	In 1941, Hilberry joined what would become the Manhattan Project, the effort to create an atomic bomb during World War II. He moved to the University of Chicago to help Arthur H. Compton in any way possible. Hilberry became associate director of Compton's Metallurgical Project. On December 2, 1942, he was present for the start up of Chicago Pile-1, the world's first nuclear reactor to achieve criticality. Because of fears that the reaction could "run away", Hilberry stood ready with an axe to cut the scram line, a manila rope connected to control rods that could quickly shut the reactor down. He was also present for the start-up of the X-10 Graphite Reactor in November 1943, and the reactors at the Hanford Engineer Works the following year. He returned to the Metallurgical Laboratory in Chicago in 1945.