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I think the doctor dies and doesn't after 12.. Basically what I am saying is once the doctor dies for the the 13th regeneration it is a new doctor in the sense he does not remember anything previously. He will be completely clueless in the sense he does not remember past enemies or companions.
It will allow them to reboot him for another 12.. In doing this, if he does come across past companions he will have no idea about them, and they can clue him in on his past that he is trying to remember.
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