Just a couple plot questions... [spoilers]

[Kedjane]

1. He was infected. He was doing fine and all, but when Philip came around I guess the Tuurngait took control of his body and turned him insane.
2. Rock worms. That's why have to block the holes in the wall to continue.
3. Philip had the "luck" of being infected with Clarence, who had somewhat different goals compared to the Tuurngait. Red I don't think ever even made it close to the Tuurngait, he escaped the Shelter when he was just a kid and have been living in the mines ever since. If he was infected he probably found some way to deal with it, but it obviously made him insane.

If the "infection" was real or not is a though question, but I believe not. At first the scientists thought it to be an infection because of all the symptoms, but later (as Howard discovered) turned out "just" to be the Tuurngait. Still you manage to get Clarence out of your head in the end by taking some sort of antidote, don't you? Can't remember exactly what happens, but it is possible that one of the ingridients were "spirit repelling" or something like that (don't you mix that mysterious "sample" into the antidote?).
I don't believe the devs can answer that question themselves. I think mysterious materials, sicknesses, spirits and general confusion about who's causing what made them a bit confused themselves in the end and there is probably no straight answer to many of the mysteries.

Lucy, you got some s'plainin' to do.

Ack. I've explained that one a whole lot of times. That's not neccessarily a plot hole, why would it be? It is fully possible that Anabel just standing somewhere in the middle of the room when Philip charged in, started running around like crazy, and she was like "?". He turns around, starts running towards the corner of the room and she goes to stop him - and passes just below the weight thing just as he drops it.
I can't remember how it works in the game, but didn't that weight drop pretty fast? If so it's very possible she just passed under it, didn't even think of it's existence and wham - was hit on the head.

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You even disproove yourself a number of times there, don't you?
Several problems with that theory:
1. Clarence does want to kill Philip, either so that he can get out of his "prison" of a body or so that he can start freely manipulating Philip's body like his own.
2. Amabels voice never sounds infected, nor is she infected when you see her dead body.

I've got to rush out into the real world now anyhow. End of post.