MOST WANTED: The Perfect Crime
Objective: Find and stop the killer displaying bodies throughout Gotham
Head for the marked location, and you will be able to hear the music. Across the street is another rooftop where the body is. If the opera music is still playing and getting louder, you are heading in the right direction. When you are close enough, some icons will appear on the screen and Batman will talk to Alfred. Use your Deep Tissue Scanner to scan the different levels (skin, muscle and bones) of the body to find three unique attributes to identify them (one on each level).
Skin: Deformed ear
Muscle: Ring in intestines
Bone: Hip replacement
Skin: Scar tissue on arm
Muscle: Pacemaker remnants in chest
Bone: Bone deformation on knee
Skin: Birthmark on chest
Muscle: Bullet in arm
Bone: Missing toes
Skin: Chemical burn on leg
Muscle: Voice box in throat
Bone: Sixth finger on hand
Skin: Tattoo removal marks on leg
Muscle: Missing kidney
Bone: Titanium plate in skull
Skin: Shark bite mark on side of chest
Muscle: Fake eye
Bone: Titanium pins and bone in arm
Objective: Investigate Pretty Dolls Parlor
Note: This quest may be bugged in your playthrough. It is still able to be completed, but read the italic text below.
Squeal your way along the streets or glide across the darkened skies towards the marked building. There will be some bad singing. Very Bad. Bear with it. And prepare for a slightly different fight. These enemies will not stay down until specifically taken out (using ground smash or other takedown methods). So use some special attacks and take them out as soon as you can. Gel and Batarangs can give you the time you need to complete the takedown, hopefully knocking back the dolls around them.
When the boss joins the fight, he will stay on the opposite side of the table (Bat Punch the table anyone?) and occasionally throw knives at you. These can be countered (you must counter all three or move far enough away to avoid damage), but Batman will probably be already in another animation as the Boss throws the knives fast and without warning. When countering the knives, Batman will deflect until there is only one left, only the last will be thrown back as a counter. If you succeed in countering and throwing a knife back, he will be stunned for several seconds, giving you just enough time to take out another of his minions without interruption.
Despite stunning him, he will still be able to avoid your attacks be circling the table in the center of the room. When all his minions are defeated, wait for the knives to stun him, walk up to the table (from the broad side), and use the prompt buttons to take him out. If you don't do this while he is stunned, he will take a few swipes at you. If your version is bugged, you may not get the prompt come up (instead displaying the quick fire explosive gel command). So when you approach the table, it will glow blue, press X and A together (Xbox) or Square and X (Playstation) to trigger the takedown despite the missing prompt.
Objective: Return Professor Pyg to the GCPD Lockup
After the battle ends, approach the fuse box on the wall and interact with it to rescue the prisoners overhead. Pick up the unconscious Professor Pyg and then leave the building. Hop back in the Batmobile and deliver the Professor to the GCPD lockup. Another one bites the dust.