Once you are through the main door, you will be attacked. Just wait and counter attack when appropriate. Once you've done that, wait for all the talking and then you will be prompted to drop smoke pellets and then use your grappling hook. Do so in that order. Thus begins your first stalker segment. This one isn't too complex (no moving parts). Hit detective mode when prompted. All of the glowing gold gargoyles are perches you can swing to using the grappling hook. Move up towards the intersection. From there you can take down the enemies on either side (one by the scaffolding and one in the confessional). Just get behind each one by gliding and then use a takedown. You can do a takedown through the back of the confessional. Once they've been taken down, go back up to the gargoyles and then drop down from the one behind the last two enemies. Come up behind them and hit the takedown button to take both out at once.
Now that the room is safe, head back towards the front door and on the left you will see a door that leads up to the bell tower (Batman will mention going up there when you are near it). Go through the door and as you go up the wooden stairs, if you turn right you can just grapple up through an archway. Walk into the tower itself and grapple your way up from ledge to ledge and then take a ladder up through the trap door (it will glow gold in detective mode).
When you get into the next room, inspect the sniper rifle using the evidence tracker. Once done, Joker will talk to you and mention something about a boom. Turn right and run towards the window. Double tap the evade button to jump out of the window.