Near the beginning of the game when you first go to the steel mill and find Joker, he is apparently dead in a chair with Harley crying over him. Batman does the detective mode scan then and Joker is indeed dead because he has no pulse. He also has bones. Clayface doesn't have bones, and when you fight Joker at the end of the game in the funhouse that Joker doesn't have bones which indicates that its really Clayface. My question though is who was that dead Joker in the beginning? It couldn't have been Clayface since the dead Joker had bones.

Robin brings the linear launcher to Batman, so apparently Robin can enter and exit Arkham City freely? So why can't Batman? Why did he have to get himself arrested as Bruce Wayne in order to get inside?

Speaking of Robin, Batman gives him the blood sample and tells him to get it to the hospital so they can work on a cure. We never find out if they actually got a working cure, and the only cure Batman had was smashed at the end of the game.

Why is Joker seemingly the only one that is dying when lots of other inmates were also injected with Titan? Also Joker said he sent his blood to the hospitals weeks ago. So he has been dying for weeks, but yet Batman when injected has only a few hours to live.

Another thing that bothers me is the Deadshot mission says Deadshot was hired by Hugo Strange to assassinate certain people in Arkham City. Why even bother to hire Deadshot when Protocol Ten was going to kill them all anyway?

Where's my No Prize?

it would probably be pretty easy to stick a skeleton into Clayface, especially if he didn't have to move. That maybe a weak answer, but it could work. Where's my No Prize?