It is a main contention of this paper that the history of science is not so much a story of the progressive advance in our understanding and discovery of ‘the facts of nature’, but rather, an account of different ways of ‘seeing’ things; where ‘the things’ thus seen are to a considerable extent themselves the result of ‘realizational’ processes operating in terms of some theory or other. But further, such theories are in turn controlled by some respective methodology which has its history: with the latter itself a record of different views about those elements believed to be essential for any adequate constructionof scientific theories. The paper then distinguishes between three views, the ‘rationalist’, the ‘empiricist’, and the ‘systemic’ processing of scientific ‘facts’; the last-named view operating under the guidance of certain leading maxims and principles. Finally, the paper formulates a triadic type of methodology whose three components mirror the three views just mentioned: the ‘probative’, the ‘explicative’ and the ‘systemic’ components; which in turn are then shown to generate three corresponding ontologies.