In 1996, the Institute for the Science of Thought decided to cease publication of its journal Shisō no kagaku (Science of thought). Launched in May 1946, the journal had not only survived the turbulent immediate postwar era, but also oversight by five different publishing companies within the space of less than twenty years. In 1962 the Institute broke away from commercial publishers, and established a new company especially to publish the journal. Self-publishing was prompted by the decision by the journal’s current publisher to cancel a forthcoming special issue on the ‘emperor system’. This was a pivotal moment in the history of Shisō no kagaku. In this essay, I outline the chronology of the “Shisō no kagaku Incident,” examine aspects of the contemporary ideological context such as the emergence of the so-called “chrysanthemum taboo,” and explore its legacy for the new publisher’s treatment of topics to do with the emperor.