Methodological naturalism is the stance almost all of us adopt almost all the time these days. We put more confidence in physicians than in faith healers; in meteorologists rather than seers; in radar rather than divination. Our experience is, that as knowledge and understanding of our universe grows, so the domain of the supernatural shrinks.
To the contrary, I assert that the natural is part of what you would consider "supernatural" and indeed, the natural declares that God exists. For instance, that there was a beginning, that the universe is intelligible at all, the unreasonable effectiveness of math, the existence of information in the universe, that order has arisen out of chaos (the void), willfulness, autonomy, semiosis and so on.
What you are speaking to is causation. Where you have looked you have found physical causation. Science depends on physical causation to understand nature, so that is not surprising.
But I doubt you have weighed the full concept of causation. For instance, were it not for A, C would not be. Were it not for space/time, events would not occur, etc. Or as Physicist remarked on another thread, existence exists.
To that I would add that everything we observe ought to be understood in that context. Intentionally not doing so, leaves one in worse shape than a blind man in the elephant metaphor (from post 529)
Considering your credentials and fields of interests which I have discerned from your postings on the forum over the years, I also suspect there are many anomalies you have not yet weighed.
For instance, you mentioned prophesy. Here's a simple one which is not part of either a Jewish or Christian canon. Consider that the book of Enoch was dated by Laurence before the rise of Christianity, most probably at an early period of the reign of Herod because it prophesied the reign of King Herod the Great which began 37 B.C. and was quoted by Jesus Christ and His apostles. In other words, the presumption of scholars is that prophesy cannot be true and therefore if something prophesied actually happened, it must have been written after the event mentioned. That is a false presupposition which leads to error. In this case, a copy of the manuscript was found in the Dead Sea Scrolls at Qumran fragment 4Q208 and was dated with a paleographic age 200 B.C. and was carbon-dated, calibrated 166-102 BC and 186-92 BC.
We could examine other prophesies in Scripture - but to do so would involve much more discussion, sources, etc. But if you are interested in such things, we can set them up and proceed to examine them one at a time.
Supernatural is by definition what is not natural.
Consider that the book of Enoch was dated by Laurence before the rise of Christianity, most probably at an early period of the reign of Herod because it prophesied the reign of King Herod the Great which began 37 B.C. and was quoted by Jesus Christ and His apostles.
Please identify the verses from Enoch that prophesy Herod the Great.