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


 * The Tenth Doctor's control room was noticeably incorrect, since 'The Runaway Bride' the control room has always been lit up, with the console glowing a heavy green colour. In the timeline, the Tenth Doctor is between Waters of Mars and End of Time, which makes no sense why the control room is A) Darker than usual. and B) The console is glowing blue, as the control room does not look like this in either episode.
 * He changed the lighting.
 * The Ninth and Tenth Doctors' console room time rotor has always been turquoise, sometimes appearing more green, sometimes appearing more blue. That's what I remember from watching their series, anyway. Any other difference than usual is simply because - if what I hear is true - they filmed his TARDIS' scenes at the Doctor Who Experience recreation of the set.


 * Why doesn't the Doctor simply dematerialise the TARDIS when it is being airlifted by the UNIT helicopter?
 * The Doctor is seen throwing levers and flicking switches as the TARDIS is picked up, it's safe to assume he at least tried. However seen as it is Kate's doing maybe he has no major objection seen as it isn't causing any harm.
 * The Doctor doesn't know its Kate!


 * Why is the War Doctor young in Night of the Doctor, yet old in The Day of the Doctor? How much time has passed, and does this affect the age of the Tennant Doctor.
 * It's supposed to be a lifetime of war.
 * The Time War lasts THAT long. I don't remember a specific time given in-show, but I the Engines of War book says 400 years. The age of the Doctor isn't any different; that was always a part of the Tenth Doctor's history, so nothing changed.


 * UNIT have been kidnapping and wiping the memories of the Doctors past companions. What time and space technology have they been using?
 * They haven't. They simply need to interview them about The Doctor, the memory wipe devices in the ceiling wipes the memory of them ever being in the archive. The companions also come there of their own free will.
 * How did the companions get to the Black Archives to be interviewed? What space and time technology was used to interview, for example, Sara Kingdom?


 * Why is the John Hurt Doctor called The Doctor at the end of Name of the Doctor, yet called the War Doctor here?
 * "War Doctor" is the name he has been given by Moffat and the media and everyone to have a name to refer to him as, equivalent to "Twelfth Doctor," "Fourth Doctor," "Meta-Crisis Tenth Doctor," etc.


 * How could so many Dalek motherships cause so little damage?
 * The war counsel states they have 'Sky Trenches' that are holding, presumably protecting the planet.
 * This might not be at the heart of the battle, either. In The End of Time, one of the Time Ladies mentions that they are far off from the true, fullest carnage. We only see a few areas in The Day of the Doctor.


 * Shortly after the Hurt Doctor reappears at the barn, two TARDISes appear. Tennents and Smiths. Where did Tennent get his TARDIS from?
 * The two Doctors leave the Tower of London and go to Trafalgar Square to where Smith's TARDIS has been since brought there by helicopter. They use this TARDIS to travel to Arcadia where Tennent's TARDIS is, as this TARDIS was used to get the Doctors into the painting.  They then each pilot their own TARDIS to the barn.
 * That is sheer prosumtion. Seems they had plenty time to waste, with that theory!
 * Well, the TARDISes can travel in time so I doubt they wasted time.


 * How did then Doctor have any memory of him killing his own species if he had stopped the war doctor from making that choice in the 50th anniversary? How did the twelfth doctor who that Galifrey was still there if he believes he had killed his own species?
 * I'm not sure what you're trying to say but as I recall the Doctor altered the past but retained his memory of his actions in the former past until the point he caused the change in his own present. But, yes, I'm not sure this makes much more sense. The implication is that the Doctor always has a memory of experiencing his life as if the change is never made and only when he gets to the point where the change was made in his own life, in eleventh he 'learns' that what he believed had happened was not actually what happened. Not quite sure how this would affect his memory at that point as the episode just glosses over it. Bother that Steven Moffat.


