This part of the monograph describes three stages of the five-stage process (Chapter 4, Table 10: Stages 2–3–4) that lead to the final form of the proposed analytical tool for the study of the text-organizing role of reference in academic writing. The first stage (Chapter 6) is an attempt to overcome the problems pointed out in Chapter 5 that undermine the use of Halliday and Hasan’s (1976) taxonomy as an analytical tool. Although Chapter 5 raised several questions regarding the analytical process, all of them cannot be handled in one single attempt if analysis is to remain consistent. This first step only intends to apply the categories of reference items arrived at in Chapter 3 (Table 8) and reshape the layout of the analysis. Ideas were borrowed from other models for the analysis of patterns in text (e.g., Hasan, 1984; Károly, 2002; Lautamatti, 1987; Thompson, 1994) to transform the taxonomy into a visual representation of cohesive chains and make it a reliable analytical tool. An analysis of 10 research articles (RAs) was carried out to check the feasibility and reliability of the analytical tool. While this empirical study proved that the tool is reliable, practical and theoretical problems were raised during the analysis, which resulted in a second version of the analytical tool.