What if the Body of Missy is actually The Doctors real next regeneration. What if somehow The Master switched bodies with him during his Regeneration, ie the sudden abrupt Regeneration rather than the usual energy stream. That might be a reason for The Darker Doctor, some Master residue left behind there. Something isnt right with the switch which is why The Master needs the Doctor to complete the Switch, hence the clips of Missy seemingly opening her eyes with a start, is that The Doctor fighting to come back through.. Maybe Peter Capaldi was really only there for the year and Michelle Gomez is The Doctor.......Just thought id throw that out there for a laugh 
