The New Organon is the second part of Bacon's larger work, the Great Instauration, which aims to offer a new method of investigating nature, called the Interpretation of Nature. A better use of the mind and the understanding is needed to investigate nature. Bacon suggests an entirely new system of logic, which is based on induction rather than on the syllogism. Induction begins with the facts of nature and works slowly towards general axioms or propositions, by building up tables of comparison. Experiments are to be used to assist the senses in this process.

Currently, men's minds are filled with various foolish and incorrect notions that prevent them from understanding nature properly. Bacon seeks to eradicate these notions, which he calls the idols, which originate in human nature, interaction between people and in the work of various philosophers, particularly Aristotle.

Book one consists of Bacon's scathing attack on current philosophy and on the scientific method. He attacks the syllogistic method, and the various idols that prevent men from investigating Nature in a reasonable way. The lack of attention paid to natural philosophy and the excessive reverence for ancient authors are key reasons why man's knowledge of nature has progressed so slowly.

Book Two is a detailed explanation of Bacon's method, using various examples. It begins by creating tables of the various instances that meet in the nature to be investigated. After the relevant instances have been presented to the intellect, the task of induction can be carried out. Induction acts by excluding various possibilities, until an affirmative has been achieved. The next stage is the consideration of privileged instances, which assist the process in terms of information or of practice.

The final section is a rough draft of the kind of natural history that Bacon argues is essential before any interpretation of nature is possible. The method of the Organon is not viable until a vast amount of information about the natural world has been collected.