At first I thought it was Radon gas (a highly radioactive gas found in abundance deep underground, and yes I see the pun), now I doubt it,maybe Ink experimented with new mutations underground and the test subjects died, we know the dead Creatures put out that haze, and the cracks could've been caused if a tunnel collapsed, or if succesful experimentations (i.e Behemoths) could have broken through the tunnel ceilings to get above ground.