An orphaned Irish boy is taken in by his mother's Scottish relations.

In the year 1900, following the death of his mother, eight-year-old Catholic Robert Shannon is sent from his home in Dublin, Ireland to live with his mother's Protestant family, the Leckies, in the small coastal town of Loganford, Scotland. Some of the Leckies, Robert soon discovers, hold a long-standing grudge against Robert's mother for running off to Ireland to marry a Catholic. While Papa Leckie, a sanitarium inspector and the sternest of the Leckies, strongly disapproves of Robert's devout Catholicism, Robert's alcoholic great grandfather, Alexander Gow, is fond of the boy and protects him from other family members. Grandma Leckie, however, is determined to end Robert's budding friendship with his eccentric grandfather and vows to turn him into a god-fearing lad. Robert's first day at school ends in humiliation as he is taunted by fellow schoolmates who ridicule the green, flowered uniform that Grandma Leckie made for him. Fearing that he will be trounced in a fistfight with Gavin Blair, the school's most notorious bully, Robert goes to Alexander for advice on self-defense. Robert defends himself honorably in the fight, after which he and Gavin become fast friends. When Robert later asks Papa Leckie for fifteen shillings to buy his first Communion suit, Papa Leckie angrily denies the boy's request, leaving Robert with no alternative but to sell his cherished microscope for the money. Alexander refuses to let Robert get rid of his microscope, however, and instead takes Papa's encyclopedia and sells it for fifteen shillings. Years pass, and Robert, now a star student in high school, receives a special science award from his headmaster, Professor Reid. Although his friends are leaving to attend university, Robert stays in Loganford to work and fulfill his obligation to the Leckies. Professor Reid, believing that Robert is too talented to be working at the Loganford Boiler, suggests that he apply for the Marshall Scholarship to study medicine. Papa Leckie rejects the idea of sending Robert to a university, but when Robert wins the scholarship, Mama Leckie and Alexander help the boy study in secrecy for the university entrance examinations. The intensive studying exhausts Robert to the point of physical collapse, however, and he fails the exam. Later, tragedy strikes when Gavin is struck by a train and dies. Having lost his best friend, and having failed in all his attempts to attend the university, Robert tells his priest that he has lost his faith in God. One day, when Alexander disappears, Robert, suspecting that he fled as a result of Papa Leckie's cruelties, berates Papa Leckie and other family members for their greedy desire to gain a profit from Alexander's life insurance policy. Alexander is eventually found but he dies shortly thereafter. Later, the Leckies are surprised when a recently added codicil to Alexander's will is discovered, in which it is stipulated that all of Alexander's life insurance money is to be used to pay for Robert's university education. With his tuition paid, the promising young scientist attends his first day at the university with his former schoolmate and sweetheart, Alison Keith, at his side.