After enumerating the shortcomings of the current and past natural philosophies, Bacon can now present his own philosophy and methods. Bacon retains the Aristotelian causes, but redefines them in interesting ways. While traditionally the final cause was held as most important among the four (material, formal, efficient, and final), Bacon claims that it is the least helpful and in some cases actually detrimental to the sciences (aph. 2). For Bacon, it is the formal cause which is both the most illusive and most valuable, although each of the causes provides certain practical devices. By forms and formal causes, Bacon means the universal laws of nature. To these Bacon attaches an almost occult like power:
But he who knows forms grasps the unity of nature beneath the surface of materials which are very unlike. Thus is he able to identify and bring about things that have never been done before, things of the kind which neither the vicissitudes of nature, nor hard experimenting, nor pure accident could ever have actualised, or human thought dreamed of. And thus from the discovery of the forms flows true speculation and unrestricted operation (aphorism 3)
In this second book, Bacon offers an example of the process that of what he calls true induction. In this example, Bacon attempts to grasp the form of heat.
The first step he takes is the surveying of all known instances where the nature of heat appears to exist. To this compilation of observational data Bacon gives the name Table of Essence and Presence. The next table, the Table of Absence in Proximity, is essentially the opposite—a compilation of all the instances in which the nature of heat is not present. Because these are so numerous, Bacon enumerates only the most relevant cases. Lastly, Bacon attempts to categorise the instances of the nature of heat into various degrees of intensity in his Table of Degrees. The aim of this final table is to eliminate certain instances of heat which might be said to be the form of heat, and thus get closer to an approximation of the true form of heat. Such elimination occurs through comparison. For example, the observation that both a fire and boiling water are instances of heat allows us to exclude light as the true form of heat, because light is present in the case of the fire but not in the case of the boiling water. Through this comparative analysis, Bacon intends to eventually extrapolate the true form of heat, although it is clear that such a goal is only gradually approachable by degrees. Indeed, the hypothesis that is derived from this eliminative induction, which Bacon names The First Vintage, is only the starting point from which additional empirical evidence and experimental analysis can refine our conception of a formal cause.
The "Baconian method" does not end at the First Vintage. Bacon described numerous classes of Instances with Special Powers, cases in which the phenomena one is attempting to explain is particularly relevant. These instances, of which Bacon describes 27 in Novum Organum, aid and accelerate the process of induction. They are “labour-saving devices or shortcuts intended to accelerate or make more rigorous the search for forms by providing logical reinforcement to induction.”
Aside from the First Vintage and the Instances with Special Powers, Bacon enumerates additional "aids to the intellect" which presumably are the next steps in his "method." In Aphorism 21 of Book II, Bacon lays out the subsequent series of steps in proper induction: including Support,s to Induction, Rectification of Induction, Varying the Inquiry according to the Nature of the Subject, Natures with Special Powers, Ends of Inquiry, Bringing Things down to Practice, Preparatives to Inquiry and Ascending and Descending Scale of Axioms. These additional aids, however, were never explained beyond their initial limited appearance in Novum Organum. It is likely that Bacon intended them to be included in later parts of Instauratio magna and simply never got to writing about them.
As mentioned above, this second book of Novum organum was far from complete and indeed was only a small part of a massive, also unfinished work, the Instauratio magna.