The Turtles got rid of the problem so quickly that the military probably just turned around and went home well before it got there.
One reason I almost wish there was a third, just to make them fix this and make Krang an actual threat, etc. Leaving it off so weak is annoying.
Good point about Shredder. Although even if his helmet was in some way made to protect him, what about when he first met Krang? No one knew he was going to end up there or that some evil alien had its eyes set on Earth. Hm.
Mostly the atmosphere thing was a weak and unnecessary reason why it had to be the Turtles to save the day, as if a reason is even needed. I couldn't buy that though... Mutants or not, you're still otherwise typical Earthlings when it comes to things like breathing oxygen. Magic ability to survive in other atmospheres... also annoying.