After Nazi Germany broke the German–Soviet treaty and attacked the USSR and the Soviet-held Polish Kresy, Boy remained in Lwów (now Lviv, Ukraine). The city was captured on the night of 4 July 1941; he was arrested and taken to the Wulka hills where he was murdered for being "a Soviet spy", together with 45 other Polish professors, artists and intelligentsia in what became known as the massacre of Lviv professors.