Interdisciplinary studies has positioned itself as an innovative approach to comprehending, navigating, and transforming knowledge. The emphasis in recent scholarship upon complex systems and integration of insights from disciplinary perspectives mark decisive progress toward the development of a cohesive theory of interdisciplinarity. Such a theory would entail establishing an epistemology of complexity through epistemological negotiation. I argue that the interdisciplinary approach to knowledge is a logical evolution of the history of Western thought and an innovative answer to the epistemological project. This project was surveyed in Welch (2009) who described how the Western canonical lineage from Plato to Hegel developed epistemological strategies founded on the principles of duality, determinism, and absolute truth. The present essay carries that historical examination forward by examining the way these strategies were problematized by the recent approaches to epistemology taken by phenomenology, post-structuralism, pluralism, and pragmatism. These schools of thought are pertinent to understanding the contrasting origins and outlooks of the critical and instrumental modes of interdisciplinarity. This essay concludes that these epistemological schools of thought are not mutually exclusive; they entwine inextricably together into interdisciplinary theory as an emergent epistemological innovation. The deep historical context provided here grounds interdisciplinary theory, and gives it a voice in ongoing debates over knowledge itself.