When Germany began the invasion of the Soviet Union in June 1941, Molodchy was a deputy squadron commander in the 420th Long-Range Bomber Regiment. Before entering combat in August he became one of the first Soviet pilots to become proficient in flying the Yer-2; or flying six daylight and seven night missions on it he was nominated for the title Hero of the Soviet Union on 20 October 1941, which was awarded two days later. From January 1942 to June 1944 he was a deputy squadron commander in the 748th Long-Range Aviation Regiment, which received the guards designation in the August of the same year and was renamed 2nd Guards Regiment. After successfully bombing Berlin in an Il-4 on 26 August 1942 he received a congratulatory radiogram from Joseph Stalin. For most of his missions in the early years of the war he flew with as his navigator.