The novel begins in Manchester, where we are introduced to the Bartons and the Wilsons, two working-class families. John Barton is a questioner of the distribution of wealth and the relations between rich and poor. Soon his wife dies—he blames it on her grief over the disappearance of her sister Esther. Having already lost his son Tom at a young age, Barton is left to raise his daughter, Mary, alone and now falls into depression and begins to involve himself in the Chartist, trade-union movement.
Chapter 1 takes place in countryside where Moss Side is now.
Mary takes up work at a dressmaker's (her father having objected to her working in a factory) and becomes subject to the affections of hard-working Jem Wilson and Harry Carson, son of a wealthy mill owner. She fondly hopes, by marrying Carson, to secure a comfortable life for herself and her father, but immediately after refusing Jem's offer of marriage she realises that she truly loves him. She therefore decides to evade Carson, planning to show her feelings to Jem in the course of time. Jem believes her decision to be final, though this does not change his feelings for her.
Meanwhile, Esther, a "street-walker," returns to warn John Barton that he must save Mary from becoming like her. He simply pushes her away, however, and she's sent to jail for a month on the charge of vagrancy. Upon her release she talks to Jem with the same purpose. He promises that he will protect Mary and confronts Carson, eventually entering into a fight with him, which is witnessed by a policeman passing by.
Not long afterwards, Carson is shot dead, and Jem is arrested for the crime, his gun having been found at the scene. Esther decides to investigate the matter further and discovers that the wadding for the gun was a piece of paper on which is written Mary's name.
She visits her niece to warn her to save the one she loves, and after she leaves Mary realises that the murderer is not Jem but her father. She is now faced with having to save her lover without giving away her father. With the help of Job Legh (the intelligent grandfather of her blind friend Margaret), Mary travels to Liverpool to find the only person who could provide an alibi for Jem – Will Wilson, Jem's cousin and a sailor, who was with him on the night of the murder. Unfortunately, Will's ship is already departing, so that, after Mary chases after the ship in a small boat, the only thing Will can do is promise to return in the pilot ship and testify the next day.
During the trial, Jem learns of Mary's great love for him. Will arrives in court to testify, and Jem is found 'not guilty'. Mary has fallen ill during the trial and is nursed by Mr Sturgis, an old sailor, and his wife. When she finally returns to Manchester she has to face her father, who is crushed by his remorse. He summons John Carson, Harry's father, to confess to him that he is the murderer. Carson is still set on justice, but after turning to the Bible he forgives Barton, who dies soon afterwards in Carson's arms. Not long after this Esther comes back to Mary's home, where she, too, soon dies.
Jem decides to leave England, where, his reputation damaged, it would be difficult for him to find a new job. The novel ends with the wedded Mary and Jem, their little child, and Mrs Wilson living happily in Canada. News comes that Margaret has regained her sight and that she and Will, soon to be married, will visit.