Congressional concern with cost overruns, or breaches, in several major defense acquisition programs led the authors, in a partnership with the Performance Assessments and Root Cause Analysis Office in the Office of the Secretary of Defense, Acquisition, Technology, and Logistics, to investigate root causes by examining program reviews, analyzing data, participating in contractor briefings, and holding meetings with diverse stakeholders. In two companion studies, the authors analyzed the reasons for six program breaches and developed a methodology for carrying out root cause analyses. This report documents that methodology, whose key components include the following steps: formulate a hypothesis, set up long-lead-time activities, document the unit cost threshold breach, construct a time line of cost growth recent events from the program history, verify cost data and quantify cost growth, create program cost profiles and pinpoint occurrences of cost growth, match the time line with profiles and derive causes of cost growth, reconcile remaining issues, attribute cost growth to root causes, and create postulates. This study represents an important chronicle of the approach to use in performing such analyses -- one that others may use in their own analytic efforts. In addition, it gathers extensive documentation on the data sources used to examine the six program breaches investigated.