To answer this question, take a look at Chapter 35. In this chapter, Jane is seriously reconsidering a potential marriage to St. John (whom she earlier refused). As the house falls into silence, however, Jane suddenly hears Mr. Rochester calling her name. This sound has a profound physical and emotional impact on Jane:
The feeling was not like an electric shock, but it was quite as sharp, as strange, as startling: it acted on my senses as if their utmost activity hitherto had been but torpor, from which they were now summoned and forced to wake.
As Jane leaves the house to search for Rochester, she tells St. John that this is the work of nature:
"This is not thy deception, nor thy witchcraft: it is the work of nature."
For Jane, then, marrying Rochester is the natural thing to do. She and Rochester are made for each other, and their union is ordained by the natural order. In contrast, Jane has no amorous feelings at all towards St. John. She would only marry him for the sake of propriety, since she could not accompany him on his mission as a friend. She would need his protection.
So, in the battle between her head and her heart, Jane's heart wins, and she marries Rochester.
St. John Rivers admires and respects Jane, but he doesn't love her with the passion of Mr. Rochester. He is cold and austere, and really loves someone else anyway, which Jane knows about. He thinks Jane would be a good wife because she is intelligent and a hard worker, so he asks her to marry him and go to India with him as a missionary.
Jane respects St. John Rivers as well, but she knows that a marriage to him would be without love. After she hears him preach one day, she realizes that he is also conflicted over his faith. His religion is also strict and legalistic, not loving and full of grace. Since Jane is a passionate woman at heart, this does not appeal to her, even though she herself questions her faith. Rochester is not a religious man, but he is a passionate one. Besides, Jane loves him and has always loved him.
Jane Eyre's choice not to go with St. John and go back to Rochester is a debated one. On the one hand, she radically dissociates herself from the masculinist missionary project of Rivers where a regimented patriarchal hegemony is at work, but on the other, she returns to Rochester thereby entangling herself in the male dominated institution of marriage nevertheless.
To the feminists, Jane's decision to reject Rivers's offer is a radical decision whereby she erases the final traces of Helen Burns and thus submissive femininity in her. She returns to Rochester, giving more importance to her desire than anything else. Her decision not to go to India and her comparisons between India and hell as well as Rivers's death at the end have been criticized by the post-colonial reader however.
She does return to Rochester, but this time on her own terms, as the dominant partner. She is in complete control of the blind and maimed Rochester. She marries her and not the other way round. this is how she subverts the patriarchal institution of marriage from within.