The revolution implied by Yukawa’s discovery of the meson in 1935 was part of a lively epistemological debate in Japan. At the beginning of the twentieth century, a radical materialist tendency represented by Taketani’s “stereo-structural logic” and a “logic of mediation” supported by Tanabe within what he called an “existentialist physics” clashed. If it seems at first sight natural to bring Yukawa’s nonlocal field theory closer to Taketani’s three-state epistemology, insofar as the two physicists co-authored some of the articles of the series crowned in 1949 by a Nobel Prize, the dialectic implied by the notion of “elementary domain” seems to us irreducible to the dialectic of nature supported by Taketani. It is from Nishida’s “logic of place” and his idea of acting intuition that we shall try to understand the theoretical synthesis that Yukawa undertakes to elaborate. Nonlocality takes on a new meaning, where emptiness is distinguished from the Epicurean vacuum in order to be understood as Śūnyatā, i.e., as a “superessential vacuity” or an “undifferentiated continuum” whose meaning and scope in physics can be clarified by Nishida’s “dialectic of nothingness” as a dialectical monadology.