The plot was very complex and involved the guy from the Wild Wild West movie as Leroy's arch nemesis building a city under LeChance, stealing resources (people, trains) and creating robotic creatures (the spiders were escapees) as lab experiments to create robotic people (think cybermen) and taking over Lechance.
The warm water, basements, forge, etc., were from the underground city's furnaces. The odd whistling and mechanical noises were when Bad Guy stole the train (and people) for his own use. The fissure was a way to get into the bad guy's lair.