Complete the puzzle in the flat chapter and reactivate B-12. To do so, find the four plugs in the lab room and insert them into the main terminal. Then head into the next room and find a box on a chelf with B-12 inside. launch it off the shelf and tehnnplace it on the main termina for the computer toupload itslef into the flying robot. As it becomes active you get the trophy as part of the main story.