Endeavour Morse is among the first on the scene when the body of Evelyn Balfour is discovered in a decommissioned old railroad car. A handkerchief embroidered with the letter "D" was stuffed in her mouth, and she was strangled with a tie. She'd told her husband, Lionel, that she was visiting her sick mother, but she was cheating on him. While Thursday and Jakes question Lionel, find Roy Adamson, the man she was involved with, and bring Adamson in, Endeavour returns, at night, to the crime scene. When the door suddenly slides closed and locks, he sees a messaged written in chalk: "Un bacio ancorra." Back at the station, he explains the message: "One kiss more," Othello's last line in Verdi's opera. Othello believes Desdemona has given her handkerchief to a lover and he strangles her in jealousy. Jakes is skeptical and disdainful of Endeavour's discovery, but they are interrupted by news of another death.
The victim is Grace Madison, found dead by her niece, Faye. Faye and her brother Philip were raised by their aunt, and Philip, a temperamental classical pianist, has lately been consumed with preparations for a solo recital. On Grace's desk, Endeavour finds a letter from a journalist named Ben Nimmo, and a 4pm appointment on the day of her death. Endeavour is again greeted with scorn when he requests that the contents of the teapot be analyzed, but the toxicological report shows the highly toxic Datura plant as the leaves brewed in Grace Madison's tea. Endeavour again returns to the crime scene and finds a hidden clue in Grace's greenhouse, a brass nametag. Inscribed on the tag are the last words sung by Lakme in the opera by Delibes before she kills herself by eating Datura leaves. Thursday convinces Bright to let him borrow Endeavour for the remainder of the case.
Bright arrives with Dr. Cronyn, a psychiatrist who specializes in the study of these kinds of deranged murderers. He notes the killer's intellect and complete absence of the notions of good and evil. Endeavour is convinced they'll succeed in catching him. He tries to interview Grace's nephew, Philip, but Faye is protective of her brother and says he can't be interrupted. However, Endeavour and Thursday track an address for Ben Nimmo to an abandoned farmhouse where, when Thursday switches on the fuse in the basement, a turntable begins playing "Aida," Ramades' final aria which he sings before being entombed alive. With a cement mixer in the yard and fresh brickwork in the basement, they understand, with grim dread, that they are about to discover another victim.
Bright, Cronyn, and the detectives listen to the pathologist describe the tortured death of old Ben Nimmo, entombed alive. Among a shrine of sorts, Jakes finds a picture tacked up on the wall from the Daily Mail of Endeavour attending a reception for the Oxford Scholars Choral Association. Found on the corpse is the score to a song known as "the list song," from "The Mikado." This triggers a memory in Cronyn of an old patient from Bellvue Sanatorium, a musical child prodigy named Keith Miller, who murdered his mother. In describing his violent fantasies about torturing members of the staff for perceived wrongs, he would say "I've got a little list." He was from Oxford.
Initial investigations into Keith Miller yield nothing, as a fire destroyed Bellvue's records several years prior, and there's no record of him in the department's files. Endeavour speculates that the victims' names indicate the mnemonic device for notes on the treble clef: "Every Good Boy Deserves Favor." So the next victim's name will start with "D." Meanwhile, Dorothea Frazil from the Oxford Mail contacts them; someone has anonymously sent an orchestral score for the opera "The Snowmaiden." A six-year-old girl, Debbie, is abducted. Left behind in her shoe is a puzzle that they have only until sunrise to solve. When Endeavour heads to the Bodleian Library and asks if the "Snowmaiden" score had been requested, and the librarian indicates that Keith Miller is there now, Endeavour pursues him in the stacks, and is stabbed before Miller escapes. Another clue, in the form of a logic puzzle called a "Bocardo syllogism", surfaces. Endeavour realizes that Bocardo is the name of the prison where martyrs were held before being burned. The martyrs' prison cell door is on display in the church tower. There, in a child's coffin, they find Debbie unharmed. Meanwhile, Dr. Daniel Cronyn's corpse is found by Philip and Faye Madison, his body melted with acid, his skin destroyed beyond recognition. He was the killer's "D". Evidence suggests that Cronyn was a morphine addict.
Dorothea has new information to share with the detectives: an old editor researched the old crime in the paper's archives, and while there was a musical prodigy who killed his mother, there was no Keith Miller – the boy's name was Mason Gull. Endeavour realizes "Keith Miller" is an anagram for "I'm the killer." Mason Gull killed the real Daniel Cronyn, stole his identity, and was killing people related to those connected to the trial: Benjamin Nimmo and Evelyn's mother, Gertrude Tate, were witnesses for the prosecution, and the judge was Justice Madison. When Endeavour receives a phone call broadcasting "Tosca," he knows that the final victim, the "F," will be Faye Madison, and that "Tosca" is the acronym for The Oxford Scholars Choral Association. They rush to Philip's performance and save Faye before realizing that they're just being toyed with again; the killer has Fred Thursday at knifepoint on the roof and is forcing him to jump. Endeavour picks his way across the roof toward Thursday and Cronyn/Gull. When the killer lunges, Thursday stabs him with his pipe stem, and the killer drops his knife. Dragged away under arrest, Cronyn/Gull taunts Endeavour, claiming that they are the same; that intelligence is a burden, and to be clever is to be alone.