The novel follows Stephen Dedalus from earliest childhood to the edge of adulthood, and it is told almost entirely from inside his head. It begins in fragments a small child would notice, a story about a moocow, the smell of an oilsheet, a song and a dance, before settling him at Clongowes, a Jesuit boarding school where he is too small for the games and homesick for his mother. There he is unjustly beaten across the hands with a pandybat by the prefect of studies, and he finds the nerve to walk to the rector and protest, a first small act of standing up for himself.
As he grows, the warmth of childhood gives way to confusion and shame. His father slides into debt and the family keeps moving to cheaper rooms. Stephen wins prizes and reads hungrily, but he is also pulled by appetites he cannot govern, and the chapter that traces his adolescence ends with him walking into the arms of a Dublin prostitute, miserable and craving at once.
Guilt over this secret life is detonated by a religious retreat. A preacher delivers long, vivid sermons on sin and the everlasting torments of hell, and the fear they raise drives Stephen to a shattering confession and a season of fierce devotion. He fasts, prays, and mortifies his senses so thoroughly that the school director invites him to consider becoming a priest, holding out the secret power of the office.
He nearly accepts, then turns away. The cold order of priestly life repels him, and walking by the sea he sees a girl wading in the shallows, gazing out to the water. The sight breaks over him as a revelation: ordinary mortal beauty, not the church, is what calls him, and he resolves there to live, to err, and to create. From this point his real subject becomes art, and he begins working out a theory of how beauty is apprehended.
In the long final chapter Stephen is a university student, sharp and aloof, arguing aesthetics with friends and sketching the artist as a god who stands invisible behind the work, paring his fingernails. He coolly declines to make his Easter duty, telling a friend, I will not serve, and resolves to leave Ireland. The book ends in his diary as he prepares to go into exile to become a writer, welcoming life and calling on the old artificer of his name to stand by him.