The gas bombs were fired from Steel Behemoths made by the Fabrication Machine. When the Machine turned on humanity, it used this toxic gas to kill everything and end the human race. During the war with humans, it shows a scene where gas bombs are fired, and wilts and kills some flowers as soon as it releases the toxic fumes. It would kill anything the second it touched it. When 5 is running, he is hit on the back of his head with one of the bombs, losing his eye. The bombs are the main reason that the Fabrication Machine was able to destroy humanity. Not only was it killing humans, but in the process, it also killed off all life.