When they attacked Achilles, Bean saw that he would be dangerous to them, and he advised Poke to kill Achilles.
Melanie reveals that she knew that Layton would have to sacrifice the prisoners, stating that such hard choices are what they have to live with for every second of their existence.
That's not it, for the most part.
With the help of Pike, Ruth leads the resistance in hiding.
Although Wilford repairs it, due to Melanie's modifications to the Engine, complications arise forcing Wilford to manually restart the Engine, revealing his presence to the train.
Bean is desgined to make you comfortable and feel at home.