At the beginning of the play, the reader learns that John Proctor has had an affair with his house keeper, the much younger Abigail Williams. Though he has decided to end it, his original dilemma has to do with how to handle Abigail. She continues to come on to him despite his instances that it's over. He wants to fire her, but he worries that she will get back at him by exposing his secret.
His troubles go from bad to worse, when Abigail accuses his wife of being a witch. At this point he deals with the dilemma of possibly having to admit to adultury and lose his reputation in order to save his wife. When the accusations shift to him, the court forces him to confess if he wants to save his life. At the end his dilemma is deciding whether he should save his life or his name.
John Proctor initially seeks to protect his secret, his affair with Abigail. As the play progresses, the internal conflict becomes overwhelming, and after his failed attempt to bring negative attention to Abigail, he comes to learn that even his admission to adultery is not enough to change the fate of the accused.
Despite John's indescretion, he is still a man of pride, and his refusal to make a false confession highlights the shift in his dilemma. In fact, because of his decision, he must suffer the same fate. In essence, his great dilemma expands from protecting himself and his reputation, or doing what he can to try to save the life of others and reveal Abigail at the same time.