Mary ends up at the home of Ben Sturgis, one of the sailors who took her to the John Cropper. When Mary enters the house, she grows pale and faints to the floor. Mrs. Sturgis takes care of her, but cannot help wondering if Mary is a fallen woman. Mary contradicts the older woman's suspicions and drinks her tea, lost in feverish thoughts, until Ben finally returns home. Mary believes that his bad mood is due to her presence, but he is angry because the wind is against the pilot boat. Mrs. Sturgis guides Mary upstairs and puts her in a bedroom, but Mary cannot sleep. She watches the weathercock all night long, dwelling on Ben’s words and wondering if Will will make it to the trial.
At nine o’clock the next morning, everyone assembles for the trial. Job has left the house early, and in the courtroom, he finds a letter addressed to him from Jem. The accused man thanks Job for all his help. He also tells Job that he is innocent and asks him to look after Jane Wilson and Alice. They have enough money, with the annuity that Jem has established, but both women will need care. Jem also asks Job to keep the secret of his innocence from Mary for now, even though Jem believes Mary hates him for it. However, Jem asks that Job tell Mary the truth only if Job is about to die. Jem cannot bear to have Mary die believing that he committed this crime. In the witness room, Job finds Mary looking hopeless and Mrs. Wilson sobbing, having heard the news that Will has not arrived.
The trial commences with Jem Wilson's plea that he is not guilty. As witnesses for the prosecution, the policemen offer up evidence of Jem's quarrel with Harry Carson, and the fact that Jem’s gun has been established as the murder weapon. When Mrs. Wilson is in the witness box, the prosecutor asks her if the gun belongs to Jem. She asks Jem what she should do. He emotionally instructs his mother to tell the truth. Jane acknowledges that the gun belongs to Jem and proceeds to declare her son’s innocence and goodness. Next, Mary Barton is called to the witness stand. She looks deathly pale, and after a few dazed minutes, confesses that she liked the attention from Harry because she had dreams of becoming a wealthy lady, but that she discovered her love for Jem after refusing his marriage proposal. She explains that her mother died before she had time to learn how to make smart decisions about love.
The prosecutor insinuates that Mary's admission of love strengthens the case against Jem. Mary answers that she stopped speaking to Harry after their final meeting, and never told Jem about him. She begs to be released from the witness stand and the judge lets her go. Mrs. Sturgis takes charge of Mary, who is becoming mad with the fear that she will have to reveal her father's guilt to save Jem’s life. Jem’s defense makes little effort to cross-examine the hysterical witness, as though the lawyer has given up hope of ever getting his client acquitted.
Later, Mary starts shouting that Jem is saved and she is mad, before convulsions wrack her body and she is carried from the court. It turns out that Will Wilson has arrived - and his entrance is the reason for Mary’s sudden outburst. The sailor forces his way to the witness stand and testifies that his cousin indeed accompanied him to Liverpool on the night of the murder. The prosecuting lawyer tries to trick Will into confessing that he is a suborned witness, a random sailor paid to give this alibi, but O’Brien, the pilot of the ship, confirms Will's identity. Later, the jury delivers the verdict that Jem is not guilty. Jem is in a state of shock, and while accepting congratulations, he asks where she is. Job assumes that Jem means his mother and brings him to Jane. Jem affectionately embraces his mother, and repeats his question. Where is she? He is looking for Mary.
Mary lies in a state of raving delirium at the Sturgis’s house, crying out for her father to save Jem. Jem realizes that she must know her father is the murderer. Jem has also known all along that John Barton was the murderer because he had borrowed his gun two days before the murder. Jem spends a night watching over his beloved until Job arrives in the morning. Jem expresses his fears to Job that Mary will die, or worse - never recover from this condition. Job tells Jem that he must go home because Alice does not have long to live. Jem reluctantly returns home to his mother who is jealous of his attention to Mary.
Alice dies a day later. Jem convinces his mother that Mary is to him what she was to George. Reflecting on those happy, loving times, Jane softens towards Mary and agrees that Jem should return to Liverpool. As Jem walks out, he sees the phantom-like figure of John Barton going into his home. When Jem gets to Liverpool, he finds Mary still hovering between life and death. She soon passes out of danger and sleeps without raving. She eventually awakens to see Jem’s loving face, her memories come flooding back to her. When Mary is strong enough to walk, she tells Jem that she must go to see her father alone. He reluctantly agrees and they say a tearful goodbye to Mr. and Mrs. Sturgis, who have been very kind.
Back in Manchester, Mary goes see her father, who is practically a ghost- and begins to care for the pitiful man. In her heart, Mary forgives her father for his crime, separating the sin from the sinner. Jem asks Mary to come see his mother, but she cannot go until her father is better. The next day, Sally Leadbitter visits and asks Mary about the trial and Jem’s acquittal. Mary tells Sally that she will not be working at Miss Simmonds' anymore and Sally calls her foolish for throwing away the only income she and Jem may ever earn - revealing that Jem has also lost his job at the foundry. Mary asks Sally to leave, but Barton overhears the whispered conversation. He tells Mary to ask Jem to come to their home at eight o’clock that evening.
