A good friend and I once had a lengthy discussion about the metaphysics of miracles. We agreed that they fit within a scientific conception of reality by simply being extremely improbable events (at least, at first), often of a good or even healing nature.
As for consciousness and reality, it is well-known that empirical science has difficulties with the former (and, relatedly in my framework, with half of the latter). I would argue that mysticism correspondingly does not handle materiality very well…its accounts often lapse too far into subjectivism, i.e. that perception alone is sufficient cause for reality’s entire existence.