Captain John Pope was in the Battle of the Head of the Passes 12 October 1861 on the lower Mississippi River near its mouth. This resulted in "Pope's Run." The Confederate ships under Captain George N. Hollins drove the Union fleet away.
On October 14th, John Pope asked to be relieved of duty due to ill health and it was granted. Later, on 16 July 1862, he was promoted to commodore at which time he retired from the service.
He died in Dorchester, Massachusetts in 1876.
Two ships in the U.S. Navy have been named after him. The USS Pope (DD-225) commissioned in 1920 and sunk during World War II in 1942. Also the USS Pope (DE-134, commissioned in 1943 and decommissioned in 1946.