It's pointed out subtly several times in the game that Greenvale has a lot of stuff in it (art gallery, big fancy hotel, sawmill, two bars...) despite being a relatively quiet small town. This is foreshadowing that Greenvale used to have a larger population that was killed off by Kasen's experiment.
Not much brilliance, since a mandatory scene with Polly early on states that Greenvale used to be much larger and have a population of over 6.000 people.
York's invisible friend Zach is actually you, the player.
Quite the observation. Wouldn't you agree, York?
Except that the game establishes near the end that this is not true.
When York opens a door he quickly looks around before going in. Why? To look for any threats before actually going in. Looks like he has been jumped before.
Becomes even more brilliant when you see the flashback to when Kaysen attacked Zach's family. Zach was watching from a doorway where he couldn't immediately see Kaysen, so York's cautiousness is a defense mechanism for his trauma as well.
Not only that, but York's signature mannerism of putting two fingers to his temple while saying "Don't you agree, Zach?" is him mimicing his father's last words and actions before shooting himself in the head.
Kaysen's final form makes sense: He doesn't need to look like a monster to be a monster.
During the autopsy scene, when York finds out that Emily was watching a movie on TV the night of the murder, he grinds his investigative questioning to a halt to ask her what it was and then rattle off the year and director before moving on. Seems like just another case of Yorkbeing York, until you poke around Emily's house and car (with a particularly telling vanity plate) and realize something about her: She's just as huge a film buff as he is. This seemingly-innocuous moment is probably when she starts to fall for him, because she realizes that they actually have something in common.
During one of the car chats in Episode 3, York is trying to work out what his feelings for Emily are. He tells Zach that she reminds him of "something he used to feel"—the feeling of wanting to protect someone, but at the same time, feeling protected by them. He wonders out loud: "Who used to make me feel that way...?" It's Zach himself. York is Zach's protector, but at the same time, Zach still helps guide him and keep him anchored in the real world.
It could also refer to his guilt toward his mother's death, and point to a desire to protect Emily to make up for how he believes he failed his mom.
Though we only see the lower half of her face, Zach's mom seems to look a lot like Emily.
During the section where you play as Emily why can you suddenly run indefinitely without the meter filling up and forcing you to stop? It's because Emily isn't a smoker like York.
Emily also exercises regularly while at home. You can peek in her windows while she is home and occasionally find her exercising in front of the mirror or on an exercise bike.
At the end of Quint and Becky's sidequest, York says "another young life saved Zach, good job". Remember that in reality, York is an alternate persona and all utterances of York and Zach reversed; so the line is actually "Another young life saved York, good job", delivered by Zach, the true persona. Who was the previous young life that York saved? Zach himself.
When Anna's ghost leads you to the Galaxy of Terror, she needlessly takes you around in a circle before getting you there. Carol described Anna as a ditz earlier in the game, so in that light it makes sense that her ghost would take you where you needed to go in such a roundabout way as opposed to the obvious quicker way.
When York finally enters George's house, we find that it's very messy and under-furnished, with all the windows boarded up. On the surface it just seems like the type of place you would expect a serial killer to live, but looking deeper, it perfectly reflects several aspects of George's persona: The messiness reflects his psychosis, the under-furnished state reflects how he had nothing of value in his life, and the boarded up windows reflect how he hid his true self from the outside world. Also, the boarded up windows prevent George from seeing the outside from within, reflecting how he was blind to certain things- namely that Kaysen had manipulated him into becoming a killer.
Michael's sidequest reveals that he is Harry's adopted son. In this light, Michael can be viewed as Harry's replacement for George, Harry's estranged biological son. George himself takes after Harry in this one respect as George was using Carol and Thomas as substitutes for Emily, the woman he loved but couldn't have. Like father, like son.
With a huge dollop of Fridge Horror: it's heavily implied that Kaysen put the sapling inside Emily by raping her. He literally spilled his seed there.
A couple of realizations concerning York's love of punk:
He and Zach didn't exactly like the same bands, but they both dislike the Sex Pistols. York never actually explains why, but here's a possible theory; what was their bassist's claim to infamy? Allegedly killing his wife. Probably hits too close to home for York.
Up to the present day, York still likes punk, as evidenced by his theme song (which plays when you're driving in his car, as well as during the racing sidequests) sounding very suspiciously similar to Green Day's "American Idiot".
Related to the above: why did York like punk rock as a teenager? Simple. Because he is Zach's conception of what a cool person is, and, to a teenager, that means rebelling against authority and social norms. Punk. His unflappable nature likely stems from this as well; the literal meaning of cool as a personality is trait is being able to keep calm no matter what, after all.
Word of God stating that Willie is in fact The Man Behind the Man as Kaysen's connection to the Red World gives a whole new meaning to plenty of things. To name a couple:
When Willie is tracking York with Emily and Kaysen in tow, Kaysen chats about how he feels like dogs are wiser than humans, and if humans were wiped off the face of the Earth, dogs would keep on going.
When Thomas is holding York in the clock tower, the last thing he says to York is that the next person who comes in through the door will decide his fate. And that is not Emily or Thomas, but Willie.
Part of the opening cutscene shows several people reacting to the news of Anna's death, including her mother, best friend and other villagers somewhat close to her. Some chapters into the game, York is investigating the Tree of Anna and notes the presence of a third party and them having taken whatever Anna was clasping tightly in her hand, prior to her death. In hindsight, the player realizes that Becky was shown holding up a pendant with the upside-down peace sign in the opening, indicating that she was the third party.
