I dont think the snake is some sort of 'god' i think it is more Abrahamic, that being a deceiver and a great evil, whichever word you wish to refer to him as. I think even it's symbolic with his apperance he's a snake on a great withered tree, and he refers to humans as fruits. And refers to an old evil, and if you are a follower of abrahamic religions that is often considered when sin was originally introduced into the world via the 'fruit'.
The way I read it is, the snake wants you to bring the other characters into despair, or allow the to suffer in their despair, that way he may 'feed' on them. The snake even claims that the MC has done that many times before, and judging from what other characters tell him about his past, the MC seems to be a bit on the calous side. I think thats what the snake wants, more tragedy, and that may be the only reason he went after Noboku, because we left her alone. I want to say that is why he made us black out, because she was closest to his influence. Though the snake also tells us to seek out the darkness, but that could mean several things in context to the story. I very well could be wrong, but it is within reason. I don't exactly remember when the headaches occur, I do know that at least two of them happen after speaking with the snake. Maybe the snake wants us to get hole, but without our emotions attached. Use the girls as objects, so to speak.
