The master is probably in a lead fridge waiting it out. Their best bet was configuring the bomb for maximum yield and doing an air blast when flying over manhattan 2 episodes ago. Most of the bombs power would be absorbed by the ground.

Am I the only one thinking that the master and henchmen could have just gone down into a bunker and wait for our heros to set off the nuke and die. Hell they could have opened all bridges to speed up the process! Or just fly somewhere else. Or take a nap in a lead lined fridge:-) After all they have plenty of warning…