The Joker burned all of the Mob's money because he wanted them to know that he is in control.  After Rachel died Harvey lost all control of himself and went from a hero to a villain.  Harvey feels that Rachel had a fifty- fifty chance to life and he thinks all the people who was involved with her murder deserves a fifty- fifty chance by flipping a coin.  Bruce decides that there is no peace without the help of Batman to fight villains like The Joker.  Joker decides he wants Gothem to experience being the villain by putting bombs on each boat.  Leaving it up to the boat fill with convicts and the boat fill with civilians to decide who's going to blow up each other first.