By insisting on explanations in terms of mechanical interaction rather than purposes, Descartes and Leibniz rejected the use of substantial forms that was at the heart of the view of science the scholastics inherited from Aristotle. Locke attacks substantial forms and the associated notion of essence from a different direction, citing our lack of direct access to the underlying structure of nature. This appeared already in his discussion of the ideas of substances in Book II, but it is stated more sharply, though again by way of a contrast with the case of mixed modes, in what he says about the meaning of our vocabulary for substances.
Bk. III ch. vi. §§1-9, 12, 14-20, 22f, 25-29, 32, 36, 51 (pp. 192-203). In ch. iii §§17-18, Locke sketched the application of his distinction between real and nominal essence to the case of substance. He develops those ideas at much greater length here in a way that prefigures what he will say in Book IV about what we can know of nature. His attitude towards classification could certainly be described as skeptical. You should think whether it is a healthy or an excessive skepticism.
Bk. III ch. ix §§1-5, 11-13, 18 (pp. 204-207). Locke’s discussion in ch. ix serves to summarize from a different point of view much of what he has said up to this point in Book III about the ability of language to communicate ideas of his three central sorts: simple ideas, mixed modes, and substances. Use it as an opportunity to organize in your thinking what he has to say about each of these sorts of ideas.