A Man Vanishes examines the concept of Johatsu, tackling the phenomenon of people missing in Japan over the years. It picks one such person from the list, someone who had seemed to disappear from the face of the earth due to embezzlement from his company, and the filmmakers begin an investigative documentary into the reasons behind and attempt at tracking him down.

The film depicts carnivalesque atmosphere summed up by the cry "Ei ja nai ka" ("Why not?") in Japan in 1867 and 1868 in the days leading to the Meiji Restoration. It examines the effects of the political and social upheaval of the time, and culminates in a revelrous march on the Tokyo Imperial Palace, which turns into a massacre. Characteristically, Imamura focuses not on the leaders of the country, but on characters in the lower classes and on the fringes of society.