Dating back to the first arc, Batman has theorized that the antidote used to clear up the infections caused by Professor Pyg was actual a trojan horse delivery system, creating addictions you can catch. The antidote would lay dormant until something triggered it, maybe just a random harmless virus. When the infection is up, that’s when the cravings and agonizing withdrawl kick in.
Penitente is the connection between everything that has come Batman and Robin’s way since the book began, from Professor Pyg to Joker and The Black Glove.
But before Batman can do anything about it, the Batmobile is shot down with him and Jim Gordon in it as Professor Pyg is broken out of jail.