I purposefully left it indeterminate so readers could fill in the blanks with their own theories. But broadly it represents a full, immediate and uncontrolled comprehension of recursive, fractal infinity. The pattern of relationships between all things at every scale, microcosm and macrocosm. 

More specifically to the story I like to think they were never human, but always those creatures dreaming they were humans, shutting out the awful truth using the dome which represents brainwashing / compartmentalization. Although I am not dead-set on this interpretation and have written other stories in this setting which contradict it. 

Incidentally this story was inspired by the following two songs: