So the broad picture is made surprisingly clear, but there are a clearly a lot of details that will probably only be clarified by replaying the game and carefully searching for clues and theorizing.
Timeline:
1. At some point prior to 1975, the "Outsider" group (of which the protag, Maciek, Trader, maybe Elephant father, were presumably a part of) sets up bases and hideouts over a broad area for unknown reasons, perhaps to study whatever strange thing is growing under the area that seems to be full of energy. They are very well equipped and, if the Doctor is to be believed, actually watched and attempted to isolate the villagers themselves.
2. In 1975, the Being (aka the woods, aka the disease, etc) starts actively trying to isolate and destroy the Outsiders. Roads are swallowed are devoured. Disease is spread, with some people being physically mutated into the living tools of destruction, while others becoming mentally deranged until they succumb to the voice calling them to go to the Being, where they are kept in a Matrix-like dreamworld (this kinda explains my theory about people in general either having strong mental or strong physical symptomps, but rarely both)
3. At some point the Outsiders try to pull out but a botched evacuation leaves some dead, others mad (Maciek) or stranded (protag, trader)
4. Protag, presumably left behind during the evacuation as well as suffering memory loss, deformed, and mute, is rescued by Doctor who also steals his key. The Trader then brings protag to the safest area in the Woods, the dry meadow, and tries to discourage him from trying to leave claiming that there is no way out (and he is entirely fucking correct)
5. Protag recovers his key and follows the calling of the Being as well as his own desperation to get home, but he ends up being tricked by the Being and ventures FURTHER into the woods towards it instead of towards the exit. From that point on one of two things happen:
6a: The player is, once again, tricked by the Being and is manipulated to come to it, and it puts him into the Matrix-like Dreamworld where he lives in the pleasant but peculiar hallucination of having come home to his appartment until the rest of his days.
6b: The player, warned by the Tree and his own intuition to investigate the Radio Tower first, is somehow able to break out of the dream at which point he can choose to willingly surrender himself to the Being's dreamworld or to burn the motherfucker down using Maciek's wonderful flammenwerfer. In the case of the latter, the woods are burned away, killing some of their inhabitants and freeing others (if there are even any left by the time you are done with the game) and ending this fucking nightmare forever, maybe.
So, what are some important details that need to be filled out?
1. What the hell is the Being, anyway? Perhaps we are not meant to know, and its something like the Strugatski Bros. Zone that is just...there, for whatever reason, an anomaly with an explanation that is beyond the feeble minds of Man.
2. What were the Outsiders doing exactly?
3. What came first, the chicken or the egg? Did the Outsiders come to the Woods to study the Being, as a result of which it lashed out at them, or did they come for reasons other than the Being, and it formed in order to combat them? The Doctor seems to imply that it might be the latter.
4. Why is the Protagonist mute, deformed, and wears clothing that he did not remember putting on?
5. Are there two factions in the Woods? The Tree, being assimilated villagers, as well as the Three (apparently intelligent, non-hostile savages) seem to be acting against The Being, attempting to block off the road to it. Plus there are weird talking growths that give you warnings in the Radio Tower as well.
6. What the fuck are up with the fleshy bullets inside the heads of the dying soldier connected with the Outsiders? Maybe they are the frankenstein radio controls the Being forms inside people in order to derange them mentally.
7. What is up with people connected to the Outsider faction being found frozen in places? This can be seen in Hideout Remains as well as the Burned House in the Old Woods. Perhaps that is just the way that the Being decided to dispatch them.
Comments and theories and shit:
-Holy fuck, this game has some good writing and interesting, complicated characters. The wolfman's story: possibly a dog named Burek originally owned by the father and the two daughters living at where the Burned Houses are now in the Dry Meadow. After eating the shroom he may have mutated into a furry. Regardless of how he came to be, though, the Hunter (who was meant to marry the Pretty Lady) tried to kill him for his bestial appearance, resulting in the Wolfman becoming very bitter at the human inhabitants of the woods. As a result the Wolfman decided to take everything away from the Hunter, which is why he wears his clothes after shooting him through the heart and covets his bride (and he gets angry if you kill her, implying that perhaps he didn't just want to eat her but also rape her...let that sink in).
-The game nails the atmosphere of cosmic horror, as the protag is ultimately a tiny, insignificant, ignorant thing in the design of a superhuman intelligent that manipulates them as well as the player. Unless the player has some luck, a set of brass balls, and a flamethrower, of course.
-The game's morality is interesting as the Wolf's path is actually required to save the most amount of people in the game, despite the fact that you assist a furry in raping and eating an invalid. The C&C in the game is definitely its best part.
-If I had to guess, the religious symbolism and defacement by applying mud, sticks, and horns over faces and eyes seems to be an extension of the madmen's desire to find bliss in ignorance of the Being's dreamworld. Maybe the devs are trying to make a statement about religion and authoritarianism given that Poland had and arguably still has problems with both? idk
-The true horror of the game is, of course, Polish communism. Having to wait in the breadline for a washing machine must have been rough for the Protag.
-Although nobody is reading this shit, I might update my thoughts if I can think of something concrete and interesting.