At the end of Penumbra: Oveture what is the thing that takes you away?

[gandalf91]

I would say the Tuurngait captured you because they want to keep expanding the hive mind. When Philip escapes from his captivity, they turn hostile towards him.

Exactly. I don't see any of this as a plot hole at all. It had to start somewhere (infecting, not killing people). As evidenced, most of the scientists working in Shelter were infected and became part of the hive mind, not killed. It probably killed those who seemed most of a resistive threat (could explain why they try to kill you after you escape).

As for its intentions, I see some good mingled with bad. (A lot in this world is gray, despite us wanting to see everything black and white. This also seems a huge theme in all of Frictional's games thus far.) Have you already played through Black Plague all the way yet..? Wouldn't want to spoil any of the details.