I would strongly recommend that you prevent Batman from losing any health points in this fight, because you're going to need those later on. Once you take care of the skeletons proceed to the next section. Keep heading to your right until you'll be forced to climb up to a higher platform.
Get ready for a challenging sprint. Wait for Scarecrow to begin turning around, climb up to a new platform and then immediately take cover behind a small brick wall located not far away. Once again you must wait for a right moment to make a move. You'll soon be forced to make a jump and to run a few meters before finding cover (screenshot #2).
Move to your right and wait for Scarecrow to complete yet another cycle. Continue moving forward, performing a new jump along the way. You'll also have to climb up to a higher platform. Once you're at the top start running right away, because you'll be allowed to use a large moving block for much needed cover (screenshot #2).
When you get to a hiding spot you'll have to prepare yourself for a new jump after which you'll climb up to an upper platform. When you're at the top immediately move to your right, taking cover behind a small brick wall. Eventually you'll have to make your way to a large elevator. Ignore the fact that the elevator will fall, because everything is advancing just like it should.
Naturally you'll have to return to the top, HOWEVER don't use your hook unless the boss has completed a new cycle. Once you're on a new platform move to your right. Eventually you should be able to locate a new spotlight, but sadly using it will end in a failure. Instead get ready for a new battle.
You'll end up standing inside a small arena. The first phase of this battle will require you to defeat a couple of skeletons. Just as before, prevent Batman from losing too much health by performing a lot of successful counterattacks.
The second phase will require you to take on a much larger skeleton. The monster will behave in a similar manner to other mutants encountered before, including Bane. It's going to be easier to injure the beast. All you have to do is to use the Batarang and avoid being hit and the skeleton will be destroyed when it'll crash into a wall.
The final third phase is by far the most difficult one. You'll have to fight several smaller skeletons and a bigger one at the same time. Use Batarangs and jumps to deal with the larger creature and then focus on the rest. Keep fighting until you're the only left standing. Doing this will allow you to defeat Scarecrow and Batman will return to Cell Block Transfer.
Once you've regained control over the main character proceed to the north and you'll end up standing in Secure Transit. Watch a short cut-scene showing the escape of the Scarecrow. Proceed down the shaft using the glide ability to avoid injuries. Turn on your detective mode when you've landed and locate enemy troops. You'll have to find them in order to proceed with the mission.
Focus on finding the stairs located near the area where you've landed. Use this new passageway and eventually you'll find the location of the inmates. Focus on eliminating the only thug armed with a gun and once he's been taken care of deal with his remaining colleagues. They shouldn't be a problem, because they won't be carrying any weapons.
Once the fighting has ended find a new control panel on one of the nearby walls and break the encryptions using your sequencer (three stages). You may head back to the main shaft. Notice a large hole. Jump over the railing and glide down to find yourself in a new area, next to enemy units.
Attack the inmates when you're ready. During the course of this battle you'll have to prevent your enemies from opening nearby gun lockers, because you would a lose of health to due to gunfire. If they do manage to pick up weapons punch them quickly to make them drop the guns. Once they're all neutralized find a nearby door (screenshot #2) leading to the Caves. You'll end up in an area marked as the Control Room Access.