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


 * Why did Time Change?


 * We saw a possible timeline in Name, just like the destroyed 1980's Earth was a possibility in Pyramids of Mars. And just like the decision to try and save the day was based on seeing that destroyed world in Pyramids of Mars, perhaps Clara knowing that if he goes through with this it will lead to the future she saw in Name made her more determined to save the day. Seeing what could happen made her so determined to stop it from happening.

in "the name of the doctor" we see the doctor's grave, meaning that in that timeline the doctor died, he did not get a second chain of regenerations. the grave of the doctor is necessary for the relationship between the doctor and clara the impossible girl.

in "the time of the doctor", however, he does not die. I do not see what the intervening factor is that caused time to change. why wouldn't the timelords grand the doctor a new chain of regenerations in the original timeline, especially when he is their only hope of returning to the universe? what is the factor that is new in this timeline?
 * This is not touched upon in the episode, and thus no concrete answer can be given. My own personal guess, however, is that it was either due to Tasha failing to fight the Dalek consciousness inside her mind (which would mean that she never retrieved Clara and therefore Clara wasn't there to answer the Question), or to Clara failing to realize that the answer to the Question was "the Doctor" for some reason or another. The former seems more likely to me, but those are the only viable branching points that I can see.
 * Or the cause of change was simply Tasha going back to get Clara. The Time Lords can smooth over paradoxes. Maybe they made sure the timeline where the Doctor died on Trenzalore somehow still existed for Clara to get scattered through the Doctor's timestream. Time really is Timey-Wimey Wibbly-Wobbly.
 * In The Space Museum, the Doctor and his companions see a future version of themselves, however, they managed to change their fate. This explains every last episode where the doctor or anyone else's future has changed. People know what could happen, not what will happen. So, Clara could go through the Doctor's whole life in the timeline where he dies and still have the Doctor be alive in the end of the war of Trenzalore.


