The novel tells the story of Harrison William Shepherd beginning with his childhood in Mexico during the 1930s. His parents are separated so he lives back and forth between the United States with his father and Mexico with his mother. During his time in Mexico he works as a plaster mixer for the mural artist Diego Rivera then as a cook for both him and his artist wife Frida Kahlo, with whom Shepherd develops a lifelong friendship. While living with and working for them, he also begins working as a secretary for Leon Trotsky who is hiding there, exiled by Stalin.
Later in life, living in Asheville, North Carolina, Shepherd becomes a novelist and is subsequently investigated by the House Un-American Activities Committee. He instructs his secretary, Violet Brown, to burn his papers and returns to Mexico. However, she saves his diaries and letters and it is these papers that form the bulk of the novel. There are gaps, or lacunae, in the story, hence the title.