Over the course of the 19th and 20th centuries, science progressed in great leaps. The rise of the scientific-materialist world-view was connected to the discovery of two worlds that people had never recognized before. One was the microscopic world of the atom. The other was the world of the unconscious. Touhou 11 - Subterranean Animism retells that modernization as it happened in the 19th and 20th centuries, especially as it concerns Japan. The modernization efforts of the Meiji era were brought about by foreign, imported ideas. Similarly, in the story of Subterranean Animism, Yasaka Kanako and the Moriya Shrine – in other words, new arrivals from the world outside Gensokyo – bring in the yatagarasu with the power of the Sun and install it inside Reiuji Utsuho, where the power begins to run wild. As we all know, the power installed within Reiuji Utsuho is that of nuclear fusion, that is, the newly discovered microscopic world. Meanwhile, Komeiji Koishi has the power to control the unconscious. And as mentioned above, this too is a creation of modernity. The microscopic and unconscious worlds have always existed around or within us. But it was only in the modern era that we became aware of, that is to say, able to see either of them. I used the word "see" here, but "seeing" actually holds special meaning when it comes to Subterranean Animism.

Reiuji Utsuho is drawn with a red eye in the middle of her chest. We can call it her third eye. Komeiji Koishi also has her third eye, but unlike Utsuho's, hers is closed. In this case, closing her third eye allowed her to discover the subconscious. This could be taken as representation of how, in exchange for the ability to see these two new worlds, there was another world that humanity lost sight of. The author believes that the world in question is the one seen by the last person in Subterranean Animism who also has a third eye: Komeiji Satori. Komeiji Satori is the mistress of the Palace of the Earth Spirits, and a powerful figure in Former Hell. Former Hell itself is a place where hated individuals, forgotten even by Gensokyo, wash up. Those hated people include some such as tsuchigumo, hashihime and oni – truly classical Japanese youkai. Komeiji Satori's third eye gazes right into the heart of that world where evil spirits run rampant: the pre-modern world-view. Ironically, this is the very world that we've become blind to as we stepped into modernity. The author believes that Subterranean Animism depicts modernization, and a certain nostalgia for the world left behind. In that sense, it is truly one of the most Touhou-like themes in all of Touhou.