During her convalescence Sue says she is beaten and must conform, and Jude asserts he belongs to "that vast band of men shunned by the virtuous-the men called seducers." She still feels she belongs to Phillotson. Jude is aware of the fact that he and Sue are going in opposite directions: she is returning to the conventional ideas she taught Jude to abandon. She insists that now she must practice "self-renunciation," but Jude argues that she has only acted out of natural instincts. She has been attending church frequently, Jude finds out, and does not want to be criticized for doing so. She doesn't want to go through the marriage ceremony with him because she feels she is still married to Phillotson. When Arabella calls, having come to Christminster to look at her son's grave, Sue insists that she is not Jude's wife. After Sue mysteriously leaves, Arabella says she is living at Alfredson with her father, now back from Australia. Jude looks for Sue, finally discovering her in church. She tells him that Arabella's child killing hers is a judgment on her. They disagree over whether she is his wife, Jude arguing that their marriage was made by nature, Sue that it was not made in heaven as hers to Phillotson was.
Jude cannot understand how Sue can have changed so, but she is convinced she has seen the light at last. She doesn't want him to return to their lodgings, but he does anyway. A conversation ensues in which each tries to take the blame for the relationship between them: Jude says he shouldn't have forced her into intimacy, though he still complains she hasn't felt for him what he feels for her; she admits she tried to attract him and through envy of Arabella gave herself to him in order to hold him. She insists they part, though Jude tries to convince her that he needs her as a defense against his weaknesses. She tells him that they must separate not because she dislikes him but because her conscience says it's right, and she suggests they can still be friends as they used to be.
After seeing Jude and Sue in Christminster on Remembrance Day, Phillotson reads of the death of the children in a newspaper while in Alfredston. Encountering Arabella there, he learns from her that Jude and Sue aren't living together, that they have never married, that Sue considers herself Phillotson's wife, and that Little Father Time was really Arabella's child. He decides to ask Sue to return to him, realizing what positive effects it might have on other aspects of his life, and writes her a letter. In Christminster Sue calls on Jude to tell him she has decided to return to Phillotson, to remarry him, and she suggests Jude go back to Arabella. Jude cannot understand this extreme penance on Sue's part. She purposely walks with him to the cemetery so they can say goodbye over the graves of the children.
Jude and Sue are shown in the scenes here to have reached the point at which their beliefs have reversed. The structure of the novel is such that the next step is for them to dissolve their relationship, with Sue the instigator. Sue now talks about the necessity of "self-renunciation" and the feeling that she still belongs to Phillotson. Jude argues that she was simply following her natural instincts in coming to him and that theirs is "Nature's own marriage." But Sue answers that it was not made in heaven, as was hers with Phillotson. The change in Sue is shown further in her attending church almost daily and in her conviction that Arabella's child killing hers was a judgment on her.
It is not surprising, then, that she accepts Phillotson's offer to return to him and remarry. It will be the right thing to do and will serve as a penance for her sins. She even suggests that Jude make things right by returning to Arabella.