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A stored program computer merely does what it is told. The computer fetches an instruction, performs the tasks dictated by that instruction and then fetches the next instruction. The instructions are stored sequentially in memory and executed in a sequential manner unless program logic dictates a branch.
Nearly all computers use zero/one logic in the hardware and therefore store their instructions and data as binary numbers. Although values may be represented as hex or decimal numbers in a program, they are stored in memory in binary representation.