When Hugo Strange tells Batman about his plans to eliminate criminals everywhere, he gets stabbed in the back and through the heart by Ra's Ah Ghul. However, no blood appears on Ra's sword and there's no hole in Strange's coat.
Just before Protocol 10 starts, you end up in a giant fight with Joker and a good number of his goons. If you activate Detective Vision during this fight, you'll see that Joker doesn't have a skeleton. This is also true when he's holding Talia hostage in front of the move theater. This offers a hint to how the plot plays out.