1.
Why are the animals so large and hostile?
There are chemicals and stuff in the tunnel system that cause that as well as the giant spiders and stuff...
2.
What exactly is Red's story?
He went to work in the mine when he was 14. He went crazy by feeding on the dogs which were all funky because of the unknown chemicals and crap mentioned above.
3.
What's up with Clarence?
Clarence is a result of Phillip being the only person to survive those levels, which simulate the virus taking over. He made it through and so he got a split personality instead of being totally overtaken. Clarence did a lot of stuff to mess with Phillip and actually was just trying to freak him out by saying he removed memories of Red. Clarence was also affected by the fact that he did not totally overtake Philip, though he may have been different all along and that is why he did not take over totally. He wanted to kill Phillip because that is what was best for the hive mind type thing, they were destroying all the humans because the humans were so hostile. Killing Phillip would actually free Clarence. He actually gets freed near the end but he does not obey the hive mind so they kill him.
4.
What's up with Dr. What's-his-face, the one who tries to saw his hand off for you?
I don't remember that at all
5.
What's with the bullet holes in the one window in Black Plague?
As mentioned above, the humans were hostile to the Tuurngait dudes, they tried to eradicate them. Presumably they had tried to do this with guns...
6.
Why is the Tuurngait seemingly omniscent?
The tuurngait is not a "he" It is the collective mind of all the infected. They are from another world and have taken over other planets/universes or whatever. They have a large amount of minds. Also, they have been around for much longer than humans, and have been able to evolve really far. Lastly, human minds are very advanced, and the tuurngait may be able to unlock the full potential for use in the hive mind.
7.
Why did Howard kill himself?
He could not take what was going on. The tuurngait allowed him to keep his human form in a similar way to Phillip. However, he didn't get an asshole, he got a regular voice that allowed him access to the hive mind, which was too much for his human mind. Right before he kills himself he writes the letter spoken about in the beginning of overture
8.
Why does Phillips try to get the Tuurngait killed at the end of BP?
He fears them, even though they seem to be the "good guys" they put him through so much that he cannot deal with it. As for Clarence, Clarence was a part of him and he kinda liked the guy...erm.... symbiote...so he was sad to see him killed. He writes a letter very similar to the one his father writes.
9.
Why does Phillips say in the email that it will be good if he dies, and "we will all perish" if he doesn't?
Phillip, went crazy through this ordeal, like his father, so he just wanted to end it. He was given access to the hive as well, which is why he hears the voices, however, he keeps his free will...Just like his daddy! He knows that him being a part of the hive only makes it stronger, so he must die. Also, if he spreads the word of the Tuurngait being good then they will be able to absorb all of mankind. He must die so he is not tempted to stop the annihilation of the tuurngait.
10.
What exactly happens in Requiem?
Phillip is going through a sequence similar to the tests in Black plague at the end, or near the beginning of BP when he is being infected, not really a dream. He is part of the hive mind so yes they can read his mind. IThe notes are presumably left by his father, somehow inscribed into the hive mind and projected into the hallucination. I didn't finish Requiem so I donno about the end...