"The Empire of Corpses" is set in an alternate 19th-century world where reanimating the dead has become a scientific reality, though the reanimated corpses lack souls and are used as laborers or soldiers. The story centers on John Watson, a young medical student in London who is secretly conducting illegal experiments to restore souls to the dead. After his mentor, Victor Frankenstein, is executed for his own forbidden research, Watson is blackmailed by the British government into locating Frankenstein's notes, which are believed to contain the key to creating a fully sentient corpse.

Watson's journey takes him across the globe, from London to Afghanistan and eventually to Japan, as he pursues the elusive notes. Along the way, he is accompanied by a reanimated corpse named Friday, who exhibits unusual intelligence and hints of a soul. Watson's quest intersects with the ambitions of various factions, including the British Empire, the United States, and a shadowy organization led by a man named Alexei Karamazov, who seeks to use Frankenstein's research for his own ends.

The narrative explores themes of humanity, ethics, and the consequences of scientific advancement. Watson grapples with the moral implications of his work, questioning whether reanimating the dead is a violation of natural order or a means to transcend human limitations. The story also delves into the political and social ramifications of corpse technology, as nations vie for dominance using reanimated armies.

Key characters include John Watson, whose determination and moral conflict drive the plot; Friday, the enigmatic corpse who becomes central to Watson's mission; and Hadaly Lilith, a mysterious woman with ties to Frankenstein's research. The series weaves together historical figures, such as Nikola Tesla and Frederick Burnaby, with fictional elements, creating a rich tapestry of intrigue and philosophical inquiry. The plot builds toward a climactic confrontation that forces Watson to confront the true nature of life, death, and the soul.