Defeat all enemies then blast the boarded wall near the glass window. Activate the airship stability controls in the end of the room. Tilt the ship fully to the left then tilt it fully to the right until you hear a large crate breaking a glass door. Do it one more time to create a pathway for you.
Go through the broken doorway and turn left. There's a riddler trophy here behind the locked crate but just press and hold the UP DPAD to take note of its location and add it to your map.
Continue further to left where you can blast another wall. You'll find yet another Riddler Puzzle you need to solve to get the trophy.First, move all crates to the left. Get inside one of the open cages then grapple through the grate above.
Now move all the crates to the left and lock the rightmost crate. Tilt the ship to the right this time to remove the crate obstructing the way. Enter the grate and collect the trophy in the bottom.
Backtrack to the main path and continue forth. You can access Stagg's research notes from the computer terminals along the way. There's another Riddler Trophy behind a cell along the way. Ignore it for now and continue forth. In the end of the corridor, you'll find yet another access terminal. Use Stagg's handprint to gain access and open the cell behind you containing the Riddler Trophy. Backtrack and collect it.
Now continue to the next large room. There's a lot of guards in this place, including a mini-gunner Brute. Batman will advise to save the brute for last since taking him down will attract a lot of attention. Get up in a vantage point and plan your approaches. It will be helpful to lay down some explosive gels on the main pathways and also taking out the guards out of sight. Take note that if the enemies notice that their numbers are dropping, they'll be more alert and will search in pairs. Use your RHD to trigger some the hackable gadgets.
Better yet, use your Disruptor to disable their guns, especially the mini-gun. It will help you'll put the explosive gels near the bodies so you can detonate them and disable whoever checks them out. Prioritize taking out the roving guards as well especially if you want to keep a low profile.
Once you have left the mini-gunner alone, keep striking him and use counter-attacks to evade his attacks. Keep pummeling him until you knock him out. Once done, you're free to explore the area. There are more Riddler Trophies here that we can collect.
One of the trophies is placed near your starting point. Hack the console with your RHD to reveal the monkey cages inside. Now hit the dot on the question mark again with your batarang to operate the pressure pads and guide the monkeys there to get the trophy.
Another trophy requires placing two more chimps on the pressure pads. This is located under the cell where Stagg is hidden. Use the Batclaw to retrieve it.
There's another one on the lower deck that's located behind a voice-locked room. Press and Hold the UP DPAD to mark its location and leave it for now. Also, there's another trophy located in a boarded up room with three unpowered generators. Just mark their locations for now.
Once you're done, head to Stagg and talk to him. Head through the door and takedown one of the Scarecrows. When you have control, beatdown all the guards and keep beating them until you trigger another cutscene. Now you have to leave the airship and save Oracle. Head to the Scarecrow's hideout in Chinatown and go down to the chamber to watch a cutscene.