I'm thinking Batman immediately goes to deal with Two Face right after the first games ends and as soon as you defeat Two Face Oracle starts relaying you messages from her Dad, Commish Gordon that something happened at Arkham...maybe they were being transported to another facility like Black Gate and on the way broke lose only to cause havoc on Gotham's streets...I think you can see a flyer on the outside of the building the Joker's in before it pans into the building and it may depict either...
I'm thinking Batman immediately goes to deal with Two Face right after the first games ends and as soon as you defeat Two Face Oracle starts relaying you messages from her Dad, Commish Gordon that something happened at Arkham...maybe they were being transported to another facility like Black Gate and on the way broke lose only to cause havoc on Gotham's streets...I think you can see a flyer on the outside of the building the Joker's in before it pans into the building and it may depict either...