The purpose of this study is to develop a 3D image map, which is an extension of a previous image map developed on a 2D plane, and to clarify how it contributes to the integration and emergence of scientific knowledge through students’ proactive problem solving. The results of this case study were analyzed in terms of the thinking process featured in “Rise Above”, as identified by Nakagomi and Kato (2020). Results of the analysis suggested that the abstract knowledge created through the 3D image map developed in this study facilitates the acquisition of a perspective that compares different contents and, moreover, fosters the thought process of integrating and generating abstract knowledge from concrete knowledge. In addition, it was suggested that abductive thinking is mediated through the comparison of different contents within the same unit, and abstract knowledge may be gradually created through this process.