User blog comment:Brandon Storm9/Alternate endings of Arkham Asylum/@comment-174.52.49.112-20130527181934

Each of your therories is wrong.

1. In Arkham City, there is a boat with a hatch that can be opened  via  Cryptographic Sequencer. If you go down the hatch, you will see a Joker thug at the end of the boat tied to a chair. He will make a noise then just sit there. As you walk to him, bugs will be crawling everywhere. At the end of the boat, if you look on the wall, there is a paper with delivery orders to Dr. Jonathan Crane. That is the only hint that he is actually still alive.

2. Killer Croc doen't even appear in this game, except for once. After fighting Ra's Al Ghul, there is a blocked off place with power button thing. If you hit it with a Batarang, Killer Croc will jump out of the water and talk to you, then return to the water. Other then that, you only hear people talking about him one and a while.

3. There is a side mission where you help Bane destroy 12 Titan Containers that Joker sent to AC. You take 6, and he takes 6. When you return to see how he is doing, he will reveal that he had taken the 6 containers so use himself, then charges at you to kill you. You get out of the way and he goes into a room. You activate a switch that brings down metal bars which traps him. You say you knew all along he'd do this, so you had used him, and you get to destroy the rest of the containers.