The first knowledge Jeanie Deans has that her sister Effie is in trouble comes just a few moments before officers of justice arrive at their cottage to arrest Effie for child murder. They tell Jeanie and her father, David Deans, that Effie bore a male child illegitimately and then killed him or caused him to be killed soon after he was born. Effie admits to the birth of the child but refuses to name her seducer, and she denies killing her baby, saying that she fell into a stupor after its birth and recovered to find that her midwife had disposed of the child in some unknown fashion. In the face of the evidence, however, she is convicted of child murder and sentenced to be hanged. Jeanie has a chance to save her sister, for the law says that if a prospective mother tells anyone of her condition she is not responsible for her baby’s death. Jeanie refuses to lie, however, even to save her sister’s life. Because Effie did not tell anyone her terrible secret, she has no defense, and she is placed in the Tolbooth prison to await execution.

Captain John Porteous is also in Tolbooth prison awaiting execution. Porteous was convicted of firing into a crowd that was attending the hanging of a smuggler named Andrew Wilson. Wilson’s accomplice, Geordie Robertson, had escaped, and the officers feared that Robertson might try to rescue Wilson. For that reason, Porteous and a company of soldiers had been sent to the site of the execution to guard against a possible rescue. Porteous fired into the crowd without provocation and killed several people. Porteous’s execution is stayed for a few weeks, but a mob headed by Robertson, who is disguised as a woman, breaks into the prison, seizes Porteous, and hangs him. Afterward, Robertson becomes a hunted man.

Although she refused to lie to save her sister, Jeanie Deans has not forsaken Effie. When she visits Effie in prison, she learns that it is Robertson who is the father of Effie’s child. He had left her in the care of old Meg Murdockson, whom many consider to be a witch, and it must have been Meg who killed or sold the baby. Meg’s daughter Madge was herself once seduced by Robertson, and she lost her mind for love of him. As a result, Meg swore revenge on any other woman Robertson might love. It is impossible, however, to prove the old woman’s guilt or Effie’s innocence, for Robertson has disappeared and Meg swears that she saw Effie coming back from the river after drowning the baby.

Determined to save her sister, Jeanie decides to walk to London to seek a pardon from the king and queen. She tells her plans to Reuben Butler, a minister to whom she has long been betrothed. Reuben has been unable to marry Jeanie, because he has no position other than that of an assistant schoolmaster and his salary is too small to support a wife. Although he objects to Jeanie’s plan, he helps her when he sees that she cannot be swayed from her purpose. Reuben’s grandfather once gave aid to an ancestor of the present duke of Argyle, and Reuben gives Jeanie a letter asking the duke’s help in presenting Jeanie to the king and queen.

The journey to London is long and dangerous. At one point, Jeanie is captured by Meg Murdockson, who tries to kill her to prevent her from saving Effie. Jeanie escapes from the old woman, however, and seeks refuge in the home of the Reverend Mr. Staunton. There, she meets the minister’s son, George Staunton, who admits to her that Geordie Robertson is his alias: He is her sister’s betrayer. George admits his responsibility to Effie, telling Jeanie that he planned and executed the Porteous incident in order to rescue Effie from the prison, but that Effie refused to leave with him. He has tried many other schemes to save her, including attempting to force Meg to confess that she had taken the baby, but everything has failed. He tells Jeanie that he was on his way to give himself up in exchange for Effie’s release when he injured himself falling from his horse. He asks Jeanie to bargain with the duke of Argyle and, as a last resort, to offer to lead the authorities to Robertson in exchange for Effie’s pardon. Geordie promises not to leave his father’s house until Effie has been freed.

Jeanie at last reaches London and presents herself to the duke of Argyle with Reuben’s letter. The duke, impressed with Jeanie’s sincerity and simplicity, arranges for an audience with the queen. She, too, believes Jeanie’s story of Effie’s misfortune. Through her efforts, the king pardons Effie with the stipulation that she leave Scotland for fourteen years. Jeanie thus secures the pardon without revealing George Staunton’s secret.

The duke is so moved by Jeanie’s goodness and honesty that he makes her father the master of an experimental farm on one of his estates in Scotland, and he makes Reuben the minister of the estate’s church. Jeanie’s heart overflows with joy until she learns that Effie eloped with her lover just three nights after her release from prison. No one knows where they were, as the outlaw’s life is in constant danger because of his part in the Porteous hanging.

Reuben and Jeanie are married and are blessed with three fine children. They prosper in their new life, and Jeanie’s only sorrow is her sister’s marriage to George Staunton. She keeps Effie’s secret, however, telling no one that George is actually Robertson. After several years, George and Effie return to London. George has inherited a title from his uncle, and, as Sir George and Lady Staunton, they are received in court society. Effie writes secretly to Jeanie and sends her large sums of money, which Jeanie puts away without telling her husband about them. She cannot reveal Effie’s secret, even to him.

By chance, Jeanie finds a paper containing the last confession of Meg Murdockson, who has been hanged as a witch. In it, Meg confesses that she stole Effie’s baby and gave him to an outlaw. Jeanie sends this information to Effie in London, and before long Effie, as Lady Staunton, pays Jeanie a visit, using a pretext of ill health to travel to Scotland. Meanwhile, George acts on the information in Meg’s letter, trying to trace the whereabouts of their son. Although it is dangerous for George to be in Scotland, where he might be recognized as Geordie Robertson, he follows every clue given in Meg’s confession. In Edinburgh, he meets Reuben Butler, who is there on business, and secures an invitation to accompany Reuben back to the manse. Unaware of George’s real identity, Reuben is happy to receive the duke of Argyle’s friend. Reuben also does not know at the time that Effie is currently a guest in his home.

As Reuben and George walk toward the manse, they pass through a thicket where they are attacked by outlaws. One, a young fellow, runs his sword through George and kills him. It is not until Reuben hears the whole story of the Stauntons from Jeanie that he searches George’s pockets and finds information proving that the young outlaw who killed George was his own son. Because Effie is grief-stricken by George’s death, Jeanie and Reuben think it useless to add to her sorrow by revealing the identity of his assailant. Reuben later traces the boy to America, where the young man continues his life of crime until he is captured and probably killed by Indians.

Effie stays with Reuben and Jeanie for more than a year. Then she travels back to London and its brilliant society. No one but Jeanie and Reuben ever know the secret of Effie and George. After ten years, Effie retires to a convent on the Continent, where she spends her remaining years grieving for her husband and the son she has never known. Reuben and Jeanie Butler, who were so unavoidably involved in sordidness and crime, live out their lives happily and carry their secret with them to the grave.