"Specimen Days" consists of three stories.

Summary of each story:

"In the Machine" (Past - 19th Century)
Set in industrial-age New York, this section follows a young boy named Lucas who begins working in a factory after his brother's death in a machine accident. Lucas starts to believe that machines are consuming people’s souls, a belief fed by his obsession with Walt Whitman’s poetry. The story explores industrialization, grief, and the spiritual cost of modern progress.

"The Children's Crusade" (Present - Early 21st Century) In contemporary New York, Cat, a black woman working for a counter-terrorism unit, investigates a series of bombings committed by children. She partners with a boy named Simon, one of the would-be bombers. The section reflects post-9/11 anxieties, child exploitation, and the search for meaning in a disoriented modern society.

"Like Beauty" (Future - Post-Apocalyptic Future) Set in a dystopian future where humans coexist with sentient androids, this story follows Simon, an android on the run, and Catareen, an alien refugee. Together, they search for a new place to belong in a devastated, increasingly inhuman world. This part delves into themes of identity, otherness, and the persistence of human longing.