According to writer and critic Shūichirō Sarashina, a common aspect of bishōjo games at the time was to treat the individual heroine routes equally, producing a coherent narrative as a result of a sum of its parts, and he notes that Kanon also followed this pattern. Maeda focused on straying from this pattern because he wanted players to experience the entire story as a whole, but he still wanted its content to be enjoyable as a bishōjo game so that as many people as possible would be satisfied by it. In doing so, Maeda kept the basic structure of having multiple heroine routes, but he realized that he could not give each character the same level of focus. When developing the plot, the basic structure of having multiple points of view and an overarching storyline had already been solidified, which according to Maeda was not something he was aware of having been done in visual novels at the time. Fellow scenario writer Yūichi Suzumoto was apprehensive about this structure when he first heard about the plot from Maeda, but Air executive producer and Visual Arts president Takahiro Baba had already given his approval for the project by then. In addition to Maeda and Suzumoto, Takashi Ishikawa is also listed as one of the main scenario writers. Scenario assistance was provided by Kai, Tōya Okano and Tomotaka Fujii.
