OK, I was curious where Arkham City managed to fit an entire naval shipyard when Harley needed one.  It’s basically in the far south, within the restricted zone (with an opening to the water in that direction).

Here’s the door as you see it in AC:

Nothin’ here but a Riddler trophy.

And here’s the same spot in Harley Quinn’s Revenge:

Batman took the time to go home and change capes

By the way, while we’re looking at the innards of Arkham City, did you ever wonder what’s behind those castle-like walls in Strange’s inner keep? This:

Are those ice cream trucks?? Probably not.

Pretty much just parking for Tyger’s fleet of helicopters.  (You can also get a glimpse of the surface when you’re going up the elevator.  Under the pavement, of course, is Wonder City.  Don’t land those helicopters too hard!)