The twist at the end of ‘Listen’ is that there never was a mysterious unknown race. Having spent too long travelling alone the Doctor invented monsters to explain his fear of the dark. It is probably important to note that this is only Clara’s theory and the Doctor never confirms this.
The Doctor might have come to the wrong conclusion but there are still some odd things here that could be the basis for further investigations or adventures.
The Doctor’s dream of a hand reaching out from under the bed is eventually revealed to be due to Clara. He retains just enough memory of this incident and so linked it to the historical records of other people having the same dream.
Clara states that everyone has that dream and the Doctor wants to know why. This question is never answered. If only the Doctor’s dream has a source in reality why does everyone else experience the same thing?
One possible, but silly, answer is that it is Clara every time. We know that she was fragmented, spread throughout history. This was supposed to be so that she could save the Doctor at various points in his life and that sometimes she’d spend a whole lifetime in that period, so she’d be in the right place at the right time, or there only for brief moments.
If Clara’s potential future was already within her then brief fragments might have materialised, reaching out from under the bed. Once she’d carried out this act the fragment would vanish, leaving very confused people.
An important fact might be that these incidents occur throughout human history. It could be that the monster under the bed is being recalled from race memory. This means that that somewhere in humanities past this really did happen. Finding this could be the source of a new adventure.
Being half-human the Doctor might really have had the same dream. Thanks to time travel his relating this event to Clara and seeking its source leads to a closed time loop. In short he creates his own explanation.
Could it be that the Doctor is the source of the nightmares? We know that he is mildly telepathic and the TARDIS has shown it is able to interact with minds around it. What if the Doctor was spreading his nightmare to every time period that he travels to? This would explain why it happens throughout history.
The nightmare might still be part of a race memory, if the Doctor is some how the progenitor of the human race. Humanity could literally be his children, which would explain his affection and protectiveness of them. This could be something that occurred in the youthful past of his 1st incarnation or something that will happen later.
While this could come about the old fashioned way ‘Evolution of the Daleks’ indicates it is possible for the Doctor to share his Time Lord DNA with humans. It is therefore not much of a leap to think he could share his Human DNA with primitive man, perhaps ensuring that humanity would develop as time demanded.
Giving how advanced Time Lords are is it possible that the Doctor is responsible for creating humans? Could they be some form of Matrix simulation brought into reality or an extension of the Land of Fiction? The Doctor might have used himself as a template for their design, explaining why they look Gallifreyan and share his nightmare.
If the Doctor is responsible for creating Earth then it would be a perfect place for him to hide from his people. They’d have no record of it and there would plenty for him to explore. It would also mean that everything humanity does is a direct result of his actions.
The other angle to explore, since there wasn’t a monster, is who wrote the message ‘Listen’ in the TARDIS? Clara’s theory is that the Doctor wrote it and forgot about it, which she indicates is not out of character for him. If this is true it is worrying.
‘Deep Breath’ had the Doctor postulating that his new face was a way for his mind to send him a message. ‘Beast Below’ similarly indicated that sometimes his mind moves so quickly he has trouble keeping up and understanding his own actions.
All this indicates that while there is a surface personality there is something deeper going on. A core Doctor who makes connections, carrying out plans and performing actions without the surface personality knowing.
This could explain why each incarnation of the Doctor seems more and more absent-minded. The core barely needs to keep the surface personality aware of what is happening. It is only the companions presence, questioning what is happening, that requires the information to be filtered to the surface personality.
When the Doctor is alone this personality could sleep. This might explain several times in which the Doctor is unaware of how much time has passed since he has last saw his companion. The only explanation he can give is that he was ‘distracted’.
‘Into the Dalek’ gives further evidence that the 12th Doctor is not always aware of what is reality and what is fantasy. He introduces Colonel Morgan Blue as Journey Blue’s uncle but can’t remember if that is something that he just made up.
The impression given is that the 12th Doctor is just try to make sense of what is happening. His core mind ensures that he is doing what is needed and is processing what is happening but the personality just floats on the periphery.
This would explain why the Doctor doesn’t plan much or at least can’t explain what his plan is. He can only say that he’ll do something very clever. This is because he is dimly aware that his mind is doing all the hard work, requiring little input from ‘him’.
If this process does continue to escalate or the Doctor spends extended periods alone would his personality shutdown altogether? Could subsequent incarnations just be mute drones saving the universe using a mind far in advance of any other life form but with no discernable personality?