Hope
Hope is a theme that doesn't seem like it exists in this film, but it is the very core of who Batman is. He wears the mask to inspire others to believe that they can make a difference in a city overwhelmed by lawlessness, crime, and violence. Batman seeks to restore the hope of the people in Gotham to believe that there is a way out of the crime that has plagued the city.
Identity
Identity plays into Bruce's story as he goes from the scared little boy trapped in the well to Batman. Bruce is seen in a Bhutan prison fighting inmates and we can understand that he's searching for something within himself that he believes he can only find through violence and crime. He literally steals products from his own company--talk about a need for identity. His training in The League of Shadows and later becoming Batman to stop crime becomes his road to discovering who he is through the things he does.
Yet, he is reminded by Rachel that it's not who he is beneath the surface that is his true identity, but rather he is defined by what he does.
Justice
Ra's Al Ghul seeks to destroy Gotham City by having it be toppled to the ground. From here he says that it can be rebuilt. But the irony is that The League is supplying power and influence to Gotham's mob boss Falcone through his link to Arkham's Dr. Crane. Thus the corruption that The League seeks to destroy is being brought on at an increasing rate by their own efforts. So Batman steps in to create the opportunity for real justice when those who are meant to be serving it are simply in league with the enemy.
Fear
Fear is a theme interwoven throughout the entire narrative. Its earliest appearance is young Bruce's encounter with bats after falling into a well. He develops chirotophobia - a fear of bats. This is pivotal to the catalyst of his story - the death of his parents - as young Bruce is frightened by the bat-like performers at the opera.
This theme is further enforced by the secondary antagonist of the film, Scarecrow, who is a literal embodiment of fear. The film's main protagonist, Ra's Al Ghul, seeks to destroy Gotham through fear. He plans to do this through Scarecrow's "fear toxin," a potent hallucinogen that causes it victims to hallucinate their fears.
An ironic twist to the theme of fear is Bruce's confrontation with his childhood fear, and his subsequent acceptance and adoption of it as his vigilante symbol. He plans to use his former fear to subdue his enemies.
