Bacon's namesake for this book is Aristotle's Organon, where Aristotle discusses syllogistic reasoning, which is Aristotle's system for logical deduction. The New Organon was originally published within a broader work called Instauratio Magna.
Bacon begins the work by discussing the philosophical issue of assumption. He addresses beliefs a priori, which is Latin for "at the beginning," as in, "they believed that from the start," which would be assumption. He says of this that by analyzing the mind, we should be able to approximate deductive reasoning in relationship to nature. Bacon continues his argument by constructing the building blocks for the scientific method.
He says that science should acknowledge the human need to hypothesize, instead of believing hypotheses a priori. Then, by examining the relationships of the parts, by limiting variables, one should conduct experiments that are replicable. He anticipates critical responses to his work and tries to circumvent them by offering counter arguments for the arguments one might use to deconstruct his system for experiment. He ends the work by discussing observation and the human experience.