The train is going deep underground to a secret tunnel where Mahogany's (Vinnie Jones) victims are eaten by humanoid creatures, the Fathers of the City, which is why no-one ever finds them. Detective Lynn Hadley (Barbara Eve Harris) is in on the secret. Jurgis (Roger Bart) is brought to the train to be eaten, and Maya, who went aboard to find out the truth, is eventually killed by the driver after trying to fight off Mahogany along with Leon (Bradley Cooper), who came aboard the train from the secret platform close to the slaughterhouse, also wearing butchering equipment.
Leon kills Mahogany, and becomes the next butcher. The train driver rips out Leon's tongue and eats it, and tells him that he envies him, and that he will serve "as we all do, without question". Hadley later sees him off from Mahogany's, now Leon's, apartment.
The film ends with a reprise of the opening sequence, in which the killer wasn't Mahogany after all, but Leon instead.