing what we're allowed to see.
And the whole point of this short post that turned into a fucking 4 page essay, is this:
Thanks for the suggestions. I'm considering letting the PC buy/rent a home somewhere in town. Bailey will still try to extort you though.
Obviously only you know where the story is actually going, but maybe when we move out, we're no longer under Bailey's "protection" and are at full risk of going insane like the rest of the town