Just a couple plot questions... [spoilers]

[Sexbad]

1:

Spoiler below!

Why did the scientist that you gave the saw to try to kill you?

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Since he, like everyone else down there was either dead or infected, and he was not dead, he was going to turn into a monster sometime or another. Possibly the pain of him cutting his own hand off made his immune system break down or something and the virus asserted itself in his mind and took over.

2:

Spoiler below!

What was the thing in the walls in The Kennels?

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A kennel is generally used to keep dogs, so it was most likely dogs who broke out of the kennel and into the walls in search of food and prey and such.

3:

Spoiler below!

If Phillip and Red were infected, how come they didn't become zombies, like everyone else?

Spoiler below!

The process of infection probably takes a long time to build that varies from person to person and there is bound to be some small population of the Earth that will be immune to a certain virus or that can resist bits of it. In fact, speaking for the phrase "black plague," there is a population of people that inherited an antibody that developed to protect against the bubonic plague that now also protects from the effects of AIDS. Don't forget: Philip was only in the mine and shelter for about twelve hours. Everyone else was in there for years.

Also, the save artifacts gave you more of the disease. Philip used like forty of them throughout his journey and was on the brink of actually turning into a Tuurngait. Red had none in any of the rooms where he lived (if I recall correctly) so he probably rarely ventured out in fear of mauling by means of evil dog. He may have been trapped in the shelter of his for years and only saw his workshop's artifact thrice.