When you're ready, head to the source of the seismic activity. After the cutscene, help Poison Ivy repel the militia forces deployed to destroy her. Eliminate the first wave of enemies and the Arkham Knight will send a battalion of Cobra Tanks. Like before, you have to sneak behind these until you get a lock-on and destroy them instantly.
Once clear, go to Poison Ivy's location and talk to her. After the cutscene, you'll have to find Stagg in the airship and find question him about a way to defeat the Cloudburst Tank.
After reaching the airship, defeat the militia guards posted in the destroyed tip of the airship. After clearing them up, you have to manually synthesize his voice print in order to access the locked up doors in the airship.
After successfully synthesizing his voice, continue inside the airship. You have to deal the militia inside too before moving forth. Once you cleared the lab, head to Stagg's cage and enter Detective Mode to follow his fingerprint trail. Once you find him under the floor, pull him out to get a Nimbus Cell.
Now you can leave the airship and find a way to repair the Batmobile. Head back to the marked location and press to dive to the toxic cloud. You have to carefully remove the Batmobile's power core and replace one of its cells with the Nimbus. A rioter will attack you so you have to counter it quickly. Now carefully return the power drive back to the Batmobile and wait until Batman crawls inside the Batmobile. Now, head to Founder's Island and trace the root which is located under the Divinity Church.
Since the Batmobile's sonar is can't reach the root's core, you have to head to Port Adams next to find an alternate way to go underground. Defeat the militia drones here to continue with your objective.