You can now let go of the helicopter, as it would just continue flying through the area. The Wonder Tower you're looking for can be found in the western part of Arkham City, beside the subway station to be precise. You need to stay careful while going there, as you can still get attacked by TYGER helicopters #1. You of course have to properly react to such situations, quickly changing location and using buildings and other objects as cover. After reaching the destination, land on the roof of one of the nearby buildings and note that the entrance gate is guarded by two snipers #2.
It would be good to attack those snipers by surprise. In order to do that, I'd suggest firstly getting above them #1, afterwards carefully jumping down and approaching each of them from behind, performing a silent takedown #2.
Stay on the balcony on which the snipers were and look around for a control panel #1 you can hack into using the Cryptographic Sequencer #2.
Choose the only possible corridor and eventually you will reach the Arkham City Processing Center, opening a passage using the Electrical Charge on your way #1. After reaching the new room, glide onto the lower balcony #2.
Here you can look for another locked passage #1 and once again use the Remote Electric Charge. Head north and soon you will reach a new room. Here you will encounter a new kind of enemy, TYGER guards equipped with stun sticks #2.
You can of course attack the first enemy from above, though the other enemies will require a special tactic to handle. You have to press A twice to jump above a guard to disorient him #1 and afterwards quickly press X to attack him #2. Try attacking the guards one at a time and evade when getting electrocuted seems inevitable.
Continue using the above tactic until you take care of all the guard with stun sticks. Afterwards listen to what Hugo Strange has to say #1 and prepare for a slightly harder fight #2.
The main difficulty of this fight is having to handle a few types of enemies at once, so you will have to keep in mind all the best tactic described in this guide and suggested by the game. I'd especially suggest focusing on the enemies with firearms (remember that anyone can pick a dropped gun from the ground!) #1 and guards with stun sticks (A, A, X button combination), who debuted a few moments ago #2.
OF course you can't ignore other enemies in this room, leading out successful counterattack #1. You also have to keep an eye on the ones throwing various objects at Batman #2, as each hit will not only deal damage, but also throw you out of rhythm. It's only worth to make an exception for the ones throwing extinguishers, as destroying it will blind the enemies (Batman will automatically switch to Detective Mode).
Also don't forget about enemies with blades. I'd recommend leaving the armoured (B followed by repeatedly pressing X) #1 and shielded guard (B and afterwards A twice) for the end #2.
After the fight, listen to Hugo Strange's comment and talk with the saved political prisoners #1. Take a look around the room and interact with the hatch in the ground to get into the sewers #2 and reach the Collapsed Streets.
Head east, eventually jumping onto the lower level #1. You goal is reaching the partially flooded area behind the destroyed buildings. Stand so that you have to south wall in front of you and use the Line Launcher on it #2.
Right after the ride begins you should slow down (left trigger) and turn towards the north-east corner and shoot the line there. You will recognize the place by the distinctive Riddle trophy found there #1. Look up and note the niche you can grab onto #2.
Move right, passing by the corner and jumping onto the new ledge in the eastern part of the Collapsed Streets. Move a bit further east, turn on the Detective Mode, search for a destructible floor fragment #2 and spray the Explosive Gel onto it. Detonate, go down and choose the door leading to the Wonder Tower Foundations.