 * I've brought up this discontinuity before for "Time and the Rani" and "Rose". Again, why does the Doctor's accent change? Accent is something that is picked up, not something you are born with. Don't say "Lots of planets have a Scotland" because they don't. Even if Gallifrey has a region which the people that come from there have the equivalent of a Scottish accent, why would only the Seventh and Twelfth Doctors have this accent? Theoretically, the Doctor's accent should stay consistent.
 * This does happen in the real world. There have been people that suffer brain injuries like blunt force trauma, stroke and even migraines among other things that upon recovery find that their accent has completely changed. A woman in Britain about 3 years ago had an extreme migraine and was rushed to hospital. She woke up to find she had a Chinese accent (that she still has to this day!). The trauma from regeneration must cause a similar effect on the Doctor's brain. But due to the mostly random nature of regeneration this wont happen every time.
 * To be honest, I think I have a better explanation for my own question. The Doctor has to ability to perform any accent perfectly, but has a default accent which can be different for each incarnation. The default accent is always from somewhere around the British isles.
 * I think that as well but i just wanted to give a real world explanation for it. I like the idea of each doctor having a different default accent.
 * Although it doesn't count because it never made it on screen, but The Christmas Invasion was going to explain that the Tenth Doctor lost his Northern accent because he imprinted on Rose and effectively adopted her's. If this is Moffat's thinking, then the Doctor may have changed to a Scots accent due to Amy. I would be very surprised if the issue isn't addressed in Series 8.
 * This theory works as the War Doctor regenerates after talking to the Northern Clara, picking up her accent as 9, 10 and 11 were born after hearing their accents, and 11 hallucinated Amy thus picking up her accent. Only one that'd confuse me following that theory is 7 regenerating into an English sounding 8 after being surrounded by American Doctors, but then again this is only a theory introduced to the new series.
 * Why did Clara not try to kill the Silents? Has she never seen the moon landing? --  jp  barrass 
 * It seems unlikely, but it is entirely possible. Nobody has to watch the moon landing footage.
 * Also, that message was about the group that invaded earth. The different context and slightly different appearance of these silents might have been enough to break the suggestion. Clara's status as time traveller and "impossible girl" might also render her somewhat immune to that kind of hypnosis.
 * Also, it is revealed in this episode that the Silents are genetically engineered to be memory-proof, and we know from "The Inforarium" that memory-proofing is artificial (or at least, it can be). If we were to get speculative, it is entirely possible that the people who designed the Silents added safeguards to their post-hypnotic abilities that would keep them from being too powerful; for instance, it could be that Silents cannot use their commands to make somebody kill themselves. Giving them that kind of power would just be asking for an uprising. So by extension, perhaps they cannot force a person to put themselves in a position with a high risk of death (similar to how the Saturnynians' perception filters in "the Vampires of Venice" were overridden by the subconscious' survival instinct, or as the Tenth Doctor said of the Sycoraxic blood control in "The Christmas Invasion", how "you can't hypnotize someone to death" since the survival instinct is too strong), which Clara certainly would have been if she had tried to attack the Silents because she was nude, defenseless, and outnumbered. Such reasoning could also explain why the Silents rely on their slower electrical attacks as opposed to just forcing their enemies to commit suicide, and could even be why the Church requires their attendees to be nude - so they don't kill their priests.
 * I have a big problem with this episode, several problems in fact. But the one that is pertinent to this discussion is that the "Silents" in this episode appear to be genetically engineered by the Church solely for the purpose of being confessional priests. The Doctor seems to know this which he did not know when he spoke to Dorium in The Wedding Of River Song. But the real problem is that the Silents in this episode are a shadow of what we have seen in the previous stories. They simply blunder around trying to extract confession from anyone and everyone they meet with minimal success it seems. They don't appear to possess any will of their own and act in complete obedience to the Church.
 * This makes perfect sense when viewed in the context they were made for but it also makes you wonder how they get from this stage to the much more advanced beings clearly called "the leaders of The Silence" at the end of series 6. This episode calls them the Kovarian faction but why do these beings need factions? They appear to operate as slaves having factions serves no purpose to what they are. The weapon the possess doesn't make much sense either, they don't seem the sort of being that need weapons and on earth priests are not allowed weapons of any kind.
 * These Silents don't seem slaves, just Priests. Perhaps in the Kovarian Chapter they were able to rise to higher positions as they could be more useful and maybe she recruited the more violent Silents. Perhaps the Silents can be given electrical powers but not usually, or it was a feature implemented for the War against the Doctor.
 * All these suggestions seem to go against the point of the Silents as they are presented in this episode: rather uncomplicated beings whose only desire is to serve the Church Of The Papal Mainframe and take confession from its members.


 * The timelords sent the Doctor a new regeneration cycle, so they must have known it was really him and that it was the right universe, so they didn't need to hear his name. Why didn't they come through the crack? --  jp  barrass 
 * The issue was not in confirming that the Doctor was on the other side. The Time Lords were intending for the Doctor to say his name in order to give them the all-clear and confirm that it was safe to come out, which it wasn't, because there was "half a universe" waiting to fire on them.
 * Ah, i like that explanation. Great: thanks. --  jp  barrass 

