Something I found on the Silent Hill Wikia. This is a comparison between Mary's normal, disease-free model, and her actual disease model, the skin not really visible in the game's last cutscene. Feel free to speculate. [spoiler]
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I've seen it before, but everytime I see a new picture of the diseased Mary skin it looks worse...Makes me feel really bad for Mary.

Wow! I new her disease was supposed to be bad but damn. No wonder she started lashing out at James and others. Poor Mary.

I nearly vomited, even though I've seen it before. Gosh, no wonder Mary and James went through all that. It's unbearable to think a disease like that might actually exist...

That's gross. What is the name of that disease again? it seems that it wasn't covered, or I forgot.

Oh dear, Mary's looking a bit worse for wear. They should of showed her appearance in more depth at the end of the game as that would give the player a clue to how bad she was.

@Mephisto ~ There was a whole topic that covered what disease it was, I think people agreed that it was some form of cancer or that it was just left up to the players imagination.

Kinda looks like leprosy to me (purely visually, I mean). I'm sure there'd be something even closer to it than that, but I don't know much about diseases at all.

There are a few more pictures here.
http://www.silenthillmemories.net/dvd_a ... ion_en.htm
http://www.silenthillmemories.net/dvd_l ... res_en.htm

Actually, I felt a spike of nausea, too... but I was already feeling nauseous, so...

Don't take this the wrong way, Mary. I love you, too.

Leprosy is what I was thinking.

I've seen it before, but it still makes me feel really bad for her.

I'm thinking it's either cancer or leprosy.

Leprosy is treatable
"'Many people have misperception that the disease is either not treatable or highly contagious or both.

'The disease will only spread after prolong contacts. With medicine, leprosy or Hansen’s disease is easily treatable,' [Malaysian Leprosy Relief Association (MaLRA) Terengganu branch president Datuk Victor Isaacs] said."

Damn. I've never seen that pic before. Poor Mary...

Kinda make you rethink whether James really was the demon don't cha?

No? Not funny? Tough crowd

Oh my, that's horrible. Poor 'ole Mary...

That really brings the argument cutscene into a new perspective for me.

Yeesh. She just looks like she'd been mugged one inch from death.

Leprosy is treatable, but what if the doctors knew that she was going to die regardless of any efforts to save her? What if it was too late? It may be the reason why they let Mary go home, because no one would contract the disease since a day wouldn't be considered a prolonged exposure-and her death would follow immediately after.

That's my theory. Feel free to correct me if I'm wrong, I'm no good at this "medical/disease" stuff, so I'll ask my Mom about it

Mary had the disease for three years. If the doctors couldn't treat it in three years, or even after the initial diagnosis after James and Mary visited Silent Hill, they should have their medical licenses revoked immediately.

So if we can rule out leprosy because it is curable... Then what does Mary have?

Facial Syphilis ?

It's generic disfiguring disease #3.

Jesus Christ....I clicked on that spoiler tag and nearly jumped out of my chair.