Once the giant tree has been woken up, you have to defend it against an army of drones. Ivy will help you but she can only target enemies in the church's courtyard. Try to bring the fight there but remember to move around to avoid getting surrounded. Once done, you have to face off Arkham Knight and his Cloudburst tank.
The cloudburst tank is surrounded by Cobra Tanks. If you haven't purchased some of the high-tier Batmobile weapon upgrades, it's a good idea to do so now. First, take out the Cobra Tank escorts.
Next, you have to do a hit-and-run to disable coolants first in the four sides of the tank. Don't get too close or the tank will detect you. Like the cobra tanks, you have to get near and get a clean lock-on to successfully destroy the coolant. Everytime the tank detects you, you have to exit Battle Mode and do your best to lose the tank's detection, even if it means going through tight alleys and corners. Repeat the
process until the tank overheats after destroying all marked targets.
Now the weakpoint of the tank will be revealed. You can go head-to-head against the tank now but you have to strike on the weakpoint in order to deal damage. You also have to keep firing your vulcan cannon to get rid of the homing missiles and you have to be careful of the area damage the tank can cause from its main armament.
After the cutscene and pummeling the Knight, you have to check on Ivy next. Head to her location to investigate. Once the cutscene is over, the city will be cleared of the toxin and more AR Challenges will become available. You also have to head to GCPD to continue with the story. If you have more unfinished missions, new intel will be available for them.
When you're ready, return to GCPD and talk to Sgt McAllister in the Communications room. Next, head to the evidence room to get another gadget: the REC (Remote Electrical Charge) device. Leave GCPD and head to the marked location.