Access to the Wonder City is unfortunately highly limited. You can't reach it at all at first and it changes only after starting Follow assassin using tracker device to locate Ra's al Ghul. It's also worth to notice that part of this location - the Wonder Tower - becomes accessible after beginning Gain access to Wonder Tower. Moreover, its top level gets destroyed after completing Climb the observation deck to stop Protocol 10, but luckily there aren't any secrets hidden there so you won't miss anything.
There are two main paths leading into Miracle Tower. The first is the door found on the main subway station (screen above). You will probably use it for the first time during Follow assassin using tracer device to locate Ra's al Ghul, as soon after getting through it you have to use the Line Launcher.
The second passage leads through the Arkham City Process Center found in the Bowery (screen above). The path gets unlocked for the first time during Gain access to Wonder Tower.
While we're at it, it's also worth to mention the elevator found in the Wonder Tower Foundation, taking passengers onto the upper levels of the Tower (screen above). You can use it for the first time during Climb the observation deck to stop Protocol 10, though if you intend to return to it in the further part of the game you will have to once again solve two hacking mini-games.
Batman Trophies - 25
Riddles - 6
Demon Seals - 12 (4 challenges)