Jude, the protagonist of the novel, is a conflicted person. However, the conflicts that exist within his character at the outset of the novel appear to be very different from those that conflict him in the end.
Early on, Jude is a person without a place. His parents are gone and he is left to live with an aunt. The aunt does not particularly like him. Jude recognizes his position with blunt honesty and without bitterness. He is driven to dream of finding a place for himself; to dream of rising up in the world. How to achieve this dream is his first conflict.
However, this conflict fades when he meets Sue. Jude allows his first and greatest dream (with its attached challenges) to fall away and he takes up a new challenge, one of love.
Sue teaches Jude that his former, uncritical moral views are not the only views available. More nuances and independent views exist. Eventually, Jude adopts these views, but not without turmoil along the way.
These changes in Jude serve as the undercurrent of the novel. In these changes, we see Judes' constant search for a place in the world and for self-value. The novel, when seen this way, becomes the story of one man's emotional maturation as he grows from a position of automatic conformity to social norms into a precarious independence of moral thought.
In particular, this is the story of a set of characters who find self-defintion in the process of coming to terms with one of society's most pervasive and important institutions:
The wrestling over the issue of marriage that takes place in Jude the Obscure is in a larger sense a function of the definition of the self which takes place throughout the nineteenth century.
The conflicts taking place within Jude (as well as within Sue and Phillotson) are concerned with the dynamics of self-definition and identity, especially as identity can be seen to be a balance between the individual and soceity.