The purpose of this paper is to examine ways of thinking about embodying deep learning in a Japanese language course that reads picture books by the same author. Another goal is to plan questions that correspond not only to simply reading but also to reading activities. The other purpose is to show the potential power of reading and thinking. In this article, we will examine the picture books “Swimmy,” “Frederick,” and “Cornelius,” which are used in the unit “Swimmy” in the second grade of elementary school, with a focus on how skills to develop ways of thinking are used in a comprehensive study class. We also highlight research on teaching materials conducted with the aid of previous studies of methods of planning questions. As a result, we are able to envision various questions with a broad view. Toward the end, we look at how “what to associate with what and what to think of” are taught. The methods of thinking and planning questions presented in this paper may contribute to the development of the ability to read. They may also help to build the capacity to learn and cultivate personality.