There was also some weirdness that came out during the Colin Baker period about The Valeyard, who prosecuted The Seventh Doctor at the Time Lords' Court.

http://www.gallifreyone.com/episode.php?id=7c2

...so we have this business of incarnations being "transferable" PLUS the possibility of The Valeyard also being one of the Doctor's incarnations.

This brings up the possibility of The Valeyard re-emerging as a villain to replace the departed Master (...do any of us really believe that the Master is gone?...).

But, when you're dealing with Time and Space, anything is possible.

Best

AA