The Duke of Portland is an aging British aristocrat who lives in seclusion on his Welbeck estate. He is a somewhat eccentric man who has always kept to himself. As he has aged, both his physical and mental conditions have noticeably deteriorated. This causes him to engage in somewhat unusual behavior. Although local folks rarely see the reclusive Duke, news of his increasingly idiosyncratic conduct makes its way into the public arena. The information is quickly exaggerated and distorted and it is often alleged that the Duke is a physically deformed monster who hides himself on his estate in order to conceal his disfigurement.

When the novel opens, it is autumn and construction of an elaborate tunnel system on the Duke's estate has been completed. It is unclear what purpose the tunnel system serves since the parts of the estate that are connected underground can be just as easily accessed above ground. It seems that the Duke built the tunnel for his own amusement.

Over the course of the winter, the Duke makes an attempt to learn more about himself. There are two ways in which he tries to accomplish this. First, he sets about exploring his estate and on his little excursions he collects artifacts that were once owned by his ancestors. Second, he is haunted by a memory and by a conviction that that there is phantom boy in his presence and he attempts to discover the significance of recurring experiences.

On one of the Duke's excursions, he finds the Fowler head, the bust of a man on which phrenological information is represented. This inspires the Duke to investigate phrenology and eventually leads him to Edinburgh where he meets with Professor Bannister, an expert in phrenology. On this visit, the Duke learns about trepanning. When a patient undergoes trepanning, a hole is drilled into his skull. According to Professor Bannister, this process was used by primitive tribesmen in Brazil to relieve the patients of evil spirits. Before leaving Edinburgh, the Duke steals Professor Bannister's trepanning kit.

Upon returning to his estate, the Duke is increasingly distressed at his physical and mental condition. His mental deterioration is even worse because the Duke seems at times to be aware that he is becoming mad. The Duke tries to take matters into his own hands and he uses the stolen trepanning kit to perform the primitive surgery on his own skull. This procedure doesn't cure the Duke, but rather, sends him spiraling into madness at an accelerated rate. In order to conceal his self-inflicted wounds, the Duke becomes even more reclusive and begins hiding from his own staff, including his valet Clement. The Duke leaves his room only at night to wander naked on his estate.

In the meantime, the Duke does manage to gain more access to the memory which has been haunting him. The Duke learns that the memory corresponds to a childhood trauma in which his twin brother drowns. The phantom boy whose presence the Duke has sensed all along is presumably his twin.

On one fateful winter night, while the Duke is out wandering on his estate naked, he mistaken by a local hunter for a wild animal. The hunter shoots him and the Duke is found dead.