In 1879 Flegel travelled about 525 miles (845 kilometres) up the Benue River and in 1880 went by way of the Niger to Sokoto, in northwestern Nigeria, where he obtained permission from the Sultan for an expedition to the Adamawa Plateau. In the course of exploring the Benue Basin (1882–84), he reached the Benue's source, near Ngaoundéré, now in Cameroon. After a short stay in Europe, Flegel returned to Africa in April 1885 with a commission to open up the Niger and Benue basins to German commercial influence and thus prevent British ascendancy in that region. He was, however, unsuccessful and died the following year. His works include Lose Blätter aus dem Tagebuch meiner Haussa-Freunde und Reisegefährten (1885; “Loose Leaves from the Diary of My Hausa Friends and Travel Companions”) and Vom Niger-Benüe (1890; “Concerning the Niger-Benue”).