Penumbra remembers me to Lost

[Kedjane]

That part about the ancient spirits was what confused me.

Ah, they are hiveminded spirits perhaps?
The hivemind always goes on about how they are many but still one. So I'm guessing they are some sort of ancient spirits (who were named "bad" by the Inuit, even if they were somewhat friendly to Philip) who all are as one. Until Clarence broke free.
Either that or I'm completely wrong and they are some sort of physical parasite and cause the illusions, the mind journey at the end and all that by manipulating Philips mind. The "telepathy" could be by sending out chemicals people can't detect into the air and communicating. But I've never looked too far into that theory as a lot of things seem a bit too supernatural to have an explanation (even though Jens or Thomas said they would make a completely "realistic" game some time around the release of Overture) in my opinion.