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Jude and Sue return to Christminster with Little Father Time, who is now also named Jude, and the other two children they have had together. They encounter a procession and see Jude's old friends Tinker Taylor and Uncle Joe. Jude tells them he is a poor, ill man and an example of how not to live. The family goes to look for lodging, but finds that people are reluctant to take them in. One woman rents them a room for the week provided Jude stays elsewhere, though when she discovers Sue's history and tells her husband, her husband orders her to send them away. Sue puts the younger children to bed and takes little Time out to look for other lodgings, but with no success. The boy remarks that he "ought not to have been born" and grows irate when Sue tells him that she is pregnant again.
In the morning Sue wakes early and goes to see Jude. They have a hasty breakfast together and then return to Sue's lodgings to make breakfast for the children. They get some eggs and place them in the kettle to boil. Jude is watching the eggs when he hears Sue cry out. He rushes in to find Sue unconscious on the floor, having fainted. He cannot find the children. He looks inside the door to the closet, where Sue collapsed, and sees all three children hanging from clothes hooks. Beneath little Time's feet lies a chair that has been pushed over. Jude cuts down the three children and lays them down on the bed. He runs out for a doctor and returns to find Sue and the landlady attempting to revive the corpses. On the floor they find a note, written by little Jude, that reads "Done because we are too menny."
Jude and Sue find lodgings toward the town of Beersheba, but Sue is despondent. She decides that she is rightly married to Phillotson, and it becomes clear that she and Jude never legally married at all. Arabella visits the house and explains that she did not feel she belonged at the children's funeral. Sue imagines that God punished her by using Arabella's son, born in wedlock, to kill her children, who were born out of wedlock. Phillotson agrees to take Sue back as his wife, and she moves into his house.
Arabella decides she will do the same and takes Jude, who is drunk, back to the house they lived in when they were married. After a few days, she and her father coerce him into marrying her again by suggesting that he has been living with them on that pretext. He agrees, and they are married. Jude is ill with an inflammation of the lungs. He decides that he wants to die but to see Sue first, so he travels to her home in the rain. Sue tells him that she still loves him but must stay with Phillotson, and he kisses her. At night she tells Phillotson that she saw Jude, but swears she will never see him again. She joins Philloston in his bed despite her lack of feeling for him, saying it is her duty.
In the summer, Jude is sleeping when Arabella goes outside to observe the Remembrance Week festivities. She wants to see the boat races, but goes upstairs to check on Jude first. Finding him dead, she decides that she can afford to watch the boat races before dealing with his body. Standing before his casket two days later, she asks the Widow Edlin if Sue will be coming to the funeral. The widow says that Sue promised never to see Jude again, though she can hardly bear her legal husband. She says that Sue probably found peace, but Arabella argues that Sue will not have peace until she has joined Jude in death.
The tragic conclusion of the novel arises as the inevitable result of the difficulties faced by the two cousins. Sue sees young Jude's terrible murder-suicide as the result of her transgressions against the institution of marriage, and her only solution is to return to her ex-husband. Sue sees all the forces of nature working against her and comes to regard her love for Jude as a sin in itself.