This paper reports on the development, self-critique and evolution of research methods for interpreting and understanding students' metacognition that were developed through the Metacognition and Reflective Inquiry (MRI) collaborative study. The MRI collaborative was a multi-year, multi-case, research study that investigated the elusive nature and character of high school students' metacognition across formal and informal science learning contexts. The study's research design comprised a series of integrated, layered, interpretive case studies which were conducted in a hermeneutic fashion over a 3 year period. The implementation of each case study provided an opportunity for the researchers to reflect critically on the research methods used to elucidate metacognition and hence refine the individual and collective capacity, responsiveness and fruitfulness of the methods used. This paper discusses the evolution of these methods and the lessons that the entire study provides for the conceptualization of other qualitative-interpretivist studies.