Philosophers and scientists often cite ontic factors when explaining the methods and success of scientific inquiry. That is, the adoption of a method or approach (and its subsequent success or otherwise) is explained in reference to the kind of system in which the scientist is interested: these are explanations of why scientists do what they do, that appeal to properties of their target systems. We present a framework for understanding such “ Opticks to his Principia . Newton’s optical work is largely experiment-driven, while the Principia is primarily mathematical, so usually, each work is taken to exemplify a different kind of science. However, Newton himself often presented them in terms of a largely consistent method. We use our framework to articulate an original and plausible position: that the differences between the Opticks and the Principia are due to the kinds of systems targeted. That is, we provide an ontic-driven explanation of methodological differences. We suspect that ontic factors should have a more prominent role in historical explanations of scientific method and development.