The Deserter starts out in a dark room in a European chateau, in early 1945. A soldier and a sergeant enter the room and have a long conversation, which comprises the first scene. As the conversation begins, the dialogue is cryptic, revealing details slowly. The sergeant says that the soldier has about an hour, so the soldier asks if he can write a letter. They discuss the soldier’s criminal record, then wonder whether the soldier’s wife will receive his pension after the soldier is killed by the firing squad. The soldier talks about his wife and the fact that they were just starting to get on their feet when the soldier got drafted. The sergeant talks with the soldier about his desertion and the soldier explains how he got separated from his military unit and tried to leave shortly after being reunited with it. The soldier asks if he can speak to a Catholic priest and the sergeant says that he will be able to soon. The sergeant finds some paper and a pen, and the soldier writes a long letter to his wife. In the letter, he tells her how he is being executed for desertion and notes that he would desert again if he had the chance, since the war is so horrible. He tells his wife to be strong and asks if she will occasionally write to his brother in prison.

The second scene begins when a Catholic priest, Father Murray, arrives and the sergeant leaves. The soldier tells Father Murray that he would like to confess, and the priest sets up an impromptu confessional. The soldier confesses to many sins, including his desertion. Father Murray asks him why he ran away, and the soldier says he was afraid. He also tells the priest that his brother is in prison because he was part of a robbery that ended in murder. Since that event, when the soldier’s hometown priest, Father Hart, told him that all murder is wrong, the soldier has been unable to carry a gun. Father Murray tells the soldier that this is not true during war. Father Murray helps the soldier say an Our Father, a Hail Mary, and a Glory Be in penance for his sins, then gives the soldier a communion wafer. They discuss the particulars of the soldier’s execution, then Father Murray tells the soldier to think about the paradise he is about to enter, not the quick death that will bring him there. The sergeant comes back to let them know it is time for the execution. The soldier and the priest walk outside, while the sergeant remains behind in the empty room and has a drink. A number of gunshots are heard before the curtain falls, signaling the death of the soldier.