We don't know when this happened. Given the number of advanced alien races who've offered technology to primeval cultures over the years, perhaps human religions throughout history have always had these specialized confessional priests. The Kovarian Chapter's time machine brought her group back to engineer the space race, and kidnap Amy and the unborn Melody, but there's nothing to suggest that they're the only "Silents" on Earth. They've always been there. Churchgoers probably saw one every time they went to church... until 1969, when we were programmed to kill them on sight... probably one of the main reasons for the decline in Church-going in modern history. Can't remember the last time you went to church? That's because you had an epic fight scene and ended up drowning the Confessional Priest in the font. And then you forgot.
 * 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.
 * Correct. This was the payoff for the various references to Clara and the TARDIS being at odds. In the end, the TARDIS protected her.
 * 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.
 * Basically, yes. What the Doctor did in the clock tower was basically the same as what he did with the wooden Cyberman earlier. The truth field doesn't appear to prevent one from telling a lie of omission, since the Doctor was able to deceive the Cyberman into thinking that he had reversed the polarity of its weapon by not mentioning that his screwdriver doesn't work on wood. In this case, he's aim is to reassure Not-Barnable by saying that he has a plan, since people "love it when he says that." He has a plan, but his plan is simply to say that he has a plan in order to ease Not-Barnable's worries. When he tells Clara that he doesn't have a plan, he is talking about something else entirely (Not-Barnable never asked if he had a plan to defeat the Daleks or even if he had a plan at all, whereas when he told Clara he didn't have one he was referring to a plan to stop the Daleks).
 * 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.
 * Well, no one else in the universe knew that he didn't still have two lives: Amy, Rory, the Silence, Madame Korvarian, and even River all believed that the Doctor still possessed two lives, and so to complete the deception, the Doctor needed to fake the regeneration.
 * 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.
 * It's also possible that the Doctor wasn't aware at the time that his partial regeneration counted.
 * The Doctor asks for a lot of things that can't happen in this scene - he asks the simulated Amelia Pond to "run away and have adventures," and he says he could be cured. It's not out of the realms of possibility to suggest that he's either a) grasping at straws, or b) flippantly hoping for things he knows he can't have. --BenCPaddon ☎  03:21, May 30, 2015 (UTC)
 * 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?
 * Who's to say they "conquered" Earth? They said they had been there since the fire and the wheel- later, in Time of the Doctor, the Doctor notes that they're genetically engineered- given that they're part of the human Church, probably genetically engineered from humans.
 * The Silence needed a spacesuit in order to control River, which they knew because they were aware of the myth of Lake Silencio. They set out to guide humanity's evolution in order to get them to the point at which they could fashion a working spacesuit for them, because the Silents are parasites who do not make anything for themselves. And since they are the self-proclaimed "sentinels of history," they would want to respect the flow of time and make as few changes to the timeline as possible. Integrating themselves into history and slowly shaping it the way they wanted would probably be a better way of achieving that end than popping out of the sky and demanding a spacesuit would have been, and taking a spacesuit from the future would have been cheating because had they not gone back in time and influenced the creation of the first spacesuits, there would be no spacesuits in the future to take.


 * 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.
 * However, Kovarian's group and the Silents in 1969 were shown to be in collaboration; Kovarian procured Melody and brought her back to 1969 to be trained and supervised, while the 1969 Silents devised the spacesuit that Kovarian would later use for the assassination attempt at Lake Silencio.
 * The Silents are not very out-in-the-open types; they tend to operate from behind the scenes as demonstrated by their spacesuit scheme on Earth. Kovarian could very well have been a public face for the group.
 * Madam Kovarian appears to be human. At least, she's affiliated with the church, which has so far only been shown to involve humans, modified humans like the Monks, and genetically engineered life forms like the Silents.  Humans reproduce, and Kovarian is a surname. She may well have been very senior in the Kovarian Chapter, by virtue of family connections, whilst still subordinate to the inner circle of confessional priests.
 * I feel that the Silents seen before were a renegade faction, who decided to abuse their power. Kovarian made contact with these more dangerous Silents. I don't think the invasion of Earth was just to get a spacesuit, perhaps these Silents also wanted power but Kovarian helped them in exchange for a spacesuit.
 * 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...
 * Actually, this is wrong. The Tardis is standing in the village during the fighting before Lem piloted it away. It is some kind of ice growing on it, though. I don't know what that is but I guess it has something to do with the doctor not using it again.
 * In The Eleventh Hour the Doctor said that if the wall was taken down the crack would still exist. The same thing would happen here, with the people taken away the papal mainframe might have taken the forcefield down and let the planet be destroyed (with no lose of life to innocent bystanders). They would then discover the crack was still there and the alien races would likely start hunting the Doctor across time and space to stop him answering the question. So to stop this he stayed on trenzalore with the people there to isolate the conflict. In a war it is easier to defend one town on one planet instead of the entire universe.
 * The simplest explanation would seem to be that they wanted to stay, to defend their home rather than relocate. The Doctor made it clear that he was going to stay, basically to protect Gallifrey from potential access by the bad guys.
 * For the first 300 years, the Doctor did not have his TARDIS, and very soon after that, the war began. He never had a good opportunity to evacuate the town (let alone the planet, as it was said that the races were willing to burn Trenzalore entirely if it meant stopping the Time Lords from coming back).
 * How could the Doctor die so young when his 10th incarnation was fast forward thousands of years to look like a small creature and still was alive?
 * We actually don't know how old the 11th Doctor was when he was dying here, as a lot of time clearly passed between Clara's trips. Plus, you'll remember that the Master mentioned that he had suspended the 10th Doctor's ability to regenerate when he artificially aged him. The 11th Doctor dying of old age here seems consistent with the similar deaths of the 1st Doctor and the War Doctor.
 * The aging was to show what the Doctor would really look like if he had never regenerated. That has nothing to do with actual regeneration.


