In a previous work the philosophical concept of Mechanism was proposed in order to characterize the kind of scientific explanations provided by the system dynamics approach.  That earlier paper positioned such idea epistemologically contrasting it with the traditional view used by mainstream management research and developed a different ontological ground based on the structuralist approach of Bertrand Russell. However, it seems to be needed an emphasis on the epistemological nature of the Mechanism thesis because of its common association with reductionism and the view of mechanistic thinking as supposedly opposed to holism and emergentism. This paper constitutes a second part; it underlines the epistemic status of Mechanism which explains why it is in no way opposed to ideas like holism or emergentism, on the contrary it is consistent with such worldviews. Based on this condition the paper explores the repercussions of such characterization for philosophy of science and for system dynamics by developing a research agenda for both fields around this topic.