The novel commences with the passage of two passengers on a ship from Portugal to Ireland: Hamilton and Edmund O'Hara. O'Hara is training to be a priest, semi-reluctantly, following the wishes of his father. He finds the priesthood as a whole to be hypocritical, but looks on Protestantism, the religion of Hamilton, with suspicion. He is melancholy because his father is ill.
After the ship sinks, the pair wash up in an unnamed coastal village in Ireland, where they are looked after by the protestant Williams family. At this point, we are introduced to a servant of the Williams called Tom Clarty, who also doubles up as a farmer, fisherman and occasional landlord, and who, unlike his neighbours, does not believe in ransacking shipwrecked goods. As a consequence, he is berated by his wife, Molly. Frederick Williams (the son of the elder Williams) gives the Catholic Clarty a Bible, which he reads. His wife, outraged, tells the priest, Father Peter. When Tom refuses to stop reading the Bible, Father Peter denies him absolution. Father Peter confronts Frederick about the fact that he gave Tom a Bible, and a debate ensues. Later in the novel, Tom abstains from church altogether.
While in the care of the Williams, O'Hara meets Frederick's sister, Emily, who runs a school in order to improve the literacy of poor children and, more specifically, to teach them to read the Bible. During this time, O'Hara needs money to get home to his father, but does not want to ask the Williams for a loan, so he requests one from Father Peter instead. Peter dishonestly claims to be too poor to be able to help, which confirms O'Hara's view of the priesthood.
Eventually, Lord Avendell lends O'Hara a horse to see his father. On the eve of his departure, O'Hara confesses his love for Emily and reveals that he no longer intends to be a priest. She neither accepts nor refuses, but asks him to think about his faith. Upon returning to his native village, O'Hara finds his father's funeral taking place. It transpires that his father has left him very little, and left the larger part of his wealth to his step-mother and step-brothers. Unexpectedly, O'Hara is charged with stealing Lord Avendell's horse, and is imprisoned until Avendell confirms his story. O'Hara then returns to the home of the Williams.
Pressing his marriage proposal upon Emily again, O'Hara receives the conditional answer that she will marry him on the proviso that he take religion more seriously. Unfortunately, O'Hara develops a fever following an ill-advised excursion during a rain shower. He dies happily, having converted to Protestantism, and two years later, Hamilton and Emily get married.
In the main, the novel serves as a satire on the perceived failures of Catholicism. While the Catholic characters are portrayed as bigoted, corrupt and/or ridiculous, the Protestant characters are generally enlightened and tolerant.

Extensive Irish English representation occurs in the speech of Tom and Molly Clarty. Molly's speech is more densely dialectal than Tom's, which may be intended to reflect either Tom's status as a more sympathetic and upstanding character or the fact that he, unlike Molly, is literate. Molly's speech features a number of consistent respellings ('tould' for 'told', 'agin' for again' etc.) and discourse markers ('sure' etc.).
The character of Nancy, Edmund's old nurse, also speaks Irish English, though her dialect is marked more by Gaelic discourse markers ('a-vourneen', 'arra') and less by respellings than Molly's.