I cried so hard at that scene. When he was leaving, something just didn't feel right. Maybe they were trying to hint at it. I don't know but the scene where they pull the plug was heartbreaking.
At this time Amelia wasn't shadow Shepard yet... In this case they were referring to the nurosurgan who was head of neurology before Derek(Jim Nelson), after Derek came he was called shadow Shepard because he was always in shepherds shadow.