The Day After Trinity is about the scientist J. Robert Oppenheimer (1904-1967) and his role in producing the first atomic bomb. The film uses newly-declassified government footage, woven together with the candid recollections of Oppenheimer's close friends and associates.

Trinity deals with the entire span of Oppenheimer's tragic and often mysterious life beginning with his early years in Europe, the heady days of atomic science in the 1920s and '30s, and the long periods of time spent with friends at an isolated ranch in the New Mexico wilderness. During the 1930s Oppenheimer was closely involved in leftist, anti-fascist politics, but these were temporarily forgotten by government authorities when he was asked to join the Manhattan project shortly after the outbreak of World War 2. Oppenheimer was named "Co-ordinator of Rapid Rupture" for the super-secret atomic bomb project, and spent 27 frenzied months as director of Los Alamos Laboratories. He brought nearly 6000 scientists and technicians to the remote lab, where the bomb was secretly designed and assembled. The device was tested in the summer of 1945 at Trinity Site, in the desert 500 km south of Los Alamos, and the film uses extraordinary new archive footage showing Oppenheimer and his team making final assembly at the site. It was only after the destruction of Hiroshima and Nagasaki that the scientists fully realized the horror of what they had wrought.

Captured Japanese films and the recollections of American scientists are used to explore the significance of the bomb's use against civilians. In the post-war years Oppenheimer was a national hero, and used his influence to limit the development of nuclear weapons, particularly the hydrogen bomb, championed by his fellow scientist Edward Teller and the U.S. Air Force. Finally, in 1954, his leftist past and his opposition to the hydrogen bomb resulted in a bizarre and ill-conceived security hearing which brought his career to a sudden and tragic end.