Thanks for mentioning Vrook and the cage, I have been trying to figure out this issue for a long time.
I am using XBOX and here is how I was able to get around this issue.
#1 Go back to a previous save and verify after you kill the Mercenaires in the cave, if Vrook's cage is still intact.
#2 If so, load the game again and choose the conversations with the Mercenaires holding Vrook hostage. Choose the conversation dark path where you strengthen his cage and get 300 credits from the Mercenaires.
#3 Leave and go back to finalize the battle plan etc. You may see some new conversations with Azual, new mines around etc.
#4 Watch out, because after the cut scene battle that used to lock up, Vrook is standing in the government lobby there and he is not very happy and you must fight him.
#5 You can try to fight him, but I could not beat him, so i grabbed my group and left for another planet, with the hope I can come back to Dantoonie after leveling up to beat him.