 * We are told that the Moment takes the form of Rose/Bad Wolf, but the teeth and hair are all wrong!
 * I don't think the Moment is taking the exact looks of Rose/Bad Wolf.


 * Clara uses Captain Jacks Vortex manipulator to rescue the Doctor. UNIT have been kidnapping the Doctors companions from time and space. Why didn't they use that device to rescue the Doctor?
 * Since when have 'UNIT have been kidnapping the Doctors companions from time and space'? they haven't, when was this even a thing?
 * How did the companions get interviewed for the Black Archives?
 * UNIT has been around for a long time and knows of the Doctor and his companions. They simply approached them throughout the years and told them "Come with us" and that's all.


 * The Moment brought the War, Tenth, and Eleventh Doctors to the Time War, but how did the other ten get there?
 * Presumably, the Moment let them in as well.
 * If this is the case, why did the Doctors come through? Where did they get instructions on what to do?  How did the Moment know to let the Twelfth Doctor in, when none of the other Doctors would even know that he existed?
 * The War Doctor didn't know about Rose (or Bad Wolf) yet, but the Moment still took her form. She/it clearly can access the Doctor's entire timeline, including the future.
 * During the 50th anniversary, the Destiny of the Doctor audio drama story arc has the Eleventh Doctor visiting his past selves in order to enlist their aid. It's very possible he did this again; indeed several of the Eleventh Doctor's cameos in the audio dramas elicit reactions from earlier Doctors suggesting this is not the first time this has happened.


 * The Tenth Doctor states to a rabbit while in Medieval England, that he is 904 years old, but he claims to not know what Eleven is talking about when he said "timey wimey," but he created that quote in Blink (third season) and said that he was 903 in the next season's premiere.
 * That was a joke; it wasn't meant to be taken literally. He knew what Eleven meant by "timey-wimey," but he was trying to play it off so that he didn't look as ridiculous by saying it.
 * There is nothing in "Blink" to indicate that this is the first time the Doctor uses that phrase. Indeed, the Fifth Doctor knows it in "Time Crash."
 * But the "War Doctor (Or whatever John Hurt's Doctor was called??) was not aware of the phrase, even though the 5th Doctor Was.
 * So he acted. Just as the Tenth wouldn't want to look ridiculous by understanding the term, so the grumpy War Doctor would have been even less willing.
 * Or go my route and discount Time Crash from the canon. Honestly, that mini-episode contradicts the main show in so many ways.


 * Why did he think the real Elizabeth was the fake one? He said that her eyes were too close together, her breath was awful and her hair was wrong which gave away that she was the fake one, when actually she was the real one! He had spent time with the real one so surely he would be able to tell that it is her. I'm trying my hardest to explain what I mean but it is difficult. Anyway, any suggestions?
 * The Doctor does occasionally make mistakes. He might have been doing what he accuses humans of doing, namely seeing patterns in things that aren't there.


 * The Doctor does know what the round things are (there seems to be hardware behind them in some classic stories which he works on)...
 * It's been awhile since he's seen them so he might have forgotten some of the details. Considering that The Eighth Doctor has lived for around 600 years and we don't know when The War Doctor reinstated the 'round things', it is hard to remember.
 * Its implied from the Tennent Doctors tone of voice, that he doesn't know what the 'round things' are.
 * Maybe they mean from a design point of view, the access panels for the hardware could have just been a hole in the wall, the question probably was aimed at the fact the repeating circular pattern is quaint.


 * Who says that the Eighth Doctor lived for around 600 years?(stated above) If this is true, then continuity is all wrong. There is a gap of 400 years between Matt Smith (1200yo) and John Hurt. Making the War Doctor 800yo, leaving 200 years between Doctor 1 and Doctor 7.


