I played if back when it first became free to play on ps3. I had alot of fun with the game at first despite some limitations (hard to use the interphase on a non Hd television, frequent lagging, occasional server crashes). Simply the mechanics of maneuvering around the cities with all three of the movement styles made the game worth playing (I particularly liked the flying).
However eventually I got to this weird point where I couldn't even play some of the scenarios I'd paid for like Central City and the defense of OA because my level wasn't high enough. At the same time it because incredibly hard to keep leveling up. That combined with my previously mentioned problems lead me to quit playing.
Definitely something I might give another chance to some day though.
I'm guessing your talking about the end of No Man's Land? The way I remember it is Lex was going to try to rebuild Gotham and establish a power base but Bruce stopped him. Still, been a while since I read that one so I'm not sure.