Amuro had no intent on killing Shiho, on the train he intend to have Shiho taken to safety by the secret police(he mentioned "my partner", so he could be referring to his secret police associates instead of BO associates). Conan also mentioned how he made no move to kill Shiho on the train(File 893_page4).bluekaitou1412 wrote:
Things I'm currently mulling over:
- Elena was good to Amuro in the past
- Yet he was so intent on killing Shiho
The one who planted the bombs and intended to kill Shiho is Vermouth.