In March 1944, he became head of a new group, E-9, which was charged with conducting the first nuclear test. In Oppenheimer's sweeping reorganization of the Los Alamos laboratory in August 1944, the E-9 Group became X-2. On July 16, 1945, Bainbridge and his colleagues conducted the Trinity nuclear test. "My personal nightmare," he later wrote, "was knowing that if the bomb didn't go off or hangfired, I, as head of the test, would have to go to the tower first and seek to find out what had gone wrong." To his relief, the explosion of the first atomic bomb went off without such drama, in what he later described as "a foul and awesome display". He turned to Oppenheimer and said, "Now we are all sons of bitches." Bainbridge was relieved that the Trinity test had been a success, relating in a 1975 Bulletin of the Atomic Scientists article, "I had a feeling of exhilaration that the 'gadget' had gone off properly followed by one of deep relief. I wouldn't have to go to the tower to see what had gone wrong." For his work on the Manhattan Project, Bainbridge received two letters of commendation from the project's director, Major General Leslie R. Groves, Jr. He also received a Presidential Certificate of Merit for his work at the MIT Radiation Laboratory. Postwar Bainbridge returned to Harvard after the war, and initiated the construction of a synchro-cyclotron, which has since been dismantled. From 1950 to 1954, he chaired the physics department at Harvard. During those years, he drew the ire of Senator Joseph McCarthy for his aggressive defense of his colleagues in academia. As chairman, he was responsible for the renovation of the old Jefferson Physical Laboratory, and he established the Morris Loeb Lectures in Physics. He also devoted a good deal of his time to improving the laboratory facilities for graduate students. Throughout the 1950s, Bainbridge remained an outspoken proponent of civilian control of nuclear power and the abandonment of nuclear testing. In 1950 he was one of twelve prominent scientists who petitioned President Harry S. Truman to declare that the United States would never be the first to use the hydrogen bomb. Bainbridge retired from Harvard in 1975. Bainbridge's wife Margaret died suddenly in January 1967 from a blood clot in a broken wrist. He married Helen Brinkley King, an editor at William Morrow in New York City,