Shchelkin's plans for further research and a further dissertation were interrupted by the Nazi's attack on the Soviet Union. He volunteered and was in the platoon of artillery intelligence of the 64th rifles division, engaged in the fighting to protect Moscow. In 1942, he was ordered to return to the Institute of Chemical Physics (which was evacuated to Kazan) by the Deputy People's Commissar for Defense, Yevgeny Schadenko. He was engaged in research into combustion in jet engines. In 1943, the Institute returned to Moscow, and the following year he was appointed head of the laboratory. In 1946, he wrote a final thesis, "Fast burning and spin detonation" (also published as a monograph in 1949). He was invited to be deputy director of the Institute for Physical Problems at the Academy, but he turned down the offer to continue scientific research. Shortly after this, however, he was part of a special committee which discussed the formation of a second nuclear weapons research centre, which became known as Laboratory B, on a peninsula of Lake Sungul', where he worked as part of KB-11 (a secret nuclear weapons development facility based in Sarov, now the All-Russian Scientific Research Institute of Experimental Physics), and where German scientific knowledge was exploited as part of the "Russian Alsos". In 1949, at the test-site in Semipalatinsk, Kazakhstan, Shchelkin supervised the placement of the first Soviet nuclear device on the tower, put the detonating cap on the sphere of plutonium himself (and supervised the later ones). For this success, he received the Hero of Socialist Labour award; several others followed in ensuing years, including for work on the first Soviet thermonuclear weapon.