For the first part, you have to keep pressing X or just tilt the left stick to incinerate Joker's corpse. (Or if you're curious, you can pause the inciderantion and check out his partially burned face.
After a few scenes, you'll be in control of Officer Owen. Walk towards the corner booth and talk to the smoking customer. During this nightmare sequence, just pull the trigger and the cutscene will end.
You'll now be able to control Batman. You have to meet Commissioner Gordon on the rooftop of the GCPD. You can glide towards the target and use your grappling hook to gain height again and glide once more. Continue doing this until you reach the rooftop.
After the cutscene, Batman will contact Oracle and ask for the location of the missing officer. Once you've reached the area, engage the thugs and defeat them. Talk to the police officer to rescue him.
After the scene, press L1 to "even the odds". Once you're inside the Batmobile, pursue the military vehicle. One of the thugs will be firing RPGs on you but you don't have to worry about it. Keep following the vehicle and fire your immobilizer rounds until you're able to shut them down. Once the vehicle is totaled, exit the Batmobile and interrogate the driver.