Mary confronts Jem about his job. He tells her that the men at the foundry did not want to work with an accused murderer, but not to worry - he has a new job prospect in Canada. As planned, the couple goes to the Barton home at 8 pm to find John Barton, Job Legh and Mr. Carson. John Barton has confessed to killing Harry Carson, and begs Jem's forgiveness for nearly letting him take the blame. Carson, furious, plans to tell the police in the morning but Mary begs him to let her father die in peace. Carson speaks emotionally about the pain of losing his beloved son and Barton, for the first time, feels empathy for a member of the upper-class. Barton feels the weight of his crime renewed, because he now sees that he killed a son and a brother, not just an enemy. He cries out that he did not know what he was doing and asks for forgiveness. Carson coldly replies that he will avenge his son's murder.
After Carson leaves the Barton home, he witnesses a scene that changes his mind; an urchin boy knocks down a little girl who is walking with her nurse. The nurse threatens to bring the boy to a policeman, when the girl tells her nurse that the boy did not know what he was doing. The words strike Carson and when he returns home, he begins to read the Bible. He regrets that he has not lived his life by Christian principles, neglecting to embrace charity and forgiveness. Meanwhile, Barton lies on his death bed and laments the fact that nobody, himself included, lives by the Bible. He claims to have grown tired of reading principles of love and forgiveness that he never saw enacted in real life. Moments later, Carson enters and holds the dying man in his arms. Carson asks God to be merciful to sinners and to forgive all their sins. John Barton dies.
The kindness of Ben Sturgis and his wife is inspired by the warm hospitality of strangers seen in Greek Mythology. Gaskell introduces this couple to add another human element to what might otherwise be a homogenous stereotyped version of a social class. In addition, the Sturgises provide Mary with much needed comfort and support, when all of her friends and family are too involved in the trial to attend to hear health.
During Jem's trial, Gaskell takes many creative liberties when fictionalizing the proceedings of an Assize court. She includes a scene where the villagers are trying to assess Jem's guilt using physiognomy, a pseudoscience, which Gaskell repudiates as nonsense. She does not believe that a person's nature can be determined by physical appearance or birth status. Here Gaskell demonstrates her belief in the natural, if not social, equality of mankind. Furthermore, Gaskell makes a case for the power of truth. In the novel, if the truth does not set Jem free in this world, she implies that it will free him in the next.
Mary’s confession in the witness box is necessary for her to purge her sinful, flirtatious ways. It is also an example of direct communication - as a contrast to the miscommunication that caused the strike, and indirectly, Harry's death. Mary finally stands up for Jem publicly - and sets the action in the right direction once again. Her admission starts the series of events that lead to the truth coming out and the characters in Mary Barton learning to abide by the tenets of Christianity. At the core of Gaskell's story is the idea that truth is necessary for happiness and freedom - and this applies to all people, no matter what social class they come from. The secret of her father's guilt weighs so heavily upon Mary's heart that she grows ill and delirious. Barton also must tell the truth to receive forgiveness before his death. Lies are like a physical virus that prey on these people's souls - and they must release their secrets in order to have a chance at happiness.
This section also marks Jem and Mary finally coming together, but their struggles are far from over. Their relationship is weighted down by the trial and John Barton's guilt. However, they are now a team, working together. After Jem is acquitted, he asks where "she" is, everyone believes that he means his mother. However, is looking for Mary Barton, because is now the most important woman in his life - not his mother. This is telling of a Freudian concept - the closeness of roles that a mother and wife play in a man’s life.
Mr. Carson, who is a victim in the murder case, has also been suffering because of his strong desire for revenge. Gaskell introduces the necessity of Christian forgiveness to heal a broken heart. Carson's drive for vengeance consumes him so that he becomes a shadow of his old self, but he frees himself from this burden when he finally is able to forgive John Barton. Through the character of Carson, Gaskell shows the human side of the upper class and that bitterness and pain can affect anyone who has lost a loved one.
The denouement of the novel occurs when Barton confesses to Mr. Carson that he murdered Harry. Barton only realizes the weight of his crime when he is able to see Mr. Carson as a father who is grieving for his son, rather than a heartless mill owner. In this way, Barton decides to forgive Carson for the injustices he committed - seeing how much he has suffered as a result. In turn, Carson must forgive Barton, who regrets taking Harry Carson's life.
However, this is not an easy decision for Carson - but when he returns to the scriptures, he finally has a change of heart. He forgives Barton to heal his own suffering. Barton confesses that he gave up on the Bible and Christian teaching because had started to feel that nobody else abided by Christianity, so why should he? These scenes highlight Gaskell’s purpose in writing this novel. She wants upper classes and lower classes to communicate with each other and acknowledge their shared humanity. For Barton and Carson, once they start speaking the common language of Christianity, they are finally able to reconcile their differences and forgive each other - and themselves.