On this page of our game guide to Batman: Arkham Knight you can find a description which explains how to infiltrate the second airship. Our walkthrough provides solutions to all riddles. Also, we provide some hints on how to get rid of your opponents.
You can now go to the main laboratory exit, because the fingerprints you acquired let you unlock the door without any problem. Hear a conversation with Alfred and use the Remote Hacking Device to hack into the nearby terminal (the password is LIPIDS).
In the adjacent room there is a group of opponents. What is new in this fight, is the fact that some enemies get into an electrified state and attacking them the usual way can hurt you. To prevent that you should attack them with the Batclaw or wait until they get back to their normal state. Regardless of how you do that, try to eliminate the two medics as soon as possible, because they can charge up their allies.
After the fight a conversation with Lucius Fox starts, in which you will be able to select another Batmobile upgrade. The available options depend on the previous decisions in this area. A new available upgrade is the EMP charge that lets you temporarily immobilize enemy machines and destroy incoming missiles.
Hack into the side terminal again (the one with the password NUCLEICACIDS). Turn toward the glass wall on the nearby airship. Since you do not have to worry about the defense turrets any more, you can freely glide there.