It’s 1955 in Grantchester, local vicar Sidney Chambers [James Norton] meets with the new archdeacon, Gabriel Atubo. Acknowledging that Gabriel’s predecessor was dispatched under some controversy and embarrassment, Gabriel questions whether he can rely on Sidney to rebuild trust in the church and lead by example. Sidney reassures him he can be counted on. Before the night is out, Sidney is on the dance floor with his old flame Amanda Hopkins [Morven Christie. Whilst they close in for a kiss, Sidney’s best friend DI Geordie Keating [Robson Green] sits nearby with wife Cathy [Kacey Ainsworth], the spark a little dimmer in their own relationship. The next day Sidney accompanies Geordie to The Round Church in Cambridge, where an elderly man, Dr Terrence Atwell, lies dead. Whilst being pestered by church caretaker Mr Harland, Geordie tells Sidney about the victim; Dr Atwell ran a soup kitchen for the homeless. On closer inspection of the body, it appears Dr Atwell died by drowning. But how does a man drown in the middle of a church and is this connected to a series of murders targeting respected figures in the community? Amanda gets a letter from estranged husband Guy [Tom Austen] saying he wants to see his daughter. Sidney can’t contain his frustration; Guy didn’t care when Grace was born. He’s clearly trying to control Amanda. But Amanda reassures him that she won’t let Guy take Grace away. As Geordie and Sidney get closer to the truth behind the murders, Sidney is forced to confront the conflict between his relationship with Amanda and his calling as a vicar, and the fact that he and Amanda must face Guy, but will it be together or apart?

Sidney and Geordie join a local cricket team to play a match against nearby Whittlesford, but team captain Geoff Towler (Peter Davison) seems to have an objection to talented young Pakistani batsman Zafar, and is even willing to forfeit the game to spite the player. After the match, a buffet ends badly when contaminated beer leaves everyone feeling ill, a matter Geoff is keen for Geordie to cover up. However, a worse fate awaits Zafar, who is later found to have received a fatal dose of the poison his teammates and spectators had received.

Leonard gets caught up in an armed robbery at the village post office, and manages to identify the masked culprit. Geordie takes no chances when going to arrest the criminal, who has a record of similarly violent crimes - but is surprised to discover that the suspect has been murdered. Meanwhile, a second robbery occurs, carried out by a man and a woman who have adopted the dead robber's trademark of disguising himself with a gas mask. Back at the Vicarage, the atmosphere is tense between Sidney and Amanda.

A factory worker dies in what appears to be a drunken accident, but Geordie suspects foul play. However, secret forces are determined to shut down his investigation. Mrs Maguire is confronted by a face from the past, while Sidney wrestles with his conscience, as his feelings for Amanda clash with his sense of duty - leading to accusations of hypocrisy from Leonard.

Sidney tries to put his life in Grantchester behind him by going in search of the man who stole Mrs Maguire's life savings, and ends up finding a new home in a travellers' community. However, he falls under suspicions when a murder rocks the camp. Geordie tracks his friend down and together they set out to solve the mystery - and hopefully give Sidney a sense of purpose in his life.

On a Sunday morning in Grantchester, Sidney visits the Archdeacon to discuss his resignation. Sidney has lost his faith in a church that won't allow him to be married to the woman he loves. With a heavy heart the Archdeacon tells Sidney he must go away and write a resignation letter in order to make it official.

A boy goes missing and the entire village heads out in search of him; and Sidney, Geordie, Leonard and Mrs. Maguire all take steps in a new direction.