 * Surely Elizabeth, being a queen in the 1700s, would not have had sex with the Doctor before marriage (it is implied heavily that they did).
 * Firstly, she was the Queen in the 1500s. Secondly, just because it wasn't considered proper doesn't mean it didn't happen. We don't know what goes on behind closed doors. And no, I don't think the Doctor mistaking the real Queen for the fake one means he believed he'd slept with a Zygon. He only thought the one at the picnic was fake.
 * Sorry yeah that was a typo I meant 1500s


 * Did the Doctor and Elizabeth have bum sex? I think it is implied as Elizabeth seems to be walking funny.
 * I don't think they had sex. When the Doctor says Elizabeth is no longer the Virgin Queen, it might just be because he married her. And I doubt the Doctor would have sex with a Zygon.
 * Well in The End of Time and The Beast Below, it is heavily implied that they had sex. And this point was specifically asking about bum sex. Maybe they had bum sex which meant that she was still a virgin but they still had sex?
 * This is the most ridiculous thing I have ever read.
 * Possibly she had a slipped disc; more likely she thought was about to break wind. See Carry On Doctor for further details.
 * well it's heavily implied that they did have sex, as in proper sex. We can only speculate as to whether bum sex also takes place. But I'm pretty sure that the doctor(s) leaves before consummating his marriage, therefore there was no sex of any kind during the 10th doctor's timeline in this episode.


 * Why does Elizabeth I sound slightly Welsh?
 * Why not? We don't know what the real Elizabeth I sounded like, so perhaps she did indeed sound slightly Welsh. After all, as a Tudor she was slightly Welsh.
 * Because the actress that played her is welsh.
 * I don't think you understand what discontinuity sections are for. Obviously everyone knows the production reasons, but we aren't here to discuss production reasons - the point of this is for in-story reasons. Educate yourself before attempting to contribute. Thank you.
 * The previous question was about "bum sex".
 * The episode "The Fires of Pompeii" explains why certain people are heard with specific accents.


 * Also, accents have changed a lot in the last 550 years. And since Cardiff's accent is a lot more conservative than the Home Counties, the real Elizabeth might well sound more south-Welsh to us than Home Counties. (Although really, she wouldn't sound all that much like either—a 20th century Virginia accent also sounds more like modern Bristol than modern London, but doesn't actually sound that much like Bristol, and you certainly wouldn't mistake it for any English accent.)


 * How can the Twelfth Doctor help save Gallifrey if the Eleventh does not receive his next set of regenerations until "The Time of the Doctor"?
 * Time travel...
 * Although the Time Lord generals are aware of his presence, we don't know whether or not the other Doctors were aware.
 * There's a whole bunch of strange timey-wimey happenings in this episode, which really can all be explained by the Moment's interference and apparent total control over time (in fact, I personally think the Moment's consciousness IS actually Bad Wolf, and have read a pretty good article going through why that is). This might be one of these things.


 * If the Capaldi Doctor makes an appearance at the end, then surely as the most recent incarnation wouldn't the Matt Smith Doctor forget events, too?
 * Not necessarily, if the episode was written in to 11's timeline, then he can remember it. as for 10, the events were never supposed to happen. Like 'A Christmas carol' the events only happened once and time changed. The Doctor was experiencing 'new memories' as it were.


 * Why does the War Doctor straight away assume that the Tenth and Eleventh Doctors are the Doctor's companions and exclaim, "They get younger all the time!" The Doctor has had younger companions than the age Tenth and Eleventh physically look, and why doesn't he think about the possibility that they are the Doctor? The Fifth Doctor was physically younger than at least Tenth, if not Eleventh too.
 * He hasn't been the doctor for several hundred years, so his memories might be a bit underused. Plus it's less about them being young, more he didn't want the idea that he would become them. General theme is every previous doctor, doesn't like their successor (except the fifth doctor, they all seemed to like him).
 * His future incarnations being physically younger is actually a theme hit on a few times during the story. There's no great continuity issue here, however. The War Doctor was simply expecting his new incarnation to be older, and from his perspective, Ten and Eleven looked pretty darn young.
 * It may also have simply been a case of the War Doctor instigating conversation with a compliment.
 * It really does not appear to have been intended or interpreted as a compliment, no. But the previous explanations seem sufficient.


