Three years after his marriage, Jude decides to go to Christminster at last. He is motivated partly by a portrait of his cousin Sue Bridehead, who lives there. He finds lodging in a suburb called Beersheba and walks into town. He observes the colleges and quadrangles and finds himself conversing aloud with the great dead philosophers memorialized around him. The next morning he remembers that he has come to find his old schoolmaster and his cousin. His aunt sent the picture of Sue with the stipulation that Jude should not try to find her, and he decides that he must wait until he is settled to find Phillotson. He tries to find work in the colleges. He finally receives a letter from a stonemason's yard and promptly accepts employment there. He thinks of going to see Sue, despite his aunt's continuing entreaties not to see her. He walks to the shop his aunt described and sees Sue illuminating the word "Alleluja" on a scroll. He decides that he should not fall in love with her because marriage between cousins is never good, and his family in particular is cursed with tragic sadness in marriage.
Jude discovers that Sue attends church services at Cardinal College and goes there to find her. He watches her but does not approach her, remembering that he is a married man. The next time he sees her, he is working on a church and sees Sue leaving the morning service. On another afternoon, Sue goes to the stonemason's yard and asks for Jude Fawley. When she is described to him, Jude recognizes who she was. He finds a note from her at his lodgings, saying that she heard of his arrival in Christminster and would have liked to meet him, but might be going away soon. He is driven to action and writes back immediately, saying he will meet her in an hour. They introduce themselves, and Jude asks if she knows Phillotson, whom he thinks is a parson. She says that there is a village schoolmaster named Phillotson in Lumsdon, and Jude is struck by the realization that Phillotson has failed in his ambitions.
Jude and Sue walk to Phillotson's house, and Jude introduces himself. The schoolmaster does not remember him, and Jude reminds him about the Latin and Greek grammars. Phillotson tells him that he gave up the idea of attending the university long ago, but invites them in. He says that he is comfortable with his current existence but is in need of a pupil-teacher. They do not stay for supper, and on the way back Jude asks Sue why she is leaving Christminster. She explains that she is quarreling with one of the women she works with, and it would be best to leave. Jude suggests that he ask Phillotson to take her on as a teacher, and she agrees. Phillotson agrees to employ her, but points out that the salary is quite low, so it would not assist her unless she viewed the job as an apprenticeship in a teaching career.
Sue begins working at Phillotson's school right away, and he is responsible for giving her lessons. According to the law, a chaperone must supervise them at all times. The schoolmaster thinks this is unnecessary because he is so much older than she is. However, one day when he is walking toward the village, Jude sees the two walking together. Phillotson puts his arm around Sue's waist and she removes it, but he puts it back and this time she lets it stay. Jude goes back to see his aunt, who is not well. Jude talks with a friend from home, who is surprised that Jude has not entered college yet. Jude decides to pursue admission the university more devotedly and writes to five professors. After a long wait he finally receives an answer from a professor at Biblioll College. The letter recommends that he remain in his current profession rather than attempting to study at a university.
Jude grows depressed and goes to a tavern to drink. Another mason, Uncle Joe, challenges him to demonstrate his academic ability by saying the Creed in Latin. Jude does, then grows angry when they congratulate him. He goes to see Sue. She tells him to go to sleep and that she will bring him breakfast in the morning. He leaves at dawn and goes back to his lodgings, where he finds a note of dismissal from his employer. He walks back to Marygreen and sleeps in his old room. He hears his aunt praying and meets the clergyman, Mr. Highridge. Jude tells Highridge of his failed ambition to attend the university and become a minister. Highridge says that if he wants, Jude can become a licentiate in the church if he gives up strong drink.
Sue serves to attract Jude to Christminster, and he seeks her out with a strange devotion, as though he is following an inevitable path carved out by destiny. Taken together with his aunt's warning that marriages in their family never end well, Jude's haste to find and fall in love with his cousin creates a sense of foreboding about the young man's fate. His marriage to Arabella prevents him from pursuing Sue fully, but she clearly captivates him.
Jude is disappointed to find that Phillotson does not remember him and has not fulfilled his ambitions. Phillotson is a foil to Jude, his complacency set against Jude's fervor. Phillotson represents a path more accessible to Jude than his aspirations toward an academic career, but Jude is loath to give up his Christminster ambitions. He also clings to Sue, arranging for her to teach with Phillotson as a way of keeping her near him.
Jude finds that the Christminster colleges are not welcoming toward self-educated men, and he accepts that he may not be able to study at the university after all. His propensity for drinking emerges. The episode in the pub, in which he recites Latin to a group of workmen and undergraduates, shows the juxtaposition of Jude's intellect with his outer appearance. Christminster will not accept him because he belongs to the working class, yet he is intelligent and well-read through independent study. The realization that his learning will help him only to perform in pubs sits heavily with Jude, and he is comforted only by the possibility of becoming a clergyman through apprenticeship.