This paper defines a theoretical framework aiming to support the actions and reflections of researchers looking for a "method" in order to critically conceive the complexity of a scientific process of research. First, it starts with a brief overview of the core assumptions framing Morin's "paradigm of complexity" and Le Moigne's "general system theory". Distinguishing "methodology" and "method", the framework is conceived based on three moments, which represent recurring stages of the spiraling development of research. The first moment focuses on the definition of the research process and its sub-systems (author, system of ideas, object of study and method) understood as a complex form of organization finalized in a specific environment. The second moment introduces a matrix aiming to model the research process and nine core methodological issues, according to a programmatic and critical approach. Using the matrix previously modeled, the third moment suggests conceiving of the research process following a strategic mindset that focuses on contingencies, in order to locate, share and communicate the path followed throughout the inquiry.