Uhmmm....
Something happened to cause the emergency brakes to activate.
Either someone accessing a manual over ride, or the on board control panel figured it was time to do so.
The part in the story, where the cell phone is used to call 911, seems really out of place, or is just some trivial fluff for no apparent reason, judging from the answer I received above.
On another subject...
No one inside the driver's cart would willingly let anyone in who is not part of the train staff. They would also not leave it unlocked accidentally to avoid someone breaking in.
The door to the driver's cart requires a conductor's key to enter.
The person who had murdered the three people inside did not have any key on him.
At least 1 death occurred in the driver's cart while the door was completely closed.
The weapon used to kill the three people inside is not something you would find 'conventional' (i.e. - not a knife or a gun).
The culprit never opened any roof panel.
I know that now I just need to put the picture together. The solution is right at my fingertips.
The author alludes that this is a train similar to the ones run by AmTrack, on the west coast of the United States. These are all powered by diesel-electrics. So that rules out carbon monoxide poisoning.
The conductor was killed / murdered first, and the next two victims could not have succumbed to poison gas so quickly - unless it is some kind of nerve agent.
Since broken glass was strewn about the cockpit, I'm guessing some at some kind of implosion / concussion device.