I've just played it through, and wow! What a game! I don't feel like I have much to add to the understanding of the overall narrative, but I would like to point out a few things I noticed, that impacted me!
Firstly, those chase scenes at the start were very intense, they really managed to make me feel terrified! I did notice however, that whenever I got caught by a human, they didn't seem to kill me, they certainly knocked me out but I didn't really get the feeling they were intent on murder - the guns they use shoot darts, like tranquilisers, if you trip on the log, the man dunks you, but I could swear he lifted me out again and if you get grabbed, you get tackled, brutally considering your age, but not something that would kill.
Next, that f... farm! Man, that really affected me. Those piles of dead pigs lying all over the place. Those worms... gah! I think though that this was not a "normal" state of affairs for the society - think about it, if you are a farmer, then those pigs are your product, and you don't leave piles of them rotting. Could those worms be parasites, nothing much to do with the narrative? The pig that attacks you, could he just have been in a lot of pain and for want of a better way of putting it, taking it out on you? I don't think we need to reach for mind control to explain it's actions. So running with these thoughts, could this farm be under quarentine, a parasite, perhaps feared to be human transmissible - hence the mask wearing men - cover all flesh the worms can attack - trying to drive you away from the area. Once on the farm, it is deserted, no signs of human activity or farming. I believe this is the first incidence of meeting the husks, which lends itself to the idea they are used for manual labour.
After the farm, I remember the streets, with all the husks marching, then performing for a human audience - jumping and "dancing" - I couldn't decide - and being in that line trying to match the rhythm was super stressful for me - if they were an audience or some sort of QC. Those buildings certainly seemed like factory buildings I wonder if the husks are made from people, or are they some sort of biological robot, grown from tissue in a lab perhaps as cheap labour? Certainly we see the lorry at the start loading them in - and I seem to remember it pulled away from those pods? small structures with a round window that we see quite a few times in the game - and at the back of that line, we see a truck, did it unload them into that line - what are those pods and why were they in the woods, are the husks harvested from them? Are they deployed to where the husks work as some sort of rejuvination? We know they are biological because of the scenes at the end, the husks in the surgical glass rooms, one is rubbing on the glass leaving blood.
The submarine section takes us down far below the street level. Those two who had the submarine, they struck me a scientists, studying something. When we get deep down, we find ourselves in long deserted man made areas - so it's almost as if those scientists meant to study humanities past - As we climb back up towards the surface, we get that room with the lights shining in and plants growing - this room has those pods again. The thing that attacks the submarine - Matt is correct, it does look a lot like the boy, but it also looked a lot like some of those people held upside down underwater (overwater... you know what I mean!). I'm wondering if those people, or husks as they turn out to be have been treated to allow them to breath under water, and maybe some of them escaped and retained, regained or developed their sentience. They have long hair because they escaped some time ago and live underwater, so it just grew and grew. The deep one at least doesn't like light, again, has it been down there so long, that it in particular dislikes light or is that common to all of them?
Breaking into the mine, it has that weight counter, is it an accident that it clocks the weight of a husk/person as 1, or is it specifically designed to count them. Why would it need a certain number of them to open that door? Maybe it's designed to open only for the big minecarts, and the wieght counter was supposed to stop anyone smaller getting into that danger area.
Considering that the explosion-pulse area had test dummies in it, but also was abandoned and flooded, was it perhaps an experimental mining technology? It's in the flooded facility connected to the pulses that we meet more of the long haired things. Could it be that the pulse intefered with the upsidedown water husks and allowed them to break free? They are certainly - perhaps surprisingly sensitive to vibrations in the water - they must be being triggered constantly by the pulses.
When you get caught by the one who you are supposed to, and it takes you deep down, it does, during your descent attach an umbilical to your belly button - and it is of the same technology that the helmets are made from, and as rightly pointed out - from this moment the boy changes - he has most notibly the ability to breath underwater, but also he can control the husks without a helmet now.
As we climb back up to human inhabited areas, our first contact is with the overhead spotlight machines. We've seen them stored previously in a warehouse and used on the rooftops around the long line of husks. It seems that these things are designed to prevent human and/or husks from accessing forbidden areas. As they are always placed where humans would normally be locked from, are husks gaining sentience so much of a problem in this world that they have these machines to prevent their escape from the facility?
That section where the father and boy come into the warehouse and a forklift picks up a cage of husks, I didn't sense the boy was scared at all, it seemed so normal, dad went out to buy some machinery, took his son and they picked up their new gear from the warehouse. The only thing that wasn't normal to my eyes was what that machinery was, but it seems that in this society, these husks are normal.
Finally, the experiment... First things first, I got the impression that the audience were excited by something, but I don't think it was the boys arrival, he is not invited in, he sneaks into the tank. The devices holding it in place, I don't think they were the same as the helmets, they has distinctive oval yellow lights around them, as did the umbilical, yet these did not. Also, I definately saw a pigs backside and tail emerging from the thing, they are not all human!
Matt was also spot on when he saw the display with the light beaming down precisely where you finish the game, but more, over the water in that diarama, were structures that you are heading towards, a farm or a mine perhaps? Is it possible that it was The Farm or The Mine you were previously in? I don't think so, too much travel left, but then I definately noticed some points, your path curved, very very subtlely - so maybe you do loop back on yourself through the entire game.
As I said, I can't get my head around the story any better than others already have, but these are the things I noticed while playing, and human memory being what it is, could easily not be remembered properly!