Head to the GCPD and talk to Gordon. You now have to escort his vehicle to the Clock Tower. Shortly after leaving the GCPD, militia vehicles will pursue Gordon. Follow them and take out the pursuers.
Once done, Gordon will enter your Batmobile. Now head to the Clocktower and defeat all the tank drones guarding the roads. After reaching the Clock Tower, get to the rooftop. However, you need to defeat the guards there first before you can safely enter it.
Stalk the guards and defeat them all. Once done, enter the Clock Tower. Watch the scene and just look around as the hallucination remains strong. Look around until you can see the wheelchair on the floor. Pick it up to start the cutscene.
After the scene, access the Batcomputer's interface. Review the CCTV videos. Select the video in the upper right-hand corner and rewind it. You should see the Arkham Knight and Barbara being carried by one of the militia soldiers. Select that cell to scan it. Then forward the footage and scan the vehicle where Barbara was taken to update your objective.
Shutdown the Batcomputer and leave the Clocktower. Enter the Batmobile and park it on the highlighted space. Use the vehicle's Forensics Scanner to track the route of the militia vehicle. Keep following the tracks and you'll eventually see a militia aircraft plant a bomb on the road. Leave the Batmobile and investigate it on foot.
After talking to Alfred, you'll learn about the tank drones sent to stop you. You have to defend the spot until the virus is successfully uploaded. Once done, use the Batmobile's power winch to pull the bomb and trigger a controlled explosion. This will unlock the "Campaign for Disarmament" mission.
Continue following the tracks until you reach the bridge. Now you have to explore the next island on foot to find the militia access point. Once there, you have to take out all the guards and access their computer. Once done, head back to the bridge and get in the Batmobile.
There's a large drone force on the bridge, including ones that fires homing missiles. Take out the smaller ones first then destory the missiles fired towards you with your vulcan cannon. Once done, resume following the tracks using the Batmobile's forensic scanner.