MISSION 21 - Confront Scarecrow
As the mission begins, you'll be walking side by side with Gordon after releasing him. Walk and talk with the commissioner until you reach the elevator and thugs begin spewing out of it. Four regular militia and an electrified bruiser will face off against you here. Don't forget the REC gun quickfire (LT + B/ Circle) to disable the bruiser's electricity, allowing you to perform a beatdown on him. The regular grunts shouldn't pose an issue after the bruiser is dealt with.
Once the bodies hit the floor, return to the elevator and Gordon. Hit the switch on the wall and begin making your way to the top floor of the headquarters. Villains always use the top floor, never some random floor in the middle where they won't be found. You'll share a few words with Gordon as the lift rises through the building. As the doors open on the top floor, you'll walk out of the lift to see Scarecrow looking out over the city.
Watch the long scene play out with Batman, Gordon and Scarecrow until you regain control on the ground.
Objective: Protect ###### (spoilers)
After being under fire for a few seconds, a quick scene will show Batman taking delivery of a new Batmobile. You'll immediately take remote control of the car when it arrives and be able to engage the twenty-four drones surrounding your position. The Batmobile will also come with a full charge of it's missile barrage, allowing you to take out up to ten enemies with a single attack, not too shabby. Try it out straight away as the cluster of drones is just begging to be hit by it.
More diamondbacks, twin rattlers and rattlers will roll in to join the fight as well as missile launchers. As usual the good old strategy of keep moving, gunning down missiles with the Vulcan Gun and aiming for turrets with your cannon will see you through.
Just remember to make use of the missile barrage to make life easier for yourself. Note that you can only move a certain distance from Batman's position before moving out of range (making it hard to see). After the tank carnage ends, walk over to the Batmobile and interact with it before jumping into the driver's seat.
Objective: Take ###### to GCPD
Wind your way through the streets as you talk with your passenger. Drive the fairly short distance to the lockup and circle down to the parking lot underneath to drop off your passenger. A fairly long scene will play out here, resulting in you finding out that Scarecrow's men have infiltrated the server room at the Clock Tower and are destroying it. Looks like it back to the Batmobile and then to the Clock Tower to stop them.
Objective: Stop Scarecrow's militia from destroying Oracle's servers
Back to the parking lot and burn rubber across the island until you reach the marked location. Park your ride, hop out and use your detective vision to examine the Clock Tower. You'll see a large number (twelve) of militia enemies spread out around the area. Your biggest immediate concern are the two snipers on top of the towers next to the building. These should be your first targets, grapple up behind them and sneak up on them for silent takedowns.
After that the idea is to basically just work your way downwards from the higher levels, silently taking down militia as you go. Use the environment to your advantage (using ducts, corners and fragile walls) to take down the swarm around the building. Just be careful dealing with the enemies around the sentry gun in front of the entrance, as it can deal nasty damage if you forget about it.
Once the area outside the Clock Tower is clear, enter the building from street level (I know, Batman not using the roof entrance for once. Shocking) to walk into the server rooms. Climb up the stairs inside to reach an office which the marker is pointing to in the corner. Use the console in the corner to secure the data and complete the mission.