The train. Have you seen "Spirited Away"?
It reminded me a lot of a scene in a Japanese animated film called "Spirited Away". If so, it's a nice homage to it, if not you'd be amazed at the parallels your animation has to it.
Your green guy looks and acts very similarly to the monster called No-face and there was a train that had black shadowy spirits on it very similar to your ones. The train ran on tracks that were submerged just under the surface of a lake. It was a very surreal part of the film.