 * What happened to the Stolen Earth continuity in the Day of the Doctor Episode?
 * It seems Davros purpose in it no longer happens.
 * Davros went missing in the first year of the time war, what we see is the last. No canon is defied.
 * It seems I was mistaken on this point. Thanks for clarification.


 * Where are the mentions of the nightmare child destroying Arcadia?
 * As we don't know what the Nightmare child is, whose to say it's not there?
 * Given the point that the Doctor remembered laughing at the Nightmare child while Arcadia fell it seems somewhat puzzling it not being mentioned.
 * The only thing to suggest that the Nightmare Child was involved in some way at the fall of Arcadia is "The Forgotten" comic, which is already contradicted by this episode in much more significant ways (as in, the Eighth Doctor being the Time War-era Doctor in the comic as opposed to the War Doctor as shown on-screen). However, as this is the Time War, it is entirely possible that the Nightmare Child was involved at the fall but then later wasn't as a result of time being rewritten so recklessly during the War.
 * To add to the above, the on-screen reference to the Nightmare Child only places it in the first year of the Time War, and says nothing of any involvement with Arcadia.
 * I want to make an opinion on what was said about the Eight Doctor in the comic "The Forgotten". It is true. He is held captive during the Time War, but this can still be canon. If you saw "Night of the Doctor", then dialogue indicated that the war was already going on, but that the Doctor hadn't joined yet (which he decided to do after he was told that there was no other choice). My belief is that this is the Doctor during the early days of the War, before he joined. And yes, it could've taken 21 days or more before he decided to join. The Doctor is sometimes very stubborn.


 * Having multiple doctors in the same are causes time paradoxes, how does this work with so many in one episode?
 * That's never been stated. Crossing one's time stream is dangerous, but the Doctor's a professional, and as stated in "The Five Doctors" it is allowed only in the most extreme emergency. I would count an entire race's destruction as an extreme emergency.
 * "The Three Doctors", "The Five Doctors" and "The Two Doctors" all occurred without great peril. "Time Crash" did have peril, but that was as much due to the Doctor misprogramming the TARDIS than anything else.
 * The Moment was in complete control over time, manipulating the time lock, crossing over all the Doctors' timelines, fixing their memories to prevent any contradictions, and sustaining any paradoxes. Personally, I think the Moment's consciousness actually IS Bad Wolf.


 * Where are the connections with the Master?
 * Off screen somewhere.
 * Not that I can see as we don't see mention of the Time Lords council and simply "the general". Also was wondering where President Rassilon is to be in this whole affair.
 * The General mentioned the high council had a mad plan, then mention it failed. Presumably Rassilon is now dead or in his next regeneration, after being blasted by the master. Who presumably was on Gallifrey when it disappeared. And knowing him is taking advantage of the chaos to steal himself another set of bodies.
 * Wasn't it established that the Master was believed lost at some point before the end of the Time War?
 * Yes, when he ran and hid at the end of the Universe (TV: Utopia). Then he was apparently taken back into the Time War when Gallifrey was returned there. (TV: The End of Time) As explained above (and below...), The End of Time is presumably taking place off screen between (or just before) the events we see here.
 * I believe it's entirly possible that The End of Time is happening at the same moment. We just never saw Rassilon because The Doctors are hanging above Arcadia with their TARDISes. And, as pointed out by the Eleventh Doctor very early in the episode, Arcadia is Gallifrey's second city. I believe that Rassilon was fighting in the capital city of Gallifrey, which is why we don't see him.

