Professor Richard Seager, a devout man in his 60s and a (former) fellow in biochemistry at Benison College, gathers his belongings from his prison cell. After serving his sentence for the accidental vehicular homicide of a young woman, Erin Cliff, he's being released, and after an awkward reunion with his wife, Martha, a reverend at Benison College, he returns home. Within 24 hours, he is dead – run over repeatedly and crushed with the same Jaguar Mark 2 that he'd been driving when he killed Erin Cliff.
When Lewis and Hathaway begin their investigation, they find that the victim had managed to scratch the number "500" into the paint of the car. And they find it noteworthy that Martha had remained fast asleep while right outside her open window a violent – and likely, noisy – murder occurred. Yet Martha claims that Erin's sister, Rachel, killed her husband. She'd left their house enraged the previous night, after a meeting between Rachel and Richard, where he asked her forgiveness, went wrong. But Rachel has an alibi, her boyfriend Adam Tibbit.
Adam Tibbit is a struggling student at Benison, desperately trying to keep up with basic concepts in Stella Drew's class. Stella, a protégé of Seager's, replaced him as Chair of Chemistry when the college revoked Seager's fellowship after the accident. Benison's provost, Graham Yardley, appears more concerned with the repair work being done on the chapel roof than the murder of his brilliant former chemistry chair. He suggests that Lewis speak to Stella, but Lewis instead encounters her husband, Carl. Himself an undergraduate chemistry teacher (in fact, Adam's old teacher), Carl had also studied under Seager. He claims that Stella had no intention of usurping Seager; in fact, Stella's best friend is Martha, and Stella has for years supported Martha in the ongoing saga of her dysfunctional marriage to Seager, who'd been trying unsuccessfully to divorce her. Meanwhile, Yardley, back in his office, shreds a letter he'd had hidden away.
Questioning Tibbit, Hathaway learns of "creepy" letters that Rachel had been receiving from Seager, requesting that she meet up with him upon his release. Adam admits going to the prison to tell Seager to stop.
Forensics show that a piece of hair recovered from the interior of the Jaguar belongs to Rachel Cliff. As Lewis and Hathaway interview her, they are interrupted and summoned to Graham Yardley. He directs them to the site of the chapel roof reconstruction, where a decayed, skeletal body and a suitcase have just been discovered in the college chapel’s dark and dusty attic. The luggage label reads "Soo-Min Chong". So it appears that Seager hadn't scratched the number "500" after all…He'd written a name.
As Lewis, Hathaway, and Hobson investigate the new crime scene, identifying the body as Soo-Min Chong, a Korean exchange student of Richard Seager's who disappeared 15 years ago. Her original missing-person file illustrates connections to many of the Seager murder suspects, as Seager was the last person to see Soo-Min alive; Carl Drew was her boyfriend; Stella was her lab supervisor; and she was Martha’s organ scholar at the chapel. It doesn't take long for the forensic anthropologist to match dried blood on the suitcase to Richard Seager.
A very distressed Adam, after arguing with his father, desperately begs Hathaway to leave Rachel alone. When Hathaway suggests that Rachel's hair must have arrived in Seager's care via someone else, ie Adam, if not her, Adam panics.
Lewis and Hathaway begin to think that Richard Seager may have been having an affair with Soo-Min Chong, in spite of Martha and Stella's denials. On his way to question Carl Drew, Hathaway discovers Adam, dead. He hanged himself in his former teacher's classroom, writing a simple suicide note on the white board: "Thanks, sir." Stella and Carl both feel guilty, and Carl states that he must have pushed the teenager too hard. Hathaway feels the same.
Meanwhile, forensics reveal that a close relative of Adam's had been in Seager's car. Adam’s father, Ron, reveals a huge scandal: Carl Drew's "Oxbridge Edge" company has an illegal side business: the purchase of admission to Benison. Ron made a hefty donation to the college in return for Adam's place, and it was in Seager's car that Ron made the deal, though Yardley and Carl were also complicit. Adam would never have known, except before his release from prison, Seager sent a letter to Ron demanding that, to address their moral wrong, he tell Adam the truth. Ron was pushed into disclosing the truth to Adam, who, devastated and humiliated, took his life. Carl and Yardley admit to receiving similar letters from Seager, all with the purpose of coming clean and righting wrongs.
Martha fishes around her drawer for her sleeping pills, then pauses, making a mental connection. She calls the police but is unable to reach Lewis. Within hours, she is stabbed to death. Lewis and Hathaway learn that she was addicted to sleeping pills; in finding her supplier, the will find the only person certain to know that she would sleep soundly through her husband's murder. The prescriber, they find, is Stella.
Confronted by Lewis and Hathaway, Stella reveals that Soo-Min had an argument with Seager and Stella over the ownership of research findings, and fell to her death in the chapel. They hid the body, terrified the story would wreck their reputations. But prior to his release from prison, Seager sent a letter to Stella explaining his change of heart; so Stella murdered her mentor and framed Rachel. Martha put the pieces together, so Stella murdered her best friend.
Lewis confirms that he intends to retire, and Hathaway announces his resignation. The two, no longer partners, now friends, enjoy a pint.