Although this is not a direct punishment on Stephen this is the second mention of punishment in the novel.
The third comes directly to Stephen in a physical form. After the boys are summoned back into the classroom they have their writing lesson, and Father Arnall begins the Latin lesson. Afterward, the prefect notices that Stephen is not working and demands to know why. Father Arnall tells Father Dolan that Stephen has been excused from class work because his glasses are broken and he cannot see well. Stephen is telling the truth, but the unbelieving prefect pandies him as well. Stephen does not understand why he is being punished when he is telling the truth and this begins his mistrust of the Jesuits. .
The next type of punishment Stephen deals with it is punishment from God and that of going to hell. Stephen has grown up a little and while at home on break from school he had his first sexual experience. Stephen is now attending a new school and to his surprise, Father Arnall, from Clongowes is the guest speaker in the chapel. Father Arnall announces to the students that he is there to announce a retreat marking the day of St. Francis Xavier, patron saint of the college. The retreat, he explains, will not be simply a holiday from classes, but a withdrawal into inner contemplation of the soul:.
But above and beyond all, let this retreat be one to which you can look back in after a few years when maybe you are far from this college and among very different surroundings, to which you can look back with joy and thankfulness and give thanks to God for having granted you this occasion of laying the first foundation of a pious honourable zealous christian life. And if, as may so happen, there be at this moment in these benches any poor soul which has had the unutterable misfortune to lose God's holy grace and to fall into grievous sin I fervently trust and pray that this retreat maybe the turningpoint on the life of that soul (103).