- How did the Zygons know when to leave the paintings again? It is to assume they all entered the paintings and broke out before the doctor was called, how did they know when to do it? - On the same level: How did the doctors know when to leave "Gallifrey falls no more" again? They were standing in the midst of the picture, with their backs to the glass, and shatter it almost immediately after. Why did they arrive exactly where they needed to? - If the pictures have a concept of time, did the Zygons really feel the hundreds of years they spent in it? Or are they frozen in time - which leads me back to the question on how to know when to leave the pictures again? - I understand why Elizabeth did write the letter to the doctor and leave her credentials: she could not expose the Zygons in her time, knew of their plan and arranged the letter. But when the doctor is brought to U.N.I.T, the Zygons had already escaped and one had taken over the commander. Even if the Zygons knew of the doctors cell carving, they could not have known about the time travel device in the vault and therefore had no reason to call the doctor in in the first place, despite the letter. - So the Zygons crash the paintings, hide beneath the cloth after smashing statues and one takes over the commander. Nicely elaborated but while the Undergallery is surely no place visited by lots of people, someone before the doctor must have wondered where the dust came from. Also, if they just had smashed the statues there would be broken limbs and pieces lying around - or the Zygons cleaned up in which case the could have cleaned the dust as well? The only explanation would be that this literally happened hours before the doctor came in and that brings back the question why they would call him in at all instead of just taking over. - where is the body of the horse the Zygon took over in Elizabeth's time? :P
 * Hey guys, I have been thinking about the episode for days now and I think it leaves us with some poorly explained and / or illogical events on which I hope to get some opinions and insight. It is not about the bigger picture but about the Zygon plot:
 * 1. The Zygons didn't "know" when to leave the paintings. Earth at the time was primitive, either they allowed an amount of time to allow Earth to develop to what they estimated would be a useful technological level or they were displaced in time and had a fair idea from their former knowledge when that would be.
 * 2. The Doctors presumably had some means of identifying the historical moment they were in discussion with. They then set the painting to release them from stasis just after that moment.
 * 3. The painting suspend beings in time, they have no concept but the suggest is that the painting can be pre-programmed to release them.
 * 4. I'm not sure I entirely know what you're saying but the Doctor was primarily called in response to the painting being broken, it was set up like a chain of events that would summon the Doctor. The Zygons had nothing to do with it except that leaving their frames was set up as the trigger. Remember as the Doctors were there when they went in they probably helped set it up.
 * 5. One had not taken over Kate, this happened when she was down there showing the Doctor what had happened. Kate called the Doctor as it was her brief to do so.
 * 6. I'm sure you're being silly but there doesn't need to be a body, it's a horse. Zygons need to sedate humans because humans are distinguishable to other humans and the original might give them away. This wouldn't likely happen with an equine.


 * Doesn't this contradict the appearance of the Time Lords in The End of Time? Rassilon and his council knew that the Doctor possessed the Moment so attempted his crazy plan to become beings of pure consciousness - this didn't happen in The Day of the Doctor. In The Day of the Doctor, the General was in charge and there was no mention of Rassilon's plan. Gallifrey did not move next to the Earth. But both these events were on the last day of the Time War.
 * The general just headed the war council he was only in charge of the military and strategic planning, the High Council was mentioned to have there own crazy plan, and it was later mentioned it failed. So nothing's been contradicted, just reset. Basically, this is how it always went.
 * But Gallifrey got moved next to the Earth in The End of Time. This never happened in The Day of the Doctor.
 * And then it was sent back. Presumably, this bit was offscreen: we don't exactly see the whole event. Alternatively destroying the process may have meant this bit was actually erased and never occurred in the time line.
 * The way I view this issue is that the high council (Rassilon) attempted this plan before all 13 doctors arrived. By the time all the doctors had arrived, the Tenth Doctor and the Master had already sent Gallifrey back into the Time War. This is backed up when the General on the War Council mentioned that the High Council were having an emergency session.
 * There are no contradictions between this episode and "The End of Time". At the beginning of "Day", the General and Androgar discuss the High Council being in emergency session "with plans of their own" (the Ultimate Sanction), although the General dismisses their plans as having already failed (however, this has to have been a metaphorical dismissal of their plans as being desperate and pointless, because the next thing that happens is the theft of the Moment, which happens before the Ultimate Sanction is enacted as evidenced by the Partisan saying that the Doctor still possessed the Moment during their session). Then, once the War Doctor is removed from the Time War by the Moment, the High Council presumably enacts the Ultimate Sanction, which would have failed shortly before the three Doctors re-entered the War. The displacement of Gallifrey would have taken place off-screen.
 * And given that Day of the Doctor confirms that certain events are forgotten (Doctors meeting themselves, etc) it's very possible that a time reset of some sort made it appear as if the "Ultimate Sanction" never occurred. At least on Gallifrey.
 * You're all forgetting one thing. The Doctors' plan was that when Gallifrey disappeared, the Daleks bombarding it would kill each other in the crossfire. If Gallifrey had already disappeared once due to Rassilon's plan, how come the Daleks didn't wipe themselves out at that moment, instead of later?
 * We don't know how long it was gone relative to the Daleks' perspective - these are Time Lords after all, jumping the planet around in both Time and Space. It could have returned milliseconds after it left. Plus, we know that at some point the Daleks intensified their bombardment. If Gallifrey disappeared before it was that intense, the Daleks may have been able to avoid their own weapons fire.


