ok I have collected the spores..and gottgen away from croK....but what do i do now....where do I go...(also forgot how to get into the batcave)......the map doesn't have any exclamation mark on it for me to go to.....the objective says"stop Joker from polluting gotham river".....help anyone plZ
Go back through the sewers, similar to to the way you first got to the batcave, it will lead you there. Then once you're in the cave and have created the antidote, a custscene will appear. Walk down to the main platform and turn left, using detective mode there should be a breakable wall. Kick down a box so you can move, then use your ultra grapple on the breakable wall and pull it down. Then you can progress to the next area.
I just got stuck after that quest. I beat up the goon, got up the elevator and the quest just stuck and not progressing, the island is now empty (as well as all the mutated trees roots) and there is an invisible thing block my way to the garden (try the tunnel right next to it also get block) so I gave up.