Unsaved Train

Even though I really liked it, the problem lies in Colter saving the train passengers as not doing so would solve the riddle of 'what about Sean's friends, families and Colter's future mission's from Beleaguered Castle?'. Via the program, Colter's consciousness was able to put all of of his know-how's into action inside of Sean's body to seek out the bomb and bomber in his allotted time. I can only assume that Sean's consciousness was not around because everyone was already dead.