In episode 10 Allison and Wil see someone with a mask on pushing one of the conductors off of the train, Allison gives chase but loses him when the train goes through a tunnel.
Allison and Wil told the other conductors about the incident along with Ker and Major Stork (Who seems to be the one who shot Allison's father) and they deduct with some persuasion that the richest man on board (can't remeraber his name) is the one being targeted so they detach the passenger carts from the train leaving them behind and go for help with only Allison, Wil, Ker, Major Stork, Fi, Rich dude and his bodyguard left on board, then a military train begins to give chase and fires upon them after Stork fired first.
I like the constant adventure in this series, its a great show.