Under the auspices of the Manhattan Project, Rafferty directed Union Carbide's efforts to enrich uranium (some of which was mined by another Union Carbide subsidiary: the United States Vanadium Corporation) for use in an atomic bomb. This effort culminated in Union Carbide designing (along with the Kellex Corporation), building, and operating the massive K-25 gaseous diffusion plant at Oak Ridge.
General Leslie Groves wrote of Rafferty: 
Stéphane Groueff, in his book chronicling the Manhattan Project, had this to say about Rafferty:On June 1, 1945, prominent industrialists, including Rafferty, were invited to the second meeting of the Interim Committee. The industrialists were introduced to the committee as follows:Tennessee Eastman also managed and operated the Y-12 facility at Oak Ridge. In 1947 Union Carbide took over the operation of Y-12.
The graphite for the Hanford B Reactor as well as the Oak Ridge X-10 Reactor was produced by another Union Carbide subsidiary National Carbon Company.