As group of schoolgirls visit a natural history museum, an elderly man is murdered upstairs with one of the museum's own artifacts, an Indian ceremonial dagger called a katar. Terence Black, a post-grad working at the museum, discovered the victim, Adrian Weiss. His empty wallet and missing watch point to robbery.
Weiss's niece tells Thursday that her uncle had devoted his life to the study of heraldry, still designing the occasional crest. Meanwhile, Morse interviews Blythe Mount schoolgirls, all summer boarders; headmistress Bronwyn Symes; and the schoolmistress Miss Danby, and inquires about the groundskeeper's son, Billy Carswell. Upon departing, he spies a fleeting ghostly figure in bloodied Victorian clothing. Later, he finds a note in his jacket pocket: Save me. Morse also interviews the Gardiners, an elderly American couple who were visiting the museum during the murder. Their son had been stationed in the village during the war.
Morse learns that the katar was not the murder weapon. From Terence Black, he discovers that it had been given to the museum by the Blaise-Hamilton family, which made its fortune in a tea plantation in India. Thursday recognizes the name in connection with an old murder case. With Dorothea's help, Morse learns of the gruesome 1866 murder of three children, their nursemaid and governess at the Blaise-Hamilton home—now the site of the Blythe Mount School. The eldest daughter, Charlotte, mysteriously survived the horror.
Weiss's former colleague reveals that he had been working with the Gardiners. With Weiss's help, they were trying to trace the grandchild they'd never met, as their son had been killed in action before they could learn the full name of his pregnant fiancée.
Morse returns to Blythe Mount School when the quirky, bright girl Bunty disappears in the night. He finds a history of the murders in Bunty's dormitory. Miss Symes confirms that everyone is aware of the 1866 murders and the alleged ghost. Miss Danby confesses that she believes it; she takes Morse to the disused, ramshackle portion of the house where the family resided, where he sees a portrait of the patriarch, his wife's bible, and the ghost! He steps on rotted floorboards and falls through. Shaken, he is certain that someone is trying to recreate the murders of 1866, whose centennial anniversary is imminent. From the history's author, Fitzowen, he learns that Weiss had contacted him in search of information about the Blaise-Hamiltons. Soon after, Edwina, the school's youngest girl, is also reported missing.
On the night of the centennial anniversary of the murders, Morse locks the Blythe Mount residents into their rooms to keep them safe, and Fitzowen arrives with equipment to record supernatural activity. The lights cut out and suddenly they see the ghost, which they pursue through the maze of corridors. Then, the ghost girl floats over the bannister of the stairs—a brief glimpse is afforded of a male figure standing behind her—and crashes to the floor below. It's Maud Ashendon, one of the Blythe Mount girls, who was supposed to be home with her parents. Now she lies dead of a wound to the throat that preceded her fall. She, Petra and Edwina had dressed in the old clothing to scare the bullying girls. A trail of blood reveals the locus of the attack was outside of Headmistress Symes' bedroom.
Morse learns from Symes that she had in fact had contact with Adrian Weiss, who had wanted to meet, but he was killed before she learned what he wanted. In Fitzowen's photographs, they see a male figure, face obscured, behind Maud as she's launched in the air: their murderer.
Bunty reveals to Morse that the "Save me" note had not entirely been part of the hoax; the girls were frightened by a man they'd seen hanging around the school. But it was just Terence Black, in assignations with Miss Darby. Black says that he too had seen a mysterious man hanging around the school at night.
Morse finds clues in Mrs. Blaise-Hamilton's old defaced bible: five stick figures, one with its face blacked out, and underlined quotes about bastards and harlots. Scanning Weiss's census papers for Blaise-Hamilton servants, he sees the family name Pickstock. He then finds, among the heraldic materials, an unnamed coat of arms with a pickaxe and other details; he overlays it with a flowering stem and has a revelation that shifts everything into place. But he's interrupted by the phone—it's Bunty, terrified and hiding from the killer, Terence Black.
Racing to the school, Morse explains to Thursday: When Samuel Blaise-Hamilton returned from India with his illegitimate son, Robert, he gave the boy to his gameskeeper, Pickstock, to raise as his own. Robert's resentment of his siblings grew until it boiled over into murder. The vast inheritance eventually made its way to Robert but a law prevented it from passing on to his descendants. With that law under review, and possibly being overturned, Terence Black, Robert's grandson, would be the sole inheritor of the massive fortune. But Weiss, in his investigation, discovered another distant Blaise-Hamilton relative who stood in the way: Miss Symes. Black killed Weiss, the only other person who knew of the connection, so that he could freely eliminate Miss Symes. Planning to kill her on the night of the centennial anniversary, he instead killed Maude, thinking she might have recognized him from the museum. The ruby ring Morse had seen on Black's finger was the same one that Blaise-Hamilton wears in his portrait—it was handed down over generations to his great-grandson.
At Blythe Mount, the police disperse in search of Black and follow the sound of a blood-curdling scream—he holds a blade to Bunty's neck as he tries to escape. In code, Morse tells Bunty to bite him, and she escapes. Black tries to flee and jump over a rotted portion of the floor but misses and crashes to his death.
Later, evidence is disturbed as hand clad in black leather gloves takes the ruby ring from Black's personal effects and gingerly lifts the gem to reveal the masonic symbol hidden inside.