The basic theory of scientific understanding presented in Sections 1–2 exploits three main ideas.First, that to understand a phenomenonP (for a given agent) is to be able to fitP into the cognitive background corpusC (of the agent).Second, that to fitP intoC is to connectP with parts ofC (via “arguments” in a very broad sense) such that the unification ofC increases.Third, that the cognitive changes involved in unification can be treated as sequences of shifts of phenomena inC. How the theory fits typical examples of understanding and how it excludes spurious unifications is explained in detail. Section 3 gives a formal description of the structure of cognitive corpuses which contain descriptive as well as inferential components. The theory of unification is then refined in the light of so called “puzzling phenomena”, to enable important distinctions, such as that between consonant and dissonant understanding. In Section 4, the refined theory is applied to several examples, among them a case study of the development of the atomic model. The final part contains a classification of kinds of understanding and a discussion of the relation between understanding and explanation.