The implication that any software is "mysterious" is problematic - there is no "woo" here - the exact state of the machine running the software may be determined at every cycle. The exact instruction and the data it executed with may be precisely determined, as can the next instruction. The entire mythos of any software being a "black box" is just so much advertising jargon, perpetuated by tech bros who want to believe they are part of some Mr. Robot self-styled priestly class.