Set in the present day, the film opens with a church service where Tomas Eriksson, a middle-aged widower is officiating. The congregation is small, including the local schoolteacher, Marta Lundberg, who is in love with Tomas, fisherman Jonas Persson and his wife, Fredrik Blom, the church organist, Algot Frovik, the church warden and Mr. Aronsson, the sexton.

After communion, the fisherman tells the clergyman he is depressed and his wife suggests he comes back to the church later alone to talk about it. Marta arrives with coffee and sandwiches. Tomas is irritated and Marta leaves. Tomas gazes at photographs of his dead wife and then opens a letter Marta sent him. The camera shifts to a close-up of Marta reciting the letter in which she confesses her agony over her unrequited love for Tomas. She goes on to say how she, as a non-believer, began to pray for a cure for her eczema after Tomas failed to do so. She concludes by asking Tomas to "use her".

Although upset by the letter, Tomas dozes off, his head and arms resting on the table. Persson appears and talks of his angst, but Tomas can only respond by talking about his own anguish, his feeling that God has abandoned him.

Persson leaves and Marta returns, at which point he breaks down in tears, in Marta's arms at the altar. A woman enters and informs him Persson has shot himself. Tomas leaves in the car to help take care of the body and Marta joins him later. They head back to the schoolhouse where Marta lives in an upstairs apartment. While Marta goes to get medicine for Tomas' cold he remains in the schoolhouse. A schoolboy appears and they have a stilted conversation.

On Marta's return Tomas again shows his irritation at her fussing. She cries but later, at his request, accompanies him to a neighbouring church in Frostnas for an afternoon service. On the way he calls into the home of the dead fisherman to inform her of the tragedy. Back in the car he begins to tell Marta of his past but noise from a passing freight train drowns out his voice.

The last section of the film takes place in the church in Frostnas. A rheumatic, Algot Frovik, talks to Tomas and tells him after studying the Gospels he has come to the conclusion his own prolonged physical suffering is comparable to the pain endured by Christ on the Cross. Christ's real suffering, says Frovik, was the sense of being abandoned by all who loved him including God.

While Frovik talks to Tomas, the organist Blom advises Marta to leave and seek alternative employment. The church bells, that summon the congregation, stop pealing but no one has arrived for the service. Tomas decides to proceed with the ceremony as Marta, kneeling in a pew, prays for peace for both of them. The film ends with Tomas intoning the words of the service, Holy, holy, holy, thy name be honoured, in Heaven as on Earth.