An enslaved woman in South Carolina is stripped and photographed. A night watchman in Cambridge is assaulted. An extra corpse turns up in a tomb. How are they connected—and who's next?

Cambridge, Mass., February–April 1858. Civil war looms in the United States as scientific frontiers are rapidly expanding across the globe. Harvard botanist Asa Gray is discerning odd patterns among his new botanical specimens. Gray's findings set him at odds with Louis Agassiz, the most celebrated man in American science, who believes that the races of humankind represent separate species—a popular notion in the slave-owning South. Gray, in contrast, fervently supports Charles Darwin (whose On the Origin of Species will be published the following year) in believing all humans are variants of one species. The conflict is particularly acute because in Gray's employ is Darius Jacobs, a fugitive slave. Gray and Jacobs expect the worst when Cambridge anticipates a visit from amateur botanist Robert Claridge, the South Carolina owner from whom Darius fled with his sister Roxanne.

An attack on a night watchman at nearby Mount Auburn Cemetery coincides with the disappearance of Claridge. When Claridge turns up dead in a tomb at Mount Auburn, botanical clues lead the cemetery superintendent, Sumner Bascomb, to his friend and colleague Gray. Bascomb, a melancholic bachelor who once hoped to marry Gray's wife, Jane, strives to unravel the mystery of this assault and a series of murders that threaten the peace of his cemetery and community. But first the embattled superintendent must contend with his eccentric intellectual mother, Adelaide, and his strong attraction to the cemetery's genial arborist, Tom McMead. Roxanne, meanwhile, finds love when she can least afford it.

As Bascomb, Gray, and Roxanne work their way to a solution, the bodies pile up. A pregnant girl drowns herself in a frozen pond; a Southerner is found in the Charles River estuary. Behind the Boston murders lie shadows of family secrets, lost siblings, and connections of blood, love, and vengeance.