In 1872, Goode started working with Spencer Baird, soon becoming his trusted assistant. While working with Baird, Goode led research sponsored by the United States Fish Commission, and oversaw many Smithsonian displays and exhibitions, for the museum itself and for expositions around the world; Goode's first of these were the preparations for the Philadelphia Centennial Exposition, for which the Smithsonian was responsible for all the government displays. He also served as the assistant secretary of the Smithsonian Institution in charge of the United States National Museum.
