Spoiler:
Pyramid Head and Maria interact rather frequently, and the end result is always Maria getting killed in some way by him or it, if you will.
First, we have to categorize Maria. What is Maria?
She is an illusion. She's a fake, a false Mary, a false face. And at the end of the game, we see that face removed, with the real face beneath. She is there to tempt James, to lead him away from Mary.
Most importantly, she symbolizes the delusion that James suffers. He spends much of the game completely unaware of what he did to his wife. He doesn't really know it, but he can't find Mary without breaking through this delusion of his. Maria is the embodiment of this delusion, for she herself is an illusion. If you stay with her, care for her, and associate too closely with her, in the end, you must instead fight Mary. James forsakes his wife and instead decides to embrace his delusion, to live in fantasy. Of course, the ending implies that it's a decision he'll soon regret.
Pyramid Head is the counter-effect. Like so many people theorize, Pyramid Head is indicative of James, but only in a passing sense. He is much more symbolic of the truth, of reality. On occasion he directly bullies James, but he never really seems like he intends to kill James. In the apartments, he gets quite brutal but he gives up rather quickly. In the Labyrinth, he appears twice. In one instance, you can pass him by without even seeing him. In the other, where he has his Great Knife, he stalks around in a circle, perhaps to keep you away from his belongings and keep you going the way you're supposed to. Note that if you go down there and do not step into the outer ring, Pyramid Head will walk right by James and ignore his presence. Even when he knocks James off the roof, it's quite clear that he's pulling his punches. What he's doing is doling out the tough love, in a sense.
But more importantly, Pyramid Head's claim to fame is that he kills Maria in particularly brutal fashion, and he does this three seperate times. In the hospital basement, Pyramid Head directly assaults Maria. He will not bother James unless James gets in the way. The final time, when there are two Pyramid Heads, James watches Maria die once again. But this time, he gets the point. He understands what Pyramid Head is, and what Maria really is. The Pyramid Heads attack again, but just as before, they don't really seem to have their heart in it. They're simply reinforcing what James seems to have realized. Once he does, they end themselves, for they have served their purpose and achieved their goal. They then open the way to Maria, the true adversary. Pyramid Head has killed Maria repeatedly as instruction to James; to tell him that he must do it himself. She is the demon, she is the illusion, and you will never get what you want while she survives.
Maria now wears a different false face, that of Mary's, but Mary she's not, and she's free to admit it. This is her last, most desperate attempt to beguile James, the last remnants of the illusion hanging on for dear life. James will have no part of it, and damns her for what she is. The illusion is finally broken, but it must be destroyed, and that's what James does. The monstrous Maria attacks, and he defeats her. The last threads of this falsehood fade away as Maria chants James' name. He severs them for good with whatever weapon he's got. The part of his mind that clung to the falsehood he perpetrated is no more, having been cast out. He is then free to face Mary, and to say what needs to be said.
What about the Maria ending?
Well, go back to the final 2 Pyramid Head battle. They still give up and give in, but not because they've served their purpose. Rather, in this case, they are no longer effective. They cannot break James of his illusion, as he is set on Maria. Therefore, the rational, truth-seeking part of his mind has one last trick left; Mary herself. Mary is the antithesis of Maria in this sense, she is desperately trying to make James realize the truth. James refuses this, and defeats the shade of his wife. He does know the truth, but he is willing to hide it away again, to imprison it for good, which he does, as Mary chants his name and he aims his gun at her head. He is now free to continue living in his delusion, along with his illusion, Maria.
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