On this page of our game guide to Batman: Arkham Knight we explain how to use the Nimbus Power Cell to repair the Batmobile.
Head back to the front of the airship where you previously dealt with a group of opponents. When you get there, you will find out that the place is being patrolled by an enemy drone. Use the Remote Hacking Device to temporarily blind the flying machine and leave the airship. Head back to Miagani Island, where you left the Batmobile. Get to the roof marked on the map and let Batman jump into the poisonous cloud.
Start SLOWLY removing the damaged battery from the Batmobile and be ready to counter an opponent who will try to interrupt Batman. When you successfully remove the battery, insert the new one, also very carefully. Wait until Batman gets inside the Batmobile.