Plot hole: Several: 1. How did Hush get Batman's fingerprints on the knife? 2. How can the likes of Mad Hatter, Zsasz, and Deadshot go through the prison city without being spotted? 3. Why wouldn't Batman suspect Ra's al Ghul being the power behind Strange once he discovered him in the prison city?
Mr. Freeze: You will bring me Nora or you will die.
Trivia: 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.
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Answer: Batman later in the game discovers that Hugo Strange has been supplying everybody with weapons, so he would have given Two-Face the vat of acid.