Pyramid Head is a symbolic punisher/executioner; he has no specific ties to any individual characters. Walter Sullivan, an infamous serial killer in the Silent Hill series, supposedly had his own Pyramid Head to deal with, although I'm pretty sure this fact has been neither confirmed or denied by any of Silent Hill's creators.
James killed his wife, and Pyramid Head was manifested as punishment. Many of the monsters in SH2 were representational of James's sexual frustration, but these emotions were only channeled through Pyramid Head in the form of his raping other monsters. PH didn't actually represent James's frustration; rather, he was only influenced by James's hidden feelings.
Hypothetically, if the main character of the Silent Hill movie had something to feel extremely guilty about, specifically about her daughter, then it would make perfect sense to have PH in the movie. "He" is a part of whoever is feeling guilt. He's the punishment that we put ourselves through whenever we feel unbearably guilty over something.
[/end geek]
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