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Vincent is a genuine member of the Order. Claudia is an insane heretic.
Look at how Vincent acts and how he talks to Claudia. He says he fears and adores God, but that he doesn't believe the Otherworld and the monsters are her handy work. He finds the idea of God being born horrifying, not just because it means an end to his hedonism, but because he considers it a blasphemy to force God into the material world, especially through such questionable means. Claudia, Leonard and Dahlia both belong to the Sect of the Holy Mother, a heretical and insane offshoot of the actual Order, and Vincent clearly disapproves of their methods.
The "Happy Birthday" voice on the other end of the phone is...
The town itself. On many occasions the town is implied to be intelligent, and self aware, and creates the puzzles and such as a way of manipulating and toying with the protagonists, while at the same time subtly guiding them towards an eventual revelation. Compare this to the voice on the other end of the phone. It's giving her information, subtly telling her "you're older than you think you", it also says "Happy Birthday Dear Who Are You?" a way of subtly pointing out "you don't know who you really are" and soon after gives her "birthday presents" which is essentially the town itself giving her them. Now with that in mind, listen to it again. Doesn't everything it's saying sound like something the town itself would know, and say, if it could speak?
Vincent's "joke" does not mean the monsters are actually people.
Isn't it strange how, if Heather really is killing people without knowing it, Vincent doesn't put in more effort to stop her? No, more likely it has to do with perception. Vincent said he finds the alternate world "fascinating," unlike Heather (and likely the player) who finds it terrifying, so it follows that he would see the monsters as fascinating creatures inhabiting/created by this world rather than bloodthirsty killing machines. Hence, "they look like monsters to you?" He retracts it when he sees it freaks Heather out. It didn't occur to her that Vincent saw the same creatures in a different light, so the thought crossed her mind that they were actually people. And rather than explain what he meant, Vincent thought it easier to say it was a joke and change the subject.
In Silent Hill 3, Heather is aware of the scenes that she doesn't show up in.
Thus explaining her "Was someone else here?" line to Vincent in the motel. Obviously, Alessa's awakening memories are causing her repressed powers to return, and she's getting visions of what's going on in other places.
Valtiel isn't a thinking creature at all, it just carries out orders directly from whatever is behind Silent Hill.
It is just a bundle of instinct, and most of that instinct is to follow the orders of the voice that sometimes talks in its head- or rather, the ideas it sometimes has just out of the blue, since a voice inside its head might be too abstract a concept for it to get. It dioesn't really understand what it's supposed to do, it just does it. Like a valet, in the traditional role of a servant, beign a part of the House that gets things done when told. Pyramid head, on the other hand, is a separate entity, and one that works toward its own gratification and release of boredom. They're both on the same level, but Pyramid Head is more of a "Silent hill tells me to do this, sure, but i'll just mess around with my own stuff until I get the chance" and Valtiel is like a flesh-robot. With instincts and a way to input instructios, but no mind of its own. (It came to me in a dream, cliche though it is.)
In Silent Hill 3, Claudia and Vincent are siblings.
Welll, it makes sense to me, at least. I mean, Vincent claimed to have the memory of Claudia's father beating her burned into his mind, so either he was a member of the household in some way, shape or form, or really liked to stalk people. Also it seemed to me like they had some sort of rivalry thing going on, but maybe I'm just weird.
Getting loads of dark points for forgiving the confessor at the Church in SH 3 has nothing to do with Heather stepping into the shoes of God as is commonly believed.
The real reason is because it shows that even after all she's been through—learning about how awful Claudia's past was, gradually gaining back Alessa's old memories which included a time when she'd loved Claudia like a sister—she still believes that murder excuses murder and revenge can be justified. Which is a belief that we know give the God a major boost in power since every time she starts raging at Claudia it gets strong enough to make her keel over from the pain of it, and is what ultimately pushes it over the edge of the amount of strength needed for it to be born if she tries to kill Claudia at the end.
