At the height of the McCarthy era, J. Robert Oppenheimer, the government’s top atomic physicist, came under suspicion as a Soviet spy. After 19 days of secret hearings in April and May of 1954, the Atomic Energy Commission revoked his security clearance. The action brought his career to a humiliating close, and Oppenheimer, until then a hero of American science, lived out his life a broken man. But now, hundreds of newly declassified pages from the hearings suggest that Oppenheimer was anything but disloyal. Historians and nuclear experts who have studied the declassified material—roughly a tenth of the hearing transcripts—say...