WARNING!! There will be spoilers from Batman:Arkham City.
Harley Quinn IS pregnant.
Calendar Man & Two-Face have a bone to pick with Catwoman.
Hugo Strange, The Joker, Talia Al Ghul, & Ra’s Al Ghul are dead(though Talia & Ra’s i think will find a way back).
Man-Bat has not been referenced in either Batman:Arkham Asylum or Arkham City, so we are left to assume Man-Bat does not exist in this universe(for now).
Apparently, Scarecrow has been M.I.A. since the last game, but watch this vid & tell me that Scarecrow wont play a big part in the next game: http://www.youtube.com/watch?v=9TiqrurnNEE seems like Falcone is financing Crane’s experiments, but i think the bugs COULD lead to
Bedbug possibly making an appearance.
Jason Todd exists in this universe(play as Robin in Joker’s carnival challenge map, Joker say’s “Robin, didnt i kill you already?” seeing the Robin in this universe is Tim Drake. Plus, i think this is an indicator that Red Hood exists.
Solomon Grundy & Clayface arent dead.
Catwoman is the daughter of Carmine Falcone(talk to Calander Man as Catwoman).
Its hinted that Superman & The Flash exist in this universe(Metropolis & Keystone were mentioned), although i dont think they exist just because the cities they protect are mentioned, does not confirm they actually exist.
Azrael(Michael Lane) warns Batman about “Dark days are coming. The prophecy is coming true. You are the warrior who will close the gates of hell. You are the one who will save the day and in doing so events will occur that you cannot stop. From the ashes of Arkham, the fires will rage and Gotham will burn. And you, you will burn too.” This also appears to be the first time Batman & Azrael have met.
Now on the decoder if you go to around 502.00 and 902.00 you will hear “You will pay for what you have done to me.” Then if you move it to around 711.00 and 501.00 it will give you number which decoded means “I will return Batman.” Last if you move to around 222.00 and 501.00 you will hear “I AM YOUR WORST NIGHTMARE, DARK KNIGHT. GOTHAM WAITS FOR ITS SAVIOUR. The letters are C T Z R Z P X A K D X I C H E B L R F P G K C J Q E M D U H.
Lucius Fox does exist in this universe.
Bane, Killer Croc, & Poison Ivy are still around.
Sal Maroni is dead, but is mentioned.
There is a design & layout of Gotham City if you go back to the observation deck at Wonder tower, similar to the plans for Arkham City that were in Quincy Sharp’s office in the first game, hinting that Arkham 3 could take place in Gotham.
The Lazarus Pit equipment was destroyed at the end of the game.
Hush is on the loose.
After hearing all 12 of Calendar Man’s stories, he is missing from his cell.