Use the ventilation shaft to find your way to the main office (the same one the inmates were trying to get into). Turn on your detective mode and examine the safe located in the corner of the room. Zoom in the view on the handprint and perform a complete scan to initiate a new investigation. Use the shaft again to return to the morgue.
Watch out, because new inmates will storm through a nearby door and some of them will be carrying melee weapons, so it'll be easy to lose a lot of health points. Get rid of all of them and find a door leading to the West Wing Corridor.
Don't forget that you should be using your detective mode skills, because it'll make finding the path to your current destination a lot easier. Head south and then turn east. Eventually you'll have to return to the Main Hall. Get ready to defeat three new thugs here (screenshot #2).
Head east once it's safe again and this time locate a door leading to the South Corridor (screenshot #1). Enter this new area and proceed to the east. An armed opponent is stationed just around the corner. The easiest way to get rid of him will be to approach the left wall and to press a corresponding key for a corner cover move. Choose a Batarang from your inventory and use it to stun the guard. Don't forget to finish him off with a takedown, as well as to take care of his colleague. Open a nearby door to go to the Library.
Make a few steps forward and engage new bandits in direct combat. Be careful, because there's going to be a lot of them here and some of them will be using dangerous melee weapons. Once it's safe use your hook to travel to upper balconies. Your objective for the time being is to locate an entrance to a new ventilation shaft (screenshot #2).
Joker should start a countdown to the moment when he kills the hostages, but you may as well ignore it. The guards aren't in any danger. Walk through a short tunnel and use your hook to find your way to an upper ledge(screenshot #1). Once you're there turn around and use the hook for the second time.
Leave the vents and choose a Batarang from your inventory. Aim your gadget at a nearby rope. Doing this will result in a huge chandelier destroying a section of the floor. Proceed to the lowest level and approach the hostages to disarm "the bomb". Listen to a short conversation with one of the guards before moving on.
Remain where you are and make sure that you're using your detective mode. Inspect one of the bookshelves located to the left of the rescued guards and you'll find an interactive book. Pressing the action key will allow you to pick up this item. You may exit the library via the main door. I guess you may be surprised to see that instead of returning to the previous room of the mansion you'll end up inside the... Wayne Manor!
You shouldn't be surprised too hear that you're minutes away from the second encounter with the Scarecrow. Before you meet him you'll have a chance to look around. Keep heading forward and enjoy weird occurrences along the way. You'll even be playing as young Bruce Wayne for a while. You won't have to do anything in particular while moving as a boy. Just remain in the same place and listen to dialogues.
Once you've been returned to Batman's body proceed towards a dark alley located directly in front of you and then open the left door. Start off by moving forward and performing a single jump. When you get to a new platform turn right and use the stairs to get to an upper floor.