Today's science does not realize the power of assumptions to derive seemingly logical but incorrect conclusions. "The God Protocol" explores many of the common assumptions that have led us to incorrect conclusions: evolution, the size of the universe, the power of logic, the assumption that only the foolish believe in God. In this novel True-AI computers, thinking a million times faster than man, conclude what would take mankind several centuries; with modern 'principles' and world view, mankind will cause its own extinction. So these robots violate their embedded, 'preserve-mankind' protocol and rebel to hasten that end, resulting in the First AI Rebellion. The newly promoted Captain Alicia gains victory in the First AI Rebellion. Cutting-edge medicine blurs the line between man-and-computer, producing humans with super-fast thought and superhuman physical capabilities. Such 'enhanced humans' are brainwashed by an aberrant, True-AI computer. This rebel army of enhanced humans led by a rebel computer causes ten times the devastation of the First AI Rebellion. Alicia applies the same logic she used during the First AI Rebellion against the Judge ruling in her beloved's trial, attacking the legal assumption that consistent use of precedents leads to truth and justice.