At the training college the previous evening there is a good deal of talk about Sue and her young man. The year before a student was seduced by a young man who claimed to be the girl's cousin, so there is some doubt about the fact that Jude is supposed to be Sue's cousin. After Sue does come in the next morning, the girls learn she has been severely punished, and they make a protest, only to learn that inquiries made have revealed Sue has no cousin. That evening they learn that Sue has gone, presumably climbing out of a back window and crossing a river. Sue turns up at Jude's lodgings wet and asking for help. He gives her a suit of his clothes until hers can dry, and after taking some brandy she falls asleep.
When Sue awakens, she and Jude talk through much of the night, the conversation beginning with what Sue has read and why. She says her unusual taste in books came from a Christminster undergraduate with whom she had a "friendly intimacy." She looked upon the two of them as intellectual companions and after she had agreed to live with him in London was surprised that he meant as a mistress. They did live together, and the young man accused her of cruelty in not yielding to him. When Jude says he believes her as innocent as she is unconventional, she replies she has never had a lover and is proud of it, though he says that not all women are like her.
Sue refuses to pray with Jude, his usual evening custom, and goes on to criticize both the religious and intellectual life of Christminster, pointing out that Jude is the very kind of person for whom the colleges were founded. Jude says he can do without Christminster and prefers something "higher"; Sue retorts that she wants something "broader, truer." After Jude says his prayers Sue speaks of the new New Testament she made for herself by rearranging the books into chronological order and decries the attempt to falsify or misrepresent the contents of the Bible. She promises not to disturb his convictions but says she hoped when she met him that he might be the man whom she had always wanted to "ennoble" to "high aims" but he is too traditional. Jude wishes he could see her as other than a woman because she would make a fascinating companion.
In the morning Sue, uncertain as to what she will do and what Phillotson will think, decides to visit a friend near Shaston until her disgrace has been forgotten. Before she leaves, Jude wants to tell her that he has been married and that he loves her, but she guesses the latter and says he mustn't love her. But as soon as she reaches Shaston she writes him, telling him that she has been cruel and that he may love her if he wishes. Not hearing from her for several days, Jude goes to Shaston, to discover she has not written him because of the reason for her not being readmitted to the training college: it is said she has been intimate with Jude. Sue accuses him of mistreating her by not revealing that he loves her, and though he realizes he is even more to blame because he is married he still doesn't tell her about Arabella. He is puzzled by her annoyance at his saying that of course she can't care about him because of Phillotson. And he is both puzzled and pleased the next day when she writes to ask forgiveness for the way she treated him when he called on her as well as to tell him she would like to see him when she comes to Melchester.
Though Hardy's handling of point of view is conventional for his time, it is noteworthy that the first part of Chapter 3 is not told from the point of view of any of the main characters, a practice which he follows in most of the novel. Much of the time, of course, the point of view is appropriately centered in Jude.
Bringing Jude and Sue together, after she flees the training college, enables Hardy further to develop the difference in their views of the world, a difference established earlier in the novel. It is true that Jude and Sue are, in a sense, counterparts, as Jude remarks; they are both sensitive and thoughtful. But Jude is still the conventional Christian in belief, though these beliefs have been little consolation to him in his times of crisis, and Sue is an agnostic, complaining of the way the Bible is falsified. Sue will not join Jude in his prayers, refusing to be a hypocrite, as she puts it. And she explains the way in which she has rearranged her New Testament in chronological order.
She is also critical of the Christminster Jude so much admires. She says that "intellect at Christminster is new wine in old bottles" and that Jude, unable to enter academic life, is the very kind of man for whom the colleges were founded. She professes a freedom of thought which cannot be confined by a university and which she implies she engaged in with her undergraduate friend.
These are the views which will undergo a reversal during the course of the novel, a reversal which is part of the structure of the novel. In this reversal Jude will learn from Sue, who will in turn seem to repudiate what she has taught him. Especially will Jude come to scorn the religious beliefs he once held. Both will increasingly feel their lives manipulated by some force which they cannot explain.
The changes in Jude especially will demonstrate the theme of the novel. Both he and Sue are, of course, caught in the changes which bring into being the modern spirit, one of questioning and doubt.