 * Did all his previous incarnations forget that they had helped to save Gallifrey too?
 * Yes, why should they be immune? This is mentioned as a consequence of being out of synch with his timestream.
 * The only exceptions would be the Eleventh and Twelfth Doctors. We do not know - and it is never stated - that the Eleventh Doctor was ever aware that the Twelfth Doctor was present. Or if he did, presumably that aspect disappeared from his memory.


 * How did the Doctors contact all their previous incarnations to get them to come and help?
 * It shouldn't be that hard considering he has a time machine and knows exactly when they would be available.
 * The audio series Destiny of the Doctors follows a similar thread, with the Eleventh Doctor contacting each of his former selves for help.
 * The TARDIS may also have assisted.
 * Don't forget the Moment's godlike control over all of time.


 * How comes all of the Doctors were there on the cloud at the end? They were all looking up at Gallifrey, but surely if they remembered that they had all saved it then it wouldn't make sense because they didn't remember.
 * It's a dream of Eleventh Doctor.
 * In some of the spin-off media it is established that after a Doctor dies and regenerates, his essence "lives on" in the mind of the new Doctor. The previous Doctors can even speak to each other within the new Doctor's mind.
 * See also "The Name of the Doctor".


 * Why were there two different versions of the Seventh Doctor shown on the screens at the War Council? - a version of him looking as he did between 1987-89 in his question marked jumper and a version of him from the TV Movie. Is this a production error? There couldn't have been two versions of him there as it is stated there is only thirteen of them there.
 * I'd chalk it up to a production error. IIUC, all of the footage of Eccleston, McGann, and the earlier actors was archival. It's possible that McCoy is the only case where clips of the same actor from multiple sources is noticeable given 1) the clips were shown in black & white and 2) most of the other Doctors had either just 1 costume or costumes that were extremely similar.
 * Likely a simple production error, but it could be explained away in-universe. For example, the 7th Doctor may have arrived there, then realised he didn't have quite the right bit of calculation done to enact his part of the plan. Years later (from his perspective) he came back, but it was just seconds after his younger self had left.
 * In his column in Doctor Who Magazine #475, Moffat chides readers for not asking him about this. Which suggests it may have been intentional, though unexplained.


 * Where are the Skaro Degradations, the Nightmare Child, and the Would-be King?
 * Presumably they were destroyed by the Dalek bombardment.
 * Assuming that they were on Gallifrey at the time. They could have been anywhere in time and space; the Doctor said in "The End of Time" that it was the entire War coming through, not just the Time Lords/the Daleks/Gallifrey.