Harry isn't really dead
Let's face it, the Missionary isn't a very difficult boss (this troper has played through the game about ten times and has been killed by him a grand total of once), and we know Harry wanted Heather to keep at least one weapon on her person at all times. Wouldn't he have done the same? And then there's the fact that he's tough enough to have taken care of the cultist that came after them years before, not to mention survived Silent Hill in the first place. At the very least, he should have put up a struggle. But the apartment, other than the chair and the blood trail, is completely untouched. Heather has already seen a number of dead bodies (one in the subway kind of reminds this troper of Travis, but all you can see is part of the legs and the feet) and she's obviously not back in the real world, because the street is blocked off so that she can't go anywhere but home. Perhaps Heather's fear that something would happen to her father and Claudia's hatred of him caused the Otherworld to produce a dead copy of him? While Heather's running around Silent Hill bent on revenge, Harry's panicking and calling the police because his little girl hasn't come home yet.
Pyramid Head and Valtiel are the same being (relates to both of the above theories that Pyramid Head is an independent manifestation of Silent Hill and Maria is the cult's God, and assumes both are true).
God's intentions towards James were to feed on his misery in order to regain her power, therefore her servant fulfilled the role of his "dark side", repeatedly killing a woman heavily resembling his wife and acting out his baser urges on the other monsters. Towards Heather however her intentions were to observe and guide her until she was able to be summoned into the world, a task again performed by a servant of hers, referred to in the Book of Lost Memories as "the God's attendant". That both Pyramid Head and Valtiel resemble humans far more than their contemporaries and resemble each other even more, the latter only possessing slightly less bulk than the former - which also exhibits limited ability to alter his form for specific objectives - is even more evidence to suggest, at the very least, a strong link between them.
Cheryl/Heather is Alessa's Nobody.
From Kingdom Hearts. This is why Cheryl merges with Alessa at the end of the first game, and Heather is haunted by Alessa's Memory in the third.
Stanley Coleman is Valtiel.
Considering the human-to-monster transition that happened with Leonard Wolf and that both Valtiel and Stanley are very fond of stalking Heather...could be interesting. Looking back at the notes, it'd make sense if Stanley/Valtiel was already a monster and just gradually lost touch with his humanity (and sanity) until he couldn't write anymore. It'd also give reason for why we don't see Stanley (human) but do see Valtiel (monster) following Heather, since the notes suggest Stanley wants to be seen. What's more, Stanley was shut in the hospital by the Organization to make him forget something—what if they deliberately created Valtiel as an obsessive attendant to protect Heather from other monsters and, by connection, ensure the birth of God?
Vincent actually does want God to be born, but for his own purposes.
Consider that when Heather confronts them both at the end of the chapel, he encourages Heather to kill Claudia. Given his position in the Order, I find it unlikely that he wouldn't know that this would bring about God's birth. My theory: he wants to control God for whatever reason, and only had Heather get the Seal of Metatron to ensure God wouldn't just go on an unchecked rampage after Her birth. He sees Claudia, with her own, more far-reaching goals, as an obstacle to this, and figures he stands to benefit from her death anyway. He doesn't actually start wanting God not to be born until after Claudia stabs him, at which point it's more out of spite than anything else (e.g. "If I can't control God, nobody can!")
Dahlia Gillespie is Claudia's biological mother.
There are so many similarities between them that the only other explanation is that Claudia at least saw Dahlia as a mother figure and was heavily influenced by her. It would also make her and Alessa (and therefore Heather) sisters, which adds a whole new level to their complex relationship.
Heather will eventually regain more of Alessa's powers.
In the beginning of the game, Heather has a premonition of the Amusement Park. This even saves her life. Although it's not canon, in the replays, Heather attains more Game Breakers than any other character in the series and is the only one to gain a special power. She also had the power to safely carry around "God" whereas Claudia was instantly destroyed by it. If you take the above theory about her heightened intuition as being true, it makes this even more likely.
It's all time travel.
Every time Heather goes into the dark world she has to touch a symbol, usually on a mirror or reflective surface. She mentions it being the symbol "of the god of time" and it isn't really mentioned after this. In the dark world, any metal is rusted and corroded, paint is flaked off, wood paneling swells with ages of moisture. Every normal place now is barricaded up, chain mesh fences, steel plates welding rooms shut. What if some horrible invasion occurred, a mutagen that turned normal people into horrible monstrosities? Imagine a world after a zombie apocalypse, anywhere that wasn't trashed would be heavily fortified. Somehow, heather has the ability to travel between the sane now and the seemingly insane then.
If Cybil had been saved in Video Game/Silent Hill1; she would have still been around and would have saved Harry.
This version of Harry didn't get 100% Completion in the first game.