 * I guess it is something bound to similarity of London's modern sleeping districts, but it seems that Clara and her relatives are celebrating Christmas in Powell Estate, as seen in "Rose". Any londoners to explain, please? Or it is an Easter Egg/Future Plot Hook/etc.? Any Mickey Smith and Martha Smith-Jones as neighbors of Clara's relatives, eh?
 * Not really a plot hole or discontinuity that she lives in a building that looks like Rose's...


 * While it's understandable for the Daleks to know about Time Lord regeneration limits, but how do they know the Doctor is at the end of his cycle, given the aborted Tenth Doctor's regeneration would not have been widely known, and the War Doctor was a "secret incarnation"?
 * You forget, the Daleks were part of both events. The Daleks were there in the Time War, and thus would have records of the War Doctor. It was also a Dalek that caused the Tenth Doctor's aborted regeneration. Thanks to the Pathweb, that information would've been shared amongst all the Daleks. Now, let me state the flaw in my own argument. All the information about the Doctor was deleted from the Pathweb. They regained their knowledge from Tasha Lem. The only way for them to have known, would be if the Doctor told Tasha about both regenerations.
 * Given that he knew her before we see them together in this episode, and it's implied that he subsequently has meetings with her often during the first 300 years that Clara is away, he easily could have told Tasha Lem.


 * The Doctor produces an item he confiscated from the Master in the Death Zone, a reference to the events of The Five Doctors. The problem is School Reunion established that the Doctor does not remember those events, and The Day of the Doctor further explained that it's not possible to retain memories of multi-Doctor encounters due to the shifting timelines. How then is the Doctor able to remember the Death Zone?


 * No, the latest incarnation CAN remember. In the three Doctors, three should be the only one to remember. In the five doctors, five should be the only one to remember.
 * Perhaps the memories sealed to his past incarnations are opened when he goes through the adventure himself. So the memories of of the Doctor in his 1st incarnation meeting his 5th would not be remembered until five has gone through that as well. So 11 wouldn't be able to remember his 10th self meeting his 11th self until he went through that too in his 11th incarnation.
 * How did School Reunion establish that the Doctor didn't remember the Death Zone? I don't recall such an establishment being made. As for the part in The Day of the Doctor, the loss of memory only applies to earlier Doctors. The latest one involved in those events retains the memories. So, the Third Doctor remembers defeating Omega, the Fifth Doctor remembers the Death Zone, the Sixth Doctor remembers the incident with the Sontarans, and the Eleventh Doctor remembers saving Gallifrey.
 * Some people assume that the Doctor can't remember the Five Doctors because Sarah Jane and the Doctor act like they hadn't met since The Hand of Fear in School Reunion. However, it was a pretty brief meeting, if you could call it that, with a future Doctor for Sarah in the anniversary story. I'm more amazed that The Doctor has carried the Seal of Rassilon around since his third incarnation. When he changes outfits, does he move all of the collecting items to his new clothes?
 * I don't think he's been carrying the Seal all this time. It's possible that after saving Gallifrey, the Doctor went rummaging through the TARDIS looking for any Gallifreyan artifacts he might still have. Upon finding the Seal, he probably kept it in the hope it might prove useful at some point.
 * School Runion does not establish that the Doctor can't remember The Five Doctors. If you mean he said he has regenerated 'half a dozen times' since they last met, it was just a preview of the Warrior.


