10 Unanswered Doctor Who Mysteries
1. How Was Gallifrey Unfrozen?
There are many mysteries related to the Doctor's home planet that have yet to be answered, including the manner in which the Master managed to destroy Gallifrey. While the planet was apparently destroyed by the Doctor in his efforts to end the Time War, we see the Doctor in fact save his home planet at the end of the 50th anniversary special, 'freezing it in a single moment'.
The planet however was revealed to be 'unfrozen' when the Master, who had apparently been sucked into Gallifrey when attacking head Timelord Rassilon, reappeared in female form. Under the new pseudonym of Missy, she revealed Gallifrey's location to the Doctor, although this initially appeared to be a lie.
The location of Gallifrey remained unclear until the Doctor broke out of a trap set for him by the Timelords in Heaven Sent. Capaldi's Doctor broke out of the trap and found himself on his home planet, with his people alive and well and very much 'unfrozen'.
Surprisingly there was no explanation of how the planet broke from its stagnant state, a mystery that could easily have been solved in a quick one liner. Show runner at the time Steven Moffatt stated that he had no intention of answering every mystery, and with the planet now destroyed it seems like it may remain unsolved.
One can only speculate that The Master had some involvement in the whole affair, although it is also a possibility that a future Doctor has yet to complete the task of unfreezing the planet.