WHY WAS A U.S. SUBMARINE FLYING THE JOLLY ROGER? “In Navy tradition, the flying of the flag typically signifies a successful mission of some sort. As the Washington Post points out, the practice for subs began in World War II, when Royal Navy submarines flew the flags as a means of signaling a successful mission. Legend has it the flag, traditionally considered the flag of pirates, was adopted after a British admiral in World War I compared submarine warfare to piracy.”