During his frightening hospital gurney ride in the intro, Alex sees several terrible things happening to some of the people in nearby rooms; physicians apparently murdering patients. One's being cut to pieces, one's being strangled, and one's being buried in a pit. Much much much later, we find out this is how the missing children died.
Lots of people rolled their eyes at the fact that Pyramid Head is even IN Homecoming, claiming that he's just there for fanservice and has nothing to do with his original portrayal by this point. Until the endgame, this appears to have at least a grain of truth to it - Pyramid Head, while still scary as hell when he shows up, doesn't really DO anything to Alex. Then you find out who PH is REALLY after, and it all makes sense. In Silent Hill 2, Pyramid Head was, depending on who you ask, either a twisted reflection of James' guilt, or Silent Hill's method of punishment for grave sins. Both of these interpretations make total sense when you realize that PH isn't after Alex, but his father.
Furthermore, the Pyramid Head in this game actually isn't the SH 2 Pyramid Head, but a similar creature instead called "The Bogeyman" (not to be confused with the Name's the Same monster from Silent Hill: Downpour). Why is there an Expy of Pyramid Head in the game? Because they belong to the same "class" of monsters; both are demons specializing in judging and punishing mortals. No wonder they look so much alike.
Which adds an extra bit of Fridge Brilliance to the "Bogeyman" ending. What seems like a fanservice-oriented Gainax Ending becomes a bit clearer when you realize PH's true purpose as covered above. Each of the parents that were marked for punishment were discovered by Alex and promptly dispatched (with Alex himself dealing with Holloway) before PH was able to reach them. By not forgiving his father or mercy killing his mother, he was ensuring they suffered as much as possible for their actions, as was PH's trademark in Silent Hill 2. In essence, Alex was doing Pyramid Head's job, and did such a great job of it that the town selected him to become one.
Moreover, the Bogeyman ending also meshes excellently with the Sins of Our Fathers theme the whole game has going on. Alex becomes a monster, because that's what his family and his community made him into. He is just as much a victim of their sins as the murdered children. It just took longer for him to be embraced by the darkness and strike back the way they did.
Homecoming initially seemed off for a number of reasons. The creatures were more prevalent and the combat more pronounced than previous entries into the series, Pyramidís appearance seemed gratuitous, the symbolism of the creatures didnít really add up to Alex the way it seemed like they were supposed to, and the cast felt more crowded than before, with an actual support group of characters helping Alex. Similarly, the reveal that Alex was never a soldier raised the question of, ďThen what was the point of telling us he was?Ē It explained the absence of the expected war themes, but it made the whole soldier thing feel unnecessary. Then it all clicked: the plotline doesnít revolve around Alex. With the exception of Josh, nothing thatís happening is actually related to him. Itís happening because of his accidental manslaughter of his brother breaking the ritual, but itís not actually directed at him in any way. Without the protection of their ritual, Shepardís Glen is being overtaken by Silent Hill. The Order is kidnapping people to try and appease their religious origins, but the cult that theyíre appealing to isnít whatís attacking them; the children theyíve killed, manifested through Silent Hill, is. The creatures donít really add up to Alex very well because they donít represent Alex; they represent the murdered children. Pyramid Headís appearance seems gratuitious because he isnít looking for Alex either, heís looking for the parents; thatís why he only appears in the hotel (where Mayor Bartlett can be found) and the church (when he kills Adam Shepard). So why the war themes, the soldier fakeout, and people with very clearly defined alliances? Because soldiers and war IS the theme, just not in the way youíd expect. The entire theme of Homecoming is ďSilent Hill marches to war,Ē with Judge Holloway and Adam Shepard preparing for a conflict that never came and were blindsided by another conflict they never foresaw: the howling fury of every child who ever died for the foundersí ritual.
Probably unintentional, but: Homecoming has a more complex combat system than any of the other games, supposedly representing the fact that Alex is a war veteran whereas every other Silent Hill protagonist was a civilian with no fighting skills. However, the combat system is so fiddly and fraught with Fake Difficulty that combat is actually harder in this game than in any of the others, where you can just flail at the enemies until they die. Which makes perfect sense once you find out that Alex isn't a war veteran at all, but a mental patient with the delusion that he is one. Combat is harder for him than for other Silent Hill protagonists because he's convinced, against all evidence, that he's a Bad Ass who can easily take down a few monsters.
As noted on the main page, generally, the best weapon in the game is the knife, as it can be quickly spammed in order to slice enemies apart. But which monster wields a knife? Why, none other than the biggest and baddest of them all; Pyramid Head, aka The Bogeyman. Furthermore, Alex can become a Bogeyman himself in one of the endings. No wonder the knife is shown as the deadliest weapon in Alex's arsenal.
As mentioned on the main Silent Hill page, the Siam enemy has so much symbolism relating to James and Mary attached to it... what if it's actually the two of them, still trapped in Silent Hill forever?
Shepherd's Glen is now a permanent offshoot of Silent Hill's haunted mess. However, the pact that results in this was made before Alessa's time. Who's really in control of Shepherd's Glen, Alessa's will or the demons?
Going on that, a majority of the game's endings are inarguably bad, but there is one good one. Except...it's still a horrible outcome for Alex. He was in a mental asylum for four years and can't prove it. Because his home is now severely and irreparably haunted, he can't prove he finished or even went to high school. Getting a job will be extremely difficult or impossible that way, and he will have to find a place to live. And that's without the borderline borderline useless leg that Holloway left him. He's likely extremely traumatized and recovery will be difficult. His life will be as a hermit who, judging by the way things have gone, will have a horrible time staying afloat.
Even worse? This means that, really, the Bogeyman ending is the best one for Alex. Yeah, he loses his humanity and becomes a demon, but he becomes an immortal avenger who will spend the rest of his existence dealing out torturous deaths to bastards who deserve it, just like the adults of Shepherd's Glen. He becomes a monster because that is what they made of him.