The term 'Pirate on the Jolly Roger' refers to a pirate who sails on a ship with a jolly roger flag, which is a black flag with a white skull and crossbones. The term can also refer to a pirate captain who commands a crew of pirates. The crossword solution for this term is SMEE, which is the name of a character from J.M. Barrie's novel Peter Pan. Smee is a pirate who serves as Captain Hook's first mate on the Jolly Roger.