 * Now hang on, are we really meant to believe that every (well almost every) Dalek in existence was destroyed when Gallifrey vanished? I mean I know they "upped their firepower", but were there no Daleks ANYWHERE else in time and space that would have escaped that initial blast. If it's true that "A Dalek is a genius", then any genius knows not to put all their eggs in one basket, anyone got any ideas?
 * The Daleks were very intent on winning the Time War. I can imagine that once they broke through the sky trenches of Arcadia, they wanted every single Dalek present in order to assure victory. Not to mention the fact that they frequently let their personal hatred of Time Lords and especially the Doctor get the best of them.
 * No this is actually a huge problem. Clearly Steven Moffat decided to dedicate his 50th Anniversary to this because being "Mr. Everybody Lives" he, quite understandably, wasn't best pleased with what Russell T. Davies had the Doctor do and opted to undo it.
 * The problem is that Russell T. Davies supported the idea but, recognizing it was difficult, went to great lengths to justify the necessity. 9th confessed it to Rose, 10th defended it to the Master, 11th practically bragged about it to House. Which first invites the question, and I may have blinked and missed it, what was so "secret" about the "secret Doctor?"
 * The idea behind the "secret" Doctor, is that it is not a secret to the viewer nor the Doctor but to everyone else in the Whoniverse, he doesn't want people to know about the incarnation of him that, up until now, committed double genocide, it's a secret that he has desperately tried to keep, think about it, he has never told any of his companions (even River Song) nor anyone else in the Universe, the only people that really encountered that incarnation (until Clara) were all dead. So there was no-one to know he even existed, hence, he wasn't the 9th Doctor, just a "War" Doctor.
 * But that's just it: when it comes down to it, this episode showed -- regardless of how justified it was -- it still wasn't right. To stop the war the doctor had to murder countless innocent men, women, and children. Nothing can make that right.
 * In RTD's era, the Doctor's ending of the Time War was justified by how involved it was and what horrors it unleashed. It was much more than just Time Lords Vs. Daleks: many races were involved and ended up in the Time Lock. The idea that it could be ended simply by Gallifrey vanishing seems highly implausible.
 * It was never stated other races were involved in the fighting, all those terrible things the doctor talked about such as the Nightmare Child could have been the weapons they were using, it was stated the war was having a horrible effect on the universe. The Time War was always described as a war between the Daleks and the Time Lords, one which had a devastating effect on the universe. That doesn't mean that other races were involved in the fighting.
 * Whilst the Daleks may well have thrown everything they had at that point in time at Gallifrey, this is a war that was being fought through all of time and space, and the consequences were that the "Universe would burn" if that continued, the simple act of Gallifrey disappearing at a singular point in time at that space would in no way cause the destruction of all Daleks throughout existence. The Moment did have the ability to do that, and to time lock it so as to make it a dedicated point in time, which would bring the war across all of Time to an end. Is it really possible that every Dalek in existence was destroyed?


