The book starts with a question, "What is Gotham City to you"? Batman of course says that he is Gotham, expresses how he knows the city inside and out. Some people fear a secret society called The Court of Owls. Batman does not believe they are real, until they send an assassin after Bruce Wayne. He feels betrayed by the city, and gets tortured so bad that it seems he is feeling fear for the first time in his life. It ends with him saying, "Gotham isn't Batman, she still has lessons to teach me".
Doubles is also used in this story, and in a very twisted way. Mr. Wayne, and Mr. Lincoln March. Wayne grew up rich once his parents died. Mr. March grew up poor when his parents died, and was raised in an orphanage run by the Court of Owls. Both are very polite, and want the best for Gotham. Wayne's best is Batman, and March's best is a secret I'll keep to myself. It is a controversial twist that Writer Scott Snyder pulled of perfectly.