At the school, five of the older boys run away. Rumors circulate among the other boys that the runaways stole money from the rector's room (the rector is the equivalent of the school principal), or that they drank the alter wine in the sacristy. Other rumors suggest that the boys were caught doing some kind of homosexual activity. Two of the boys are to be flogged; three of them are given the choice of being flogged or being expelled. Two opt for expulsion; the third, named Corrigan, chooses to be flogged. Stephen wonders what the pain from a beating would feel like according to the different implements used-the "pandybat" (a leather strap) and a cane.
Stephen is in a Latin class with Father Arnall. The Father is in a bad mood because he considers that the boys have produced very poor work. He makes one boy, Fleming, kneel in the middle of the class, saying that he is one of the most idle boys he ever met.
Father Dolan, a prefect, enters the classroom. He is carrying a pandybat and is ready to thrash some boys. He interrogates Fleming and then gives him six strokes of the pandybat on the palm of each hand. Dolan then comes across Stephen, who is not writing like the others. This is because his glasses were broken a few days' previously, and Father Arnall exempted him from work. But Dolan believes Stephen is lazy and is just trying to evade work. He gives him one extremely painful stroke on each hand, and then makes the weeping Stephen kneel.
Stephen feels keenly the injustice of the punishment. He had written home that morning, asking his father to send him new glasses, and Father Arnall had excused him from work. The other boys encourage him to report Dolan to the rector. After supper, Stephen plucks up his courage and knocks on the door of the rector's office. The rector receives him kindly and listens to his complaint. He accepts Stephen's explanation, says the punishment was a mistake, and promises to have a word with Dolan and stop him from beating Stephen the next day, as Dolan had threatened. When Stephen returns he is cheered by the other boys after he tells them what happened.