Theory:Doctor Who television discontinuity and plot holes/The Time of the Doctor


 * Why was Clara fine after hanging on to the TARDIS in the vortex? Captain Jack died!
 * The Doctor specifically noted that the Tardis extended the shields to cover her. Given that it was trying to shake Jack off during his trip, while she's the one who saved the Tardis' Doctor throughout his whole timeline, it's understandable that she'd be treated differently.
 * How could the Doctor lie about having a plan at the end of the episode? --  Ransom Time 
 * Technically, he didn't say what kind of plan he had, or which situation it may pertain to. His comment about not having a plan to Clara was to clarify he didn't have a plan for what she thought he meant. Also, moments later he reminds Clara that they already supposedly saw what happens here, so they can't change it. It's likely that he did have a plan of sorts- to die. Or in contrast, perhaps his plan was to "talk very fast, hope something good happens, take the credit".
 * Or maybe his plan was to lie about having a plan.
 * The Doctor is on his last life, so why did the Teselector have to imitate his regeneration in The Impossible Astronaut, it would have been believable enough if he just died as he had no remaining regenerations.
 * Perhaps the doctor didn't realise he was on his last life until he realised that he had lived significantly longer than all his other incarnations and then put 2 and 2 together and came to the conclusion that 10 had used two regenerations, resulting in the eleventh doctor being the thirteenth incarnation.
 * Neither the War Doctor, whose adventures were mostly time locked, nor the aborted regeneration which created the MetaCrisis, were particularly widely known of. While it would have been historically accurate to show that incarnation dying without regenerating, the Doctor's goal was to create a plausible enough "final end" to preserve the fixed point in history of this being his recorded death.  Not depicting a failed attempt at regeneration would have led to doubt and a suspicion that he might well have survived in a new body, since historical record still showed him as the "Eleventh" at this point.
 * Why did he ask the TARDIS if he could regenerate after being poisoned in Let's Kill Hitler? Even though the poison prevents regeneration, he doesn't have any regenerations remaining anyway!
 * Perhaps the doctor didn't realise he was on his last life until he realised that he had lived significantly longer than all his other incarnations and then put 2 and 2 together and came to the conclusion that 10 had used two regenerations, resulting in the eleventh doctor being the thirteenth incarnation. This would also explain why the TARDIS says that regeneration is disabled.
 * The Doctor has claimed that he tried very hard to forget the War Doctor ever existed. Given how good he is at erasing memories, and that at the time he was poisoned, very sick, and quite possibly a little delirious, it's understandable that he might forget that his standard escape from certain death was no longer an option, until reminded by his TARDIS.
 * If they Silence really worked for the papal mainframe, and were specially made as priests for confession. Why did the conquer the earth all those thousands of years ago. It was explained that it was renegades who tried to kill the doctor, but how does conquering the earth fit into there plan? Surely its a bit much to start a thousands year plan to kill the doctor, aren't there easier ways?
 * The renegade chapter of the church that tried to kill the doctor, was referred to as Krovarian chapter implying she was there leader, but it was made clear that Krovarian was a servant of the silents.
 * She thought she was their leader, and it suited them for her to think that. So they let their faction be called after her.
 * The silents who invaded earth were likely a splinter group of the splinter group, who had goals beyond Krovarian's plan to kill the doctor.
 * Why didn't the Doctor take the people of Christmas away from the planet so they weren't in danger?
 * He never had the means to do so. The Tardis was away from Christmas almost the entire time, and in the end he was dying anyway...