Mary Dedalus dies from cancer between the end of A Portrait of the Artist as a Young Man and the opening of Ulysses. Stephen returns home from Paris to see her. In her dying moments, she asks Stephen to pray over her and he refuses. As a result, Mary dies without her son's blessing.
In Portrait, Mary comes across as something of a religious and overbearing mother, but at the start of Ulysses, Stephen is wracked with guilt over her death. When Mulligan makes light of it in "Telemachus," Stephen is extremely offended. In "Circe," Stephen has an absinthe-induce dream in which Mary rises from the grave and asks him to repent. He refuses adamantly, but is horrified and rushes out of Bella Cohen's brothel.