As I understand it, a chipset (CPU, etc.) will have a set of registers for storing data, and understand a set of instructions for manipulating these registers. The instructions will be things like 'store this value to this register', 'move this value', or 'compare these two values'. These instructions are often expressed in short human-grokable alphabetic codes (assembly language, or assembler) which are mapped to the numbers that the chipset understands - those numbers are presented to the chip in binary (machine code.)
Those codes are the lowest level that the software gets down to. Going deeper than that gets into the architecture of the actual chip, which is something I haven't gotten involved in.
