In December 1940, Bacher joined the Radiation Laboratory at MIT, although he did not immediately cease his research at Cornell into the neutron cross section of cadmium. The Radiation Laboratory was organized into two sections, one for incoming radar signals, and one for outgoing radar signals. Bacher was appointed to handle the incoming signals section. Here he gained valuable experience in administration, coordinating not just the efforts of his scientists, but also those of General Electric and RCA. In 1942, Bacher was approached by Robert Oppenheimer to join the Manhattan Project at its new laboratory in Los Alamos, New Mexico. It was at Bacher's insistence that Los Alamos became a civilian rather than a military laboratory. At Los Alamos, Bacher headed the project's P (Physics) Division, and later its G (Gadget) Division. Bacher worked closely with Oppenheimer, and the two men discussed the project's progress on a daily basis.