Are we absolutely certain that Missy is the Master?
Maybe Donna regenerated?
A Template of the Master was forced onto every human being in the world except Donna (and Wilf?), just because Donna had the precautions installed to ignore the "upgrade" it doesn't mean that she didn't keep a copy of his "brain" on file for later use, or that she was forced to stick the Master's Psyche into her trash folder like everyone else had.
Maybe Donna regenerated?
A Template of the Master was forced onto every human being in the world except Donna (and Wilf?), just because Donna had the precautions installed to ignore the "upgrade" it doesn't mean that she didn't keep a copy of his "brain" on file for later use, or that she was forced to stick the Master's Psyche into her trash folder like everyone else had.