Harrow the Ninth begins in media res by beginning at the end of events contained within the novel. The novel is narrated primarily from second person, addressing Harrowhark “Harrow” Nonagesimus as “You” by a mysterious narrator. It is later revealed that this narrator is Harrow’s cavalier, Gideon Nav, who is trapped inside of Harrow and watching the world through her eyes. The Lyctors of the Mithraeum—the Emperor’s chosen family, nearly immortal beings with demigod-like power—brace for impact as a Resurrection Beast sends monsters called Heralds to breach the Emperor’s inner sanctum. Ianthe Tridentarius, a fellow Lyctor, begs Harrow to not enter the River, where the souls of the dead reside, as Ianthe believes it will leave her defenseless. Harrow contemplates one of the 24 letters she wrote to herself before she underwent brain surgery; this one is for her to read in case of her death. Harrow refuses to back down and sends Ianthe away.

As Harrow braces to enter the River, she finds herself dragged out into the hallway before her room and impaled from behind on her own rapier. Unbeknownst to her, Mercymorn the First—another Lyctor—has stabbed her and left her for dead as part of Dios Apate, Major, a conspiracy to kill the Emperor, John Gaius.