 * How Come the Daleks remember the Doctor in this episode even though the Doctor was wiped from their memory banks
 * They harvested information about the Doctor from Tasha Lem's mind, but I don't see why they wanted to do that.
 * It would make sense for the Daleks to extract whatever information they could about the person down on that planet who was the very source of their dilemma (Why can't we destroy the planet? Why does this old guy in a bow tie keep stopping us? Who is he?) at that time.


 * Tasha was able to take out three Daleks with a single blast each from a Dalek gunstick, but in Evolution of the Daleks it took dozens of blasts to destroy one.
 * Those weren't just any Daleks in Evolution, they were from the Time War era - and even more so, they were teh Cult of Skaro, a speciel elite unit. Plus, we don't know that it was the same type of gun, what settings were being used, etc.


 * The prophecy says that during these events "no living creature can speak falsely or fail to answer." The Truth Field in this episode does prevent anyone speaking falsely, but it does not prevent failure to answer. "Doctor Who?" is asked many times, but the Doctor doesn't answer.
 * Not all prophecies are meant to be taken literally word for word. Alternatively, it's possible that the Doctor is sufficiently strong-willed that he was able to overcome that part of the Truth Field.
 * At no point is the question actually directly asked of the Doctor. And while the context is clear, even if it was the Doctor could work his way around the answer to a question like "Doctor who?" The problem arises if he were to be asked "What is your real name?" which does not actually happen.
 * To add to the above, even though I'm sure that this episode is of course what the prophecy was intended to refer, it seems that the scene in The Name of the Doctor where the GI was trying to get into the tomb doors was a little more in keeping with what was said.
 * Steven Moffat clearly stated that the question (in the context presented by the prophecy) was not asked in The Name Of The Doctor. And when you have a criteria that "no living creature can...fail to answer" you can't then say, "unless they're strong willed enough not to. The Wedding Of River Song made clear that when the question, which was identified as `Doctor Who?` was asked on Trenzalore the Doctor would be unable to refuse to answer it. That was the crisis that led to him nearly letting The Silence kill him.
 * I agree with the person who said that the question is never asked of him directly. After all, he's not the only person in the universe who could answer it. River could've if she'd been there with him.
 * Of course the question was addressed to him. It is quite explicit that the reason "Doctor Who?" is the question is because it is presumed that only the Doctor can answer it. (River could not have answered. If you're thinking of when the Doctor supposedly told River his name at their wedding, he didn't, as she later revealed to Amy. The only time he actually told her his name was when she was headed to her death.) As for Moffat's claim that the question was never asked, the prophecy explicitly stated that it would be, so we're still left with the prophecy being untrue.
 * He can't fail to answer otherwise trenzalore will be destroyed. He can delay answering and hope something happens (such as Clara somehow persuading the time lords to give him more regenerations) but he cannot refuse to answer because otherwise he would not be acting in the name of the doctor by protecting the people.


 * After it is established that the truth field exists, a woman turns to Clara (fortunately she doesn't turn to the Doctor! See above) and asks for her name. Instead of answering "Clara Oswald", Clara said stuff about being a control freak. Shouldn't she have been compelled to properly answer the question?
 * We don't know that, because the exact functionality of the truth field isn't explained. We know it compels you to state the truth, and initially it appears to make Clara and the Doctor give away more information than they intend.


 * When Tasha Lem heard the question "Doctor Who", she instantly links it to Time Lord's attempt to return. But how did she know about them? Time Lords are believed to be extinct in the last day of the Time War. Even the Doctor didn't know real ending of Time War before "The Day of the Doctor". The fact that the signal means "Doctor Who" doesn't necessarily mean that Time Lords are actually survived, frozen in another universe, and making attempt to return to this world.
 * It's established that Tasha has met the Doctor before, just not the Eleventh Doctor. It's possible that she met the Tenth Doctor and he told her about the Time War. About how the Time Lords became corrupt and tried to destroy all of reality by means of the Ultimate Sanction.
 * This is possible even though The End of Time is Ten's final episode; The Doctor might have met Lem in his Final Reward. However, even if Tasha did know about the Time Lords, and thought they might be able to escape the Time Lock again, why would she instantly connect the Time Lords to the question 'Doctor Who'?
 * First of all, the Doctor's known about the Ultimate Sanction since the end of the Time War. That's why the War Doctor was prepared to destroy Gallifrey. As for the Doctor Who? question, it's possible that the Doctor might have told Tasha that his real name is a secret and only his fellow Time Lords know what it is. Why would he tell her that? Maybe she tried to get him to confess and he resisted.


