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.
Which adds an extra bit of Fridge Brilliance to the "Judgment" 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.
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.