And now for the big meta question: Why don't the game's low graphical fidelity, glitches, overly re-used animations, and questionable audio choices diminish its impact? Because the overall feel and tone the game is going for is surreality that switches between comedy and horror - and that's exactly what all those things contribute too. They make the game feel disconnected from reality in a way that is sometimes silly, and sometimes disturbing. The game doesn't succeed in spite of those shortcomings, it succeeds because of them.
Almost every married couple on Greenvale are next to each other in the alphabet. The one exception is Jack and Gina, and they are also the only couple who seem emotionally distant towards each other.
When you are at the final battle, Zach ends up running DOWN a whole flight of circular stairs away from Kaysen, only to end up at the TOP of the roof of the clock tower... huh?
Well, given that Kaysen is implied to be an Eldritch Abomination, and he might very well be warping space-time, combined with the whole Through the Eyes of Madness thing in the dark world, there's at least two reasons why this might have happened.
In Spy Fiction, Kaysen is killed by Lauder. This never made any sense to me, because he was still alive back when the gas was released meaning he was super paranormal for a while. If that's the case, how did the Lauder kill him. If the Lauder did kill him, either the events of Greenvale shouldn't happen, or Spy Fiction took place after DP and never happen because Zach killed Kaysen.
This is because Kaysen is part of Swery65's Reused Character Design group. Deadly Premonition and Spy Fiction are not canon to one another. The same thing goes for General too, who was eaten by piranhas.
During the second victims death York just stands there watching her die. Alright he made a mistake assuming she was dead the first time I can forgive that (although he does the same damn thing for the third victim too) but after seeing she was alive and after the trap had been sprung he didn't think, maybe he should attempt to support her weight to stop her strangling to death two feet in front of him. Don't say it was an instant death either, we clearly see her still alive even before York starts seeing things from behold the grave.
By the time the trap is sprung, it's too late...It's not INSTANT, but, like with 'Power Rangers' transformations and such, it's quicker then it looks.
Not to mention that the murder was literally committed in front of them, and Emily and York didn't know it.
George completed the New Raincoat Killer ritual and turned into a powerful monster, yet he still had a weakness with his scars. One could perhaps draw the conclusion that it was never meant to succeed, but there is another possibility: One of the components of the rituals is that the sacrifice must not speak while they are being killed. George cut out tongues in order to do this, but several of the victims spoke as they were dying: Becky was mumbling gibberish, but both Diane and Carol spoke words. The ritual wasn't down correctly, so it didn't work.
How come Greenvale is still inhabited? Given how Harry remembers the incident with the purple fog, why would anyone willingly remain in a location where not only a massacre has occured, but is also full of poisoned soil? Certainly, the military and government hushed it up, but what about the kids? Wouldn't they remember? And Harry keeps making mention to the people to not leave during rainy days because of the fog. Why hasn't the place been abandoned? Harry has money, can't he just relocated everyone and give some hokey reason? Maybe even go so far as to tell the government that, if they don't agree to this sudden relocation of an entire (albeit small) town population, he will reveal the entire purple fog mess?
Harry explains things somewhat. The military arrived the next day and issued a gag order. Nobody was allowed to mention what had occured and the surviving townspeople followed that order. The townspeople began to stay inside when it rains, likely a safety mechanism, in case something like the massacre happened again on a rainy day. Nothing was mentioned to the children or grandchildren, leaving only the tradition of staying inside on rainy days to remain. And the Raincoat Killer becoming a folklore. Simply put, those that remembered never mentioned it and the people born after were never told.
Given the method we see for creating red tree saplings, does that mean there's someone buried in a shallow grave under George's lawn?
That's just the methods to get the seeds to sprout. After becoming saplings, they can be planted like regular trees.
Although that's not the only fridge horror at George's house. Remember his mother's corpse in the basement? Kaysen most likely raped her. Is that why George become so fanatic about the red trees?
More Fridge Horror comes in when you consider the possibility that it wasn'tKaysen who raped his mother... Guess he might have gotten back at her for all of those beatings...
If you check the Galaxy of Terror late at night, sometimes you can see Thomas or Carol head to a room you can't enter. If you check the map you'll notice they're with someone else George, and later you find out that it's the secret BDSM room. With the way the game treats Thomas as a fellow victim despite his antagonism and death at your hands, and his comments on George's cruelty, you realize that meek and gentle Shrinking Violet who cooks lunch for you daily is a Love Martyr who was probably being sexually and physically abused right under your nose the whole time, and it's implied his eventual psychosis is partly the result of Break the Cutie.
Likewise, Carol's abrasiveness may also be the result of similar abuse.
Pay close attention to Brian Xander Morgan's gun, it's a magnum, now take note the prize in Willie's Doghouse after completing his sidequest with all seven bones, a magnum. Kaysen likely stole that Magnum from Xander's dead body.
It's mentioned that Forrest Kaysen is particularly close to the Ingram family, especially Isaac and Isaiah. Considering his modus operandi, what are the chances that he's plotting to make Lily his next victim?
Keep an eye on the nameless background people through the game. They start out looking normal, but as time goes on, more and more of them will have pale skin and dark rings around the eyes, making them look like the Shadows.
As if there weren't enough unpleasant sexual implications about what exactly is needed to make a red sapling sprout, note that the only people we know for certain that happened with were all women.