 * The First Doctor died of old age at about 300 years old, correct? Then how come the Elleventh Doctor can live so long? And why does it take so long for his age to show, yet it only took 100 years for the Tenth Doctor's age to show? Honestly, I couldn't stop thinking about this whenever I saw the episode.
 * He actually died at a little after 600 years. I have a similar question. Since the first incarnation died at a little after 600 years, why did the Eleventh Doctor? In Deep Breath, the twelfth Doctor stated that he has lived for over 2000 years. With some math, that means the Eleventh Doctor has lived for at least 1006 years. If one of his bodies can only last a little over 600 years, he should have died way before Clara and the TARDIS's second trip back to Trenzalore.
 * The First Doctor didn't die of old age, he regenerated, he could have chosen to regenerate because he wanted a younger body, not because he had to, but in The Time Warrior (TV story) the Third Doctor said he was 300 but the First Doctor regenerated at 600?


 * The First Doctor died of exhaustion at 450 as the Second states that as his age in the next story; I believe the Eleventh died at 1200. War also said his body was "wearing thin" so it's possible that One and War died of extreme fatigue and still prematurely before old age, whereas the 11th truly died of old age. It's also possible that the Doctor adapts to his previous deaths every regeneration (4 died falling off a tower yet 10 was much more durable to a skydive, and while 3 died from radiation in a cave it took a fall from a ship and extremely concentrated radiation to kill 10.) It's possible his body adapts to old age and his personal incarnation's lifespans get gradually longer.


 * When the Church destroyed the Sontarans, they said "Your respective afterlives have been notified", or something similar to that. This implies that there are indeed afterlives, and that the CotPM has access to them, at least in form of communication. The Doctor has met Tasha Lem before this episode, as stated above, and probably as 10, so she has most likely told him about the fact of the afterlife. So why does the Doctor basically say he is Atheist in both The Impossible Planet/Satan Pit, and The God Complex?
 * This may have been alluding to something that may occur in Series 8. Especially with the facts of "Heaven"/"The Promise Land"'s existence.
 * When they mention afterlives they may not have proof that the afterlives are real, they just believe they are, also the Doctor may not agree with the Church on the matter and by afterlives The Church of the Papal Mainframe might have been referring to a form of artificial reality like River Song's afterlife as the church could have changed significantly in the future so they may believe the afterlife is something they must provide not something they must receive.


 * Due to the question's phrasing and the truth field, only The Doctor should be able to answer it. After the TARDIS is returned to Trenzalore 300 years into the doctor's stay, why doesn't the doctor just leave? The townspeople shouldn't be in danger because the various alien races wouldn't be able to do anything with the crack, and as such would stop besieging Trenzalore and instead would try to find the doctor (and since he has a whole universe to hide in, it would take an extremely long time for them to catch him.)
 * To quote the Doctor from this episode "Well, it's a standoff. They can't attack in case I unleash the Time Lords, and I can't run away, because they'll burn this planet to stop the Time Lords." He can't leave, or Trenzalore, and Christmas, will be destroyed by the alien fleet to prevent the time lords' return.
 * Surely, destroying the planet wouldn't actually destroy the crack though. Realistically, this should have been addressed.
 * The Doctor and whoever he discusses it with seem to be the only people who know the crack will never be destroyed with the planet, and despite there being a truth field to confirm he isn't lying, I doubt any of the aliens would've cared if he told them the crack wouldn't go away. Plus, we've got Daleks, Slitheen, Cybermen, war-obsessed Sontarans, Weeping Angels...who's to say they wouldn't attack the planet even if the Doctor left without releasing the Time Lords?