Throughout the novel, the Dedalus family makes a series of moves into increasingly dilapidated homes as their fortunes dwindle. His mother is a devout Catholic. When Stephen is young, he and the other Dedalus children are tutored by the governess Dante, a fanatically Catholic woman. Their Uncle Charles also lives with the family. The book opens with stream of consciousness narrative filtered through a child's perspective; there is sensual imagery, and words approximating baby talk. We leap forward in time to see young Stephen beginning boarding school at Clongowes. He is very young, terribly homesick, un-athletic and socially awkward. He is an easy target for bullies, and one day he is pushed into a cesspool. He becomes ill from the filthy water, but he remembers what his father told him and doesn't tell on the boy. That Christmas, he eats at the adult table for the first time. A terrible argument erupts over politics, with John Casey and Stephen's father on one side and Dante on the other. Later that year, Stephen is unjustly hit by a prefect. He complains to the rector, winning the praises of his peers.
Stephen is forced to withdraw from Clongowes because of his family's poverty. The family moves to Blackrock, where Stephen takes long walks with Uncle Charles and goes on imaginary adventures with boys from around the neighbourhood. When Stephen is a bit older, the family moves to Dublin, once again because of financial difficulties. He meets a girl named Emma Clere, who is to be the object of his adoration right up until the end of the book. His father, with a bit of charm, manages to get Stephen back into private school. He is to go to Belvedere College, another institution run by the Jesuits.
Stephen comes into his own at Belvedere, a reluctant leader and a success at acting and essay writing. Despite his position of leadership, he often feels quite isolated. He continues to be a sensitive and imaginative young man, acting in school plays and winning essay contests. He is also increasingly obsessed with sex; his fantasies grow more and more lurid. Finally, one night he goes with a prostitute. It is his first sexual experience.
Going with prostitutes becomes a habit. Stephen enters a period of spiritual confession. He considers his behavior sinful, but he feels oddly indifferent towards it. He cannot seem to stop going to prostitutes, nor does he want to stop. But during the annual spiritual retreat at Belvedere, he hears three fire sermons on the torments of hell. Stephen is terrified, and he repents of his old behavior. He becomes almost fanatically religious.
After a time, this feeling passes. He becomes increasingly frustrated by Catholic doctrine. When a rector suggests that he consider becoming a priest, Stephen realizes that it is not the life for him. One day, while walking on the beach, he sees a beautiful girl. Her beauty hits him with the force of spiritual revelation, and he no longer feels ashamed of admiring the body. He will live life to the fullest.
The next time we see Stephen, he is a student at university. University has provided valuable structure and new ideas to Stephen: in particular, he has had time to think about the works of Aquinas and Aristotle on the subject of beauty. Stephen has developed his own theory of aesthetics. He is increasingly preoccupied with beauty and art. Although he has no shortage of friends, he feels isolated. He has come to regard Ireland as a trap, and he realizes that he must escape the constraints of nation, family, and religion. He can only do that abroad. Stephen imagines his escape as something parallel to the flight of Dedalus, he escaped from his prison with wings crafted by his own genius. The book ends with Stephen leaving Ireland to pursue the life of a writer