MISSION 15 - The Cloudburst
Objective: Equip a new secondary weapon for the Batmobile at the facility near Merchant Bridge
Now that the Joker infected are under control, you can leave the building and walk out of the VIP entrance on to the rooftop. Skydive off the edge of the roof and start working your way across the city skyline towards the new marker. Hop in the Batmobile and park it on the glowing square to open the garage door, allowing you access. Drive inside to obtain the upgrade you selected in the earlier story mission.
Note: New Most Wanted: Friend in need mission chain unlocks here
Objective: Investigate the seismic activity on Miagani Island
Once the upgrade is complete, slam down the accelerator and rocket out of the garage. Tear through the streets towards the marker on Miagani Island. As you cross over the bridge, you will likely run into the Arkham Knight's forces on the streets. The main nuisance is the new flying drones/ helicopters that fire targeted missiles at you. Use the vulcan gun to destroy the incoming missiles and then blast them away.
Keep racing through the streets until you reach the rectangular marker at the end of the trail. When you arrive, you'll have a quick chat with Alfred before watching Poison Ivy's plant demolish several of the Arkham Knight's drones. After the inevitable call for backup by the Arkham Knight, it looks like you'll have to work together with Ivy to keep her plant safe.
Main Objective: Work with Poison Ivy to defeat the militia forces attacking the Botanical Gardens
A few seconds later, you'll see by the counter that 24 various drones are incoming. Enter battle mode and position yourself near the Botanical Gardens. Doing this will allow you to receive support from Ivy during the fight (she will occasionally take down drones near you). By now you will likely have the drone hack secondary ability which can be quite useful in dealing with large numbers of enemies as it gives them more targets to spread their firepower on. Of course, the regular missile barrage is also good for just taking down enemies quickly as well.
Use whichever secondary attacks you can as you duck and weave amongst the predictive missile lines. As long as you stay near the gardens, you shouldn't have too many issues with Ivy tearing drones apart. Keep on the move, time your shots and stay close to emerge victorious.
Seconds after the first wave ends, you'll be confronted with five Cobra tanks. Yep, the ones you have to shoot in the exhaust pipe. Unlike previous encounters, the Cobra tanks here tend to be fairly close together which makes them much more difficult to bring down.
You'll need to be very cautious as you sneak up on them from behind as they like turning around at intersections suddenly. As their numbers thin, they will become easier to single out and destroy. The hardest part is taking down the first one or two. Use the small areas between buildings and shortcuts as hiding places before emerging behind them and blasting them after the lock-on is done.
Objective: Pick up Poison Ivy and return her to GCPD
Now that the mechanical nightmares are gone, you'll need to return to the Botanical Gardens to collect Ivy. When you get close to the gardens, you'll need to get out of the Batmobile (if you aren't already) and grapple up over the walls. Drop down to the base of the gigantic tree and approach the marker for a prompt to appear. After pressing the button, watch the long scene play out. Things just went to hell in a handbag. Great.
Main Objective: Destroy the Arkham Knight's Cloudburst Tank
Objective: Interrogate Simon Stagg to find a way to defeat the Cloudburst Tank
When you regain control of Batman, you'll be on a rooftop far above the streets of the city. As you look down over the ocean of orange and brown gas covering Gotham, keep in mind that dropping down into it is a bad thing to do.
Looks like we need to revisit Stagg's airship to terrify him into telling us how to solve this problem. Traversing the city is now more difficult due to the clouds of gas below. You cannot use the Batmobile anymore so you will need to use your glide and flight abilities to cross over the gaseous death below.
When you get close to the airship, you'll spot a crane directly oposite the huge hole that scarecrow blew in the front of it. Grapple to the top of the crane and carefully glide across the gap to land amongst a group of six or seven enemies.
Immediately take down the medic if you can. The other main threat of the group is a bruiser with a shield, making him difficult to take down. You need to use the aerial attack (B + AA/ Circle + XX to bypass the shield and then tap X/ Square to begin beating him down like a normal bruiser. If you can take out the shielded bruiser early, the rest of the enemies are just regular militia who will fall in quick succession.
After the battle ends, walk up the stairs to the doorway at the top. When you reach the door, you'll see Stagg has upgraded the door to use voice commands instead of the ealier fingerprint scanner. This means you'll have to play the voice synthesizer minigame once again, using Stagg's voice instead of Harley Quinn's. Adjust the left column so the bar is just slightly below the top. Adjust the bottom one so the bar is about a quarter of the way along from the right side. Verify the voice print and use the synthesizer to open the door lock.
Open the fingerprint door beyond to reach the container where Stagg was last incarcerated. Seems like he managed to get out of the container, so we'll need to find him. First things first however, you'll want to introduce your fists to each of the eight enemies on the other side of the room. The duct system on the lower level works very well here for silent takedowns. You can also use the remote hacking tool to take control/ disable the pair of drones some of the militia use.
Don't forget you can use your disruptor gadget as well to disable enemy weapons before attacking. Basically if you use your gadgets correctly here, the enemies shouldn't even know you are there. One of the funniest strategies is setting up a conga line of takedowns, with each enemy investigating the unconscious enemy you just took down which you then immediately take down. After glomping the final enemy, return to the container that Stagg was imprisoned inside.
Objective: Track down Stagg using his fingerprint trail
After a quick animation, you will be prompted to enter detective mode. When you do, you'll see Stagg's handprints scattered all over the place. Follow the trail down the stairs to the lower level of the room, around the walls and even through one of the vents until you reach a floor panel you can interact with (not a duct cover). Wrench it aside to meet Stagg once more. Batman is so happy to see him again. After picking up the new power generator/ cell for the Batmobile, this mission will be over.