So I just watched IGN's breakdown of the trailer and just came up with a theory.

Some points I have to make first: Arkham Knight's a new villain created by Geoff Johns apparently. From the trailer we see 1) Scarecrow's back "Leave this city or I will unleash your greatest fears". 2) all the villains are working together and 3) their new combined gang's name is apparently "Hell's Gate".

Pooling all this together thinking the initial story is that Scarecrow's going to be the one to unite the gangs together into some super gang for a plot to destroy the city and kill Batman. But if I remember correctly in City Azrael mentioned something about "opening Hell's Gate" and seeing as how the dude shares his name with the title of the game I'm willing to bet this Arkham Knight is the main villain of the game.

My theory is it's going to work out a bit like Origins we're lead to believe Scarecrow's the one running the show then half way through we find out he's been manipulated the whole time by Arkham Knight who takes over Hell's Gate then that's going to lead into the main plot of the game something way bigger that's going to involve Azrael and some cataclysmic stuff.