Plagge was drafted into the Wehrmacht (German Army) as a captain in the reserve at the beginning of World War II, and stopped paying Nazi Party membership fees at the same time. Serving initially in Poland after the German invasion, he witnessed atrocities that caused him to decide "to work against the Nazis". In 1941, he was put in command of an engineering unit, "Heereskraftfahrpark 562" (vehicle maintenance unit 562, or HKP 562; literally "Army motor vehicle park"), which maintained and repaired military vehicles. After the German invasion of the Soviet Union, HKP 562 was deployed to Vilna, Lithuania, in early July 1941. Plagge witnessed the genocide being carried out against the Jews of the area.