"I don't want to endanger anyone on the train by setting him against us. So far he's been working in the same direction as us on board." And that's... a strange situation, but they have enough problems so she prefers it to the alternative.

"Better to have the train neutralize him as part of the mission preparation. It might see a problem with having two of him in the same world anyway." Really, it would just be smart to have the train do it.