Cooling Tunnel B
As soon as you enter you'll overhear three enemies chatting. Use the Freeze Blast to freeze the first thug in place and knock him out, then deal with the other two thugs. Drop down to the platform below, and double-tap RT/R2 to throw a Freeze Blast grenade and make a sturdy platform. In order to move the platform, you need to use the Batclaw to pull yourself towards latch-able rings. Latch onto the ring to your left, then duck, and make your way towards the platform on the right. You should be facing more sewage with a large saw-like cylinder in the middle. Make another Freeze platform and use the Batclaw on the rings to the left or right to move around the cylinder. Use the Grapnel to reach the next platform, then go through the vent on your left.
Enter the next fight by moving over to the left side, so you are across from the window, then glide kick through the window to take out one of the thugs. You'll be facing five regular thugs and an armoured thug, all with access to a weapons locker. Keep the thugs away from the locker and you should be fine. Continue through the door on the left of where you came in, or stick around to listen to a funny message from the Joker: it's your choice.
Cooling Tunnel D
You'll see an armoured thug and a regular thug, both in Joker's employ, torturing a thug employed by Two-Face. Take out the regular thug then Beat Down the armoured thug for some easy experience points. If you try to free the Two-Face thug, he will remain neutral until your back is turned, at which point he will attack. Detonate the wall to the left of the acid bath with Explosive Gel and drop a Freeze Grenade down into the sewage. Head right, moving around the cylinder and underneath the ring in the back. Look to your right for a hard-to-see platform, and use the Line Launcher to get over to it, because the current from the water will be too strong to get the platform over.
Oracle will bring more bad news from City Hall; use the Line Launcher to get around here. Use the Freeze Blast to block the steaming pipe, then slide under it and do the same thing to a second pipe. Once Hugo Strange starts giving a broadcast, look to your left and you'll see a platform. Save yourself a lot of trouble and use the Line Launcher to get over there instead of a Freeze Grenade.
You'll then need to use your Remote Controlled Batarang to power the switch you can see to your left. You need to pass the Batarang through the electrical current in front of you, then make a U-turn and go through the small gap to the right of Batman and hit the switch, which will open the door in front of you. Throw a Freeze grenade down, and step onto the platform. Move forward until you see a platform above you on your right, and Grapnel up to it. Use the Cryptographic Sequencer on the console there to lower the bridge behind you. Cross the bridge and turn right to trigger a cutscene, then head through the door.
You have another Predator section ahead. Some of the guards here are armed with proximity mines, which will detonate when you get close to them.
Walk forward, then left, and immediately take down the guard walking carefree ahead of you. The fastest way to get the guards to split up is to use a loud Knockout Smash on the first guard to get their attention. You can then take everyone out one by one, avoiding the mines (you'll get an optional upgrade for the Disruptor to deactivate mines later). You can also take out guards who are standing on or near mines, since the mines don't detonate when they step on them. Take out the rest of the guards as you see fit. When everyone's down, exit through the old battery-powered shutter on the far side of the room, heading back towards the Loading Bay.
The next room has a sniper and a room full of mines. Use the Firearm Disruptor to neutralize the sniper and try to avoid the mines, exiting out the door on the other side. Head up to the left of the sniper and you'll find Harley Quinn, bound and gagged. You can't help her. Move past her and down, into the Loading Bay.
Just keep running forward and open the door. You'll see two snipers on the elevated platform, so use your Firearm Disruptor on them while you deal with the three regular thugs to the right of the other door. Zip up to the snipers, take them out, and follow the green arrows to the door on your left.
BOSS FIGHT: The Joker
Beat up the Joker a bit, until he pretends to surrender, at which point he'll summon some more goons. The first wave has you fighting regular goons, and one goon with a knife. Eventually, Mr. Hammer will join the fight, and then a Titan. In addition, trains will occasionally run through the map, knocking you and any thugs in the way over. This is a purely skill-based fight: if you've made it this far, now's the opportunity to show off your combat skills. Just keep your combo, use every move at your disposal and, when the Titan arrives, focus on Stunning him and using his attacks to knock out the other thugs.