In the last part of the walkthrough, you learn from Selina (Catwoman) after questioning her regarding protocol 10 that Prof' Strange has been put in charge of running Arkham City and working with Joker. Your goal now is to interrogate the Joker to uncover Protocol ten.
You need to locate where the bullet entered the court and where it impacted. Scan the crime scene for ballistic evidence. Enter detective mode and use the Evidence Scanner.
Detect where the entered through the window. Then look for where it hit. Detect the spot on the floor. The trajectory the bullet traveled will lead you to the shooter. Locate the source of the sniper shot. Batman realizes the shot came from the tower of a nearby church.
You hear a message from Strange that Protocol 10 will commence in 10 hours so you don't have much time!
Exit the courthouse by going to the balcony and dropping on the thugs below.
Head towards the church (green marker on your compass). You'll hear in Local Surveillance that Joker's crew got into the church.
When you reach the church, jump onto a wall then drop attack on the thugs guarding the entrance.
You will communicate with Alfred telling him that you are in the church and that Harley Quinn is inside. Alfred will warn you that Quinn is setting up a trap for you. Enter the Church (which also acts as a medical center)
Open the door and enter the church. In the corridor, you will be attacked by Harley Quinn. When you knock her to the ground, an inmate will threaten you that if you don't let her go they will kill the hostages.
To defeat the thugs, you will need to disappear, and then pick then off silently one by one. Use a Smoke Pellet to escape when discovered by armed enemies.
Drop the Smoke Pellet. Once you have "vanished" from their sight, use detective mode to survey the room and plan out your tactics. You will see four thugs, all armed, two hostages. This is gonna be easy.
Swing between Vantage Points.
One of the inmates will threaten that if you try and get them the hostages will die.
One of the thugs is holding a hostage inside the confessional, hiding. But he is not safe in the confessional, it actually makes it easier for you to get in behind him.
Observe the inmate and hostage behind the glass panel. Smash the panel and defeat that thug. There will be another inmate holding a hostage nearby. Glide to the scaffolding above him without being seen and take him down from there. Use the Silent Takedown when directly above the target.
If you can get behind the two thugs in the main corridor without being seen, you can take them both down in one move.
The room will now be secure and the hostages can escape
Aaron Cash will thank you for the help. Talk to Doctor. Batman will explain that Quinn's only priority is to protect Joker and that she is dangerous.
You need to locate the source of the Sniper Shot.
Talk M.P.T. Anne Bishop and to M.P.T. Officer listen to what they have to say.
Talk to Medic Adam Hamasaki in the room nearby.
Open the door to the Bell Tower and start making your way up the tower.
Get to the top and find the room with the remote controlled gun. Scan the sniper rifle for forensic evidence.
Joker will appear in the televisions and warn you about bombs in the tower. Dive through window just before the bombs explode.
You will tell Alfred that you got a lock on the signal used to remotely control the sniper rifle and that Joker is behind this.
The radio signal should lead you right to him.
