This study aims to deepen the understanding of the challenges students face in using theory during thesis writing in teacher education and to explore the potential of a systems theory approach to explain these challenges. Data were collected via focus group discussions, informed by the analysis of approximately 70 purpose statements used to develop an interview guide. Nine students participated in three focus groups. The writing process is viewed as an operationally closed, self-referential system, regulated by the internal logic emerging from students' communication and actions. Findings reveal that effectively using theory requires recognizing the mutual influence between theory and the phenomena being theorized, which necessitates non-linear and complex thinking. Students must adopt the perspective of an observer and consider the factors shaping their own knowledge creation. A significant insight is that theory is not merely a tool for understanding phenomena but also shapes how observers perceive knowledge. This highlights the importance of addressing "the blind spot"- what remains unseen in scientific processes - and the inherent limitations of language in articulating complex, interdependent relationships. These insights underscore the need for a reflective approach to theory in thesis writing.