Batman may have beat up the bad guys and saved the day (night?) again in Arkham City, but there are still some secrets that remain. At the Kapow! Comic-Con in London, Game Director Sefton Hill commented:
Some of them we put in there that were really obscure were found within a week [like the Scarecrow code]. We didn't think anyone would ever solve that, but it only took people two days. But there are still 3 or 4 things that people haven't seen – some of them very subtle things. There's one that we had right in one of the first demos that we did that nobody has found – it's in there if you look hard enough.
I can't say the chances we'll ever know just what these secrets are, are great. Rocksteady are infamous for teasing Arkham City in Arkham Asylum in a secret room no one ever actually found. Naturally, I'm also sure whatever it is we won't discover hints at the inevitable third chapter in the Arkham series.
via IGN
