The central conflict in Jane Eyre can be boiled down to man vs. society. Though many personal conflicts occur throughout the novel, at its core, the book is about Jane determining and sticking to her own values in a world of people that constantly mistreat her and try to shape her behavior to fit their purposes.
As a child, Jane is accused of being wicked, full of passion and vice. She is mistreated by her family and punished for any attempt to defend herself. Despite being a generally inquisitive, good-natured child who prefers to keep to herself, Jane is criticized by her aunt and cousins, as well as their servants, for being impudent and disrespectful. She endures slander, such as when Mrs. Reed tells Mr. Brocklehurst that she is a liar and when Mr. Brocklehurst then names her as such to the whole of Lowood School. Through all this she must fight to retain her sense of identity and not give in to what the world around her tells her that she is. She fights to be good and honest and dutiful, despite her frustrations in striving to please a world that does not accept her.
When Jane arrives at Thornfield Hall, she faces a very different obstacle. Mr. Rochester expects a governess to be mild and accommodating and is shocked by Jane's frankness and independence. His behavior towards her is often bizarre, seeming to goad her into speaking out of character or revealing things she does not want to, and she must avoid these traps he lays for her, such as when he dresses as a gypsy woman to trick her into telling him her feelings for him. Later, when they are engaged, he tries to alter her in other ways, describing her as a fairy or an angel. Jane fights back on this count.
“I am not an angel,” I asserted; “and I will not be one till I die: I will be myself. Mr. Rochester, you must neither expect nor exact anything celestial of me—for you will not get it, any more than I shall get it of you: which I do not at all anticipate.”
Jane must constantly assert her identity and her independence, with Rochester and with others. She has an excellent sense of self and must struggle to make sure it is recognized by those around her.
We see this later in the novel in her relationship with St. John Rivers. He has set expectations of her behavior and identity, expecting her to marry him and become his missionary partner as a dutiful Christian woman. When she argues back and offers to go as his sister or cousin rather than as his wife, he becomes unsettled and even angry, but this does not stop Jane. She will not be forced to do something that goes against her nature.
The conflict is resolved when Jane returns to Rochester at the end of the novel. When she hears his voice in a vision, she knows that in her heart she wants to be with him and decides to follow that passion rather than allow herself to be dictated by the expectations of society. Despite Rochester's physical limitations, despite his age, he is the man that she wants, and she defies societal conventions to pursue her own desires. Though she has spent the whole novel establishing her identity in contrast to the expectations and criticisms placed on her by the outside world, it is not until this moment that she is able to fully assert her independence and dictate her own future.