Environmentalist and senior fellow Dr Julian Dear is on his way to give a rare speech at an Oxford Union debate when he is attacked, later dying in hospital. Morse and Lewis are encouraged by Chief Superintendent Rennie to wrap up the case quickly because the cause of death was a heart attack and because Matthew Copley-Barnes, the Master of Beaufort college, is on the police oversight committee.
The fractious relationship between the Master and his mentally fragile daughter and her husband becomes apparent when Sylvie Maxton, a newspaper columnist who used to live with the Master's family, arrives to stay with them. As Morse begins to question the family about Dr Dear, he finds that a series of unusual and disturbing packages has been arriving at the Master's lodge.
Dr Jake Normington, whom Morse knows through musical connections, confides to Morse that Dr Dear had something important to say at the debate, and implies that he may have been stopped from doing so. After Morse departs, Normington and young man Mick McGovern listen to a tape in which Dear outlines his planned comments at the debate, which he stresses have "grave and far-reaching implications".
Lewis is told by a college porter that Copley-Barnes has significantly increased the college investment income, particularly through CORBI, a chemical company that also funds Copley-Barnes' research. After Dear's funeral, the porter recognises McGovern as the young man he saw running out of the college around the time of the murder, so McGovern is brought in for questioning. At the same time, men are setting fire to McGovern's home. Normington leaves Oxford to return to his position in America, but leaves Morse a letter advising him to trust McGovern.
McGovern remains silent until after his mother, who has been dying in the hospital, passes away. He insists that he did not attack Dr Dear and explains that he used to work for a subsidiary of CORBI and that he told Dr Dear about a cover-up the company's promising new fertiliser was causing cancer. Dear was planning to disclose that information at the debate.
Morse finds the Master dead in his lodge, and Sylvie Maxton reveals that he had sexually abused her as a child and that she sent the mysterious packages to remind him. The Master's daughter had been aware of her father's behaviour and confided in her mother, who killed her husband. Mrs Copley-Barnes prepares to throw herself from the chapel organ loft but is talked down by Morse and taken away.
Forensics from the original crime scene leads Lewis to conclude that the culprit was the Beaufort College gardener, Phil Hopkirk. He had discovered that his daughter, who took piano lessons at the Copley-Barnes' home, was also being abused and attacked Dear while drunk, mistaking him for the Master.