Into the Church
If you stuck with the grinding like I did, you should have picked up a few levels and have some new combat moves and better armor. Once you are ready, head to the Church (follow the marker on our compass) and go inside!
Additional Silent Take-down Training
After you enter you have a face-to-face with Harley who lets you know that the Big J is not taking visitors at the moment... She then departs, and you get to use a smoke pellet for the first time as you disappear up into the shadows above, and learn about silent takedowns from above! Do a few of those, and then glide down behind the confessional to take out the thug by completing a smash-through-the-wall takedown, and that just leaves one armed thug you can drop down behind and put to sleep for the win! Uh huh!
Taking the last thug down unlocks the Achievement "Savior" (10 GS) for saving the medical volunteers, and now you are just left with what to do next?
--== Investigating the Tower ==--
We still need to investigate the tower where the shot originated -- who knows, Joker could still be up there! Probably not, but still... So after talking to the Doctors and the Cops here, head to the door that is helpfully marked Bell Tower and go in -- then Grapnel up to the top level and use the ladder there to enter the Bell Section itself.
Here is the gun but wait -- it is a remotely controlled setup! But hey, the Joker IS here -- kinda -- but so are a bunch of bombs and, clearly, his plan is to blow us up! So Left-Stick double-tap 'A' to smash through a window and escape the explosion then a brief chat with Alfred to fill us in on the plan, and away we go!
Follow the radio signal using its strength to guide you -- but you should have guessed the area we will be heading in since the Joker has clearly already staked-out his piece of Arkham City... On the way you should get the prompt for Augmented Reality Training (AR Training) -- go ahead and take a look at that and use the map to check out the distress flare location, and the AR spot -- you can do that now if you like but I chose to wait.