So, everything is explained, nothing is resolved. More later, maybe.
Oh, and also: I heard Shizuku (and Mikoto) saying "あやつられていろ" (it means "is being manipulated"). I knew that studying passive would come handy one day. There was casuative too, although I didn't jot it.
UPDATE: A decent blow-by-blow write-up is available at Blue Blue Wave. Parts of what Kaede says wasn't clear, in particular what does Natsuru's sex has with anything, but this explains it (nothing, as it turned out: it's only an indicator).