I like how the movie has plotlines with moral implications. Joker wants to see people get corrupted and to "watch the world burn."
He succeeded in corrupting Dent, and he won't kill Batman until he corrupts Batman as well (if Batman still remains good and dies, then Joker loses). He also hoped that the people in the ferries would kill each other off, thus proving his point that people have no morals.
But in the end of the movie, the director shows that people, in general, are good and that there is hope despite all the chaos and crap that goes on. I liked that, especially with the scene of the prisoner throwing away the detonator. The second ferry with the guy was good too, as it showed that even though it would make "sense" to blow up the ship of criminals, it would be jacked up to go through with it, knowing that you blew up the other ship to save your own, you would have blood on your hands.
In the end, you have to read into the moral implications. I believe that the director wanted to show that not everything is black and white (i.e. what two-face ultimately personifies). Even though there is no clear cut line that is drawn morality wise, there still is a zone you need to stay in that is "right."
Batman himself falls into this category. The director questions his morality as a vigilante. Batman is clearly not going by the books; he's broken a bunch of laws already (i imagine, Breaking and Entering, Trespassing, illegal search and seizure, assault, embezzeling money, all be it from his own company, I'm sure dropping someone from a building simply to break his legs isn't legal either, and etc. etc.).
Also Batman does things like use that weird cell phone sonar thing (which I don't believe would work, but I'll suspend my belief on that) on everyone's cell phone, which invades everyone's privacy. That is a device that is handy, but I don't think it was absolutely necessary to move the plot along. But it does bring up the question of giving up privacy for the sake of security (Lucious Fox in fact makes this plot device explicit by expressing his displeasure in Batman's meddling with people's cell phones).
In the end he "kills" Two Face (i say kill because that's what the audience is lead to believe), then tells Gordon to lie to the police and to the public; to tell them that Batman killed the 5 people, including two cops. And also to lie to the public about Dent's turn to being a crazy two face guy.
I enjoyed the fact that the director planned these things out so well; portraying Joker and Batman as intellectual equals, but taking opposite philosophical positions. Joker believes that everyone is an animal, and "when the chips are down," they will reveal their true colors and will throw out all the rules. Batman believes the opposite, that people, despite living in crappy situations (i.e. the ferry), are still inherently good.
/end of my disorganised rant
