Jump back into the compound and you'll see Batman mention about improvising, so make your own entrance by blasting the wall with the 60mm Cannon. With that done, go back up to the crane controls and move the ramp to where you can use it to jump into the hole you just created. Once you've done that, take out the two Diamondbacks right around the corner, then grapple up and over the first large gate.
There will be two armed guards here, who are being watched over by a sentry gun, so you'll need to find a way to quickly take out the guards without becoming a piece of Swiss cheese. On either side on the walls are two vent openings that you can grapple to if you hold the button down, which will put you underneath those very same guards. Monitor the turret and when it sweeps past the guards' line of sight, use a Fear Multi-Takedown to put the guards to sleep, then jump down into the grates, then back up once more when the coast is clear to destroy the turret.
Find the fuse box nearby and use it to open the gates, letting you drive your Batmobile further into the plant, where you will meet another gate. The bad news is that there are a total of 20 unarmed thugs on the other side, with two of those being Medics. This fight can be a pain, especially if playing on Hard, as you need to watch out for double counters, enemies throwing objects and it's possible that the Medics can revive some foes to have you defeat another six of them.
One good tactic to use is to get on the ledge before dropping down and hitting the fire extinguisher with a Batarang, which will cause some enemies to gather just below you, allowing you to perform a Fear Multi-Takedown, hopefully with two of the targets you get being the Medics. Whatever method you choose, use the fuse box to open the next set of gates and drive to the final one. To get over this one, you'll have to eject from the Batmobile and glide over the spikes on the edge.
Welcome to the final area, which is now a predator section against eight armed enemies. They may appear to be split into sections, but they are connected, so you will want to always return to the top of the room after taking down a guard. After defeating all of them, it's a good idea to go around and destroy the sentry guns, just as a precaution. Find the door into the central chamber and enter it to find Scarecrow.
Welp, it looks like the crap has just hit the fan. Seeing as how you're locked in this room, go to the central computer and begin creating a neutralizing agent. This will make four cylinders pop up on the one side of the room, and as Batman mentions, they are highly volatile and require you to move them very slowly. This means that it has to be removed slowly, carried slowly to the four receptacles, and pushed in slowly as well. Do this for the first three and after removing the final one, an old friend shows up...
It looks like you're in control of Commissioner Gordon, so walk down the stairs and to the elevator, only to have no luck when you try to use it. When it finally opens, go inside and take the elevator down to find some kind of containment cells. Go up to each one to reveal who's inside, then walk around until Batman decides to appear. Back in the present day, use the remote to switch to the Batmobile and use the winch to create an opening. Hop into the Batmobile and get out as fast as you can, which will finally end this mission.
