The film opens with the final moments of Tomas's noon service. In attendance are only a handful of people, including fisherman Jonas Persson and his wife Karin (von Sydow and Gunnel Lindblom), and Tomas's ex-mistress, the atheistic Mrta (Ingrid Thulin). After the service, Tomas, though coming down with a cold, prepares for his 3 o'clock service in another town.
Before he leaves, however, the Perssons arrive to speak to him. Jonas has become morose after hearing that China is developing an atomic bomb. Tomas speaks to the man briefly, but asks Jonas to return after taking his wife home. No sooner have the Perssons left than Mrta enters, attempts to comfort the miserable Tomas, and asks if he's read the letter she wrote to him (he hasn't). Tomas tells her of his failure to help Jonas, and wonders if he will have anything to say, since he is without hope as well. Mrta states her love for Tomas, but also her belief that he doesn't love her. She leaves, and Tomas reads her letter.
In an unbroken shot lasting almost six minutes, Bergman has Mrta face the camera and speak the contents of the letter. In it, she coldly attacks Tomas for his neglect of her, relating a story of how a rash that disfigured her body repulsed him, and neither his faith nor his prayers did anything to help her. Tomas finishes the letter, and falls asleep. Awakened by the return of Jonas, Tomas clumsily tries to provide counsel, before finally admitting that he has no faith as well. He tells the depressed man that his (Tomas's) faith was an egotistical one God loved humanity, but Tomas most of all. Serving in Lisbon during the Spanish civil war, Tomas could not reconcile his loving God with the atrocities being committed, so he ignored them. Tomas finally tells Jonas that things make more sense if we deny the existence of God, because then man's cruelty needs no explanation. Jonas leaves, and Tomas faces the crucifix and declares himself finally free.
Mrta, who has been lurking in the chapel, is overjoyed to hear this, and embraces Tomas (who again does not respond to her affections). They are interrupted by the widow Magdalena, who tells them that Jonas has just committed suicide with a rifle. Tomas drives, alone, to the scene. Shot in an awkward, distant style (as contrasted with the claustrophobic close-ups of the rest of the film), Tomas stoically helps the police cover Jonas's body with a tarp, then stands guard while waiting for the "van" to collect the body, which arrives shortly. Mrta arrives on foot, and she and Tomas drive off to her home where she invites him in to take some medicine for his cold.
Waiting in the classroom attached to her house (Mrta is a substitute teacher), Tomas finally lashes out at her, telling her first that he rejected her because he was tired of the gossip about them. When that fails to deter her affections, Tomas then tells her that he was tired of her constant talking, and that Mrta could never measure up to his late wife, the only woman he has ever loved. Though shocked by the attack, Mrta agrees to drive with him to the Persson house. Informed of Jonas's suicide, Karin collapses onto the stairs and wonders how she and her children will go on. Tomas makes a perfunctory offer of help, and leaves.
Arriving for the 3 o'clock service at the second church, Tomas and Mrta find the building empty except for Algot, the hunchbacked sexton, and Fredrik, the organist (who arrives late and slightly inebriated). Fredrik tells Mrta that she should leave the small town and Tomas and live her life, rather than stay and have her dreams crushed like the rest of them. Meanwhile in the vestry, Algot questions Tomas about the Passion. Algot wonders why so much emphasis was placed on the physical suffering of Jesus, which was brief, versus the many betrayals he faced from his disciples (who denied him, did not understand his message, and did not follow his commands) and finally from God, who did not answer him on the cross. Wasn't God's silence worse, he asks. Tomas, who has been listening silently, answers "yes". Fredrik and Algot wonder if they should have a service since no one showed up, but Tomas replies that someone has shown up: Mrta. Tomas speaks the first lines of the service as the film ends.