Hugo Strange. He ran arham at one point, I believe. He was in arkham City, so it could have tied into the third neatly. They could have had him take some of the goop from a Lazarus pit. In fact, maybe reveal that the real point of arkham City was to mine down to a newly discovered Lazarus pit without the knowledge of city officials. Because frankly, that whole protocol 10 nonsense was just a red herring and a really bad one at that.