 * Oh this has got weird. I wish my post hadn't been butchered somehow; it would be a lot easier for me to reply. I absolutely agree the idea was always difficult, but it doesn't change the fact the RTD tried his best to present it differently to how SM clearly does. It was always highly questionable, the fact of that was never the problem. The idea behind it was why the Doctor thought it was necessary and how deep the damage was. The idea was that the war was so protracted that whatever happened the result of letting it continue would be the destruction of everything, the Doctor saw a different path, the only one he could see at the time, and took it. The Time Lords tried to take yet another path which was what finally pushed the Doctor's hand - such was suggested in The End Of Time.
 * I repeat the "secret" was not kept well at all, why does it matter that the Doctor doesn't identify it was a different incarnation that committed double genocide, he admitted it to Rose, he specifically admitted the genocide of the Daleks to the Dalek in "Dalek": 'I made it happen!', he admitted the genocide of the Time Lords to House in "The Doctor's Wife": 'Fear me, I've killed all of them."He admitted both genocides frequently and used the first person pronoun on so many occasions so what really did we discover that we didn't know before and we would have lost if 9th had done it? It's a great episode to watch, but I can't see how that works.
 * The Time War wasn't a secret, according to this episode the Zygons lost their home during it, thus the sub-plot. Races were mentioned, the Time Lords were absolute masters of time and on all evidence of sense much better at it than the Daleks. It's hard to see the Daleks conducting anything other than a standard war without help even if very violent. Although the Time War is a hard and little-explained concept (and a rather strained idea perhaps) it's still impossible to believe that all the Daleks would destroy each other: there were too many of them, they'd eventually notice what was happening. Note the distinctive shape of Dalek ships we've always been shown.
 * It is not the time war that is secret, he's happy to admit to that and to committing double genocide, but the incarnation of the Doctor, the one who did it, that is what he keeps secret, the fact that he did it is different to the incarnation that did it. The War Doctor is the secret, what the War Doctor did is not, therefore the fact that the Doctor had a secret identity is what's so mysterious, because he did not take the name of the Doctor he is an incarnation of that time lord that does not exist within the known universe, no one knows that he even existed.  However the issue of the Daleks destroying each other is still in my eyes a massive plot hole.
 * The implication is that this is pretty much it, the fighting has reached the Time Lords' home planet. From the look of the War doctor, the fighting's been going on for at least centuries. The Daleks are on the verge of victory; they've thrown pretty much everything -- no, everything -- they have at them, because as far as they're concerned they are about to win, and they're not going to let anything stop them now. Then the Doctors grabbed Gallifrey while the massive bombardment was going on. Now that Gallifrey is gone the bombardment simply hits the other Daleks. Their weapons wiped out them all out too fast for them to realize that Gallifrey is gone. They're blown to kingdom come, and everyone assumes that the two races must have annihilated each other, as there is no sign of either of them on the battlefield.
 * But essentially if the Time War has only just now reached Gallifrey, where's it been taking place for the past few centuries? Well anywhere else and doing huge damage to the rest of the universe such as the disappearance of the Zygon homeworld. Whether or not either species was allied with other species or not, when Russell T. Davies established the idea of the Last Great Time War he made it very clear that the whole universe, and every species therein, was involved. It was like a nuclear war except on an infinitely larger scale over a much larger area. The consequences of the protracted battle between the forces of Skaro and Gallifrey were about to destroy the universe, the Time Lords had one way to survive this, the Doctor came up with another. The point was that the Doctor didn't use the Moment lightly. He created the time lock to cut off the universe from all these horrors that threatened to destroy it. In short he didn't use the Moment to protect the universe from Gallifrey he did it to save the universe from the effects of the Time War and it's those effects that really continue unaddressed.
 * With the War ended, Time would right itself and the Universe was safe.
 * Define the terms "time" and "right". The major crux of the problem, of course, is that the Time War resulted in a host of great wrongs the Doctor had put a stop to. This episode plays off one of those wrongs: the disappearance of the Zygon homeworld. No one is meant to believe that it reappeared just because the Time war ended.
 * Or as this is the Last Day, all the other races involved are gone and the war is no longer being waged throughout history. Both sides are enacting their final plans. The Daleks are bombarding Gallifrey and Rassilon is trying to enact his Ultimate Sanction. This could be the final stage in a war of attrition.


 * * PLEASE PUT SEPARATE QUESTIONS IN SEPARATE THREADS! To answer the original question, we do indeed know that a number of Daleks survived after the assault on Gallifrey.
 * * * Indeed, it's a major emotional pivot point for the Ninth Doctor when he realizes he killed Gallifrey (or so he believed) for nothing.


 * If the paintings are a slice of time - stasis - how did the Zygons move to exit the paintings? How did the three Doctors fight a Dalek off an exit the painting?
 * Aspects of this question were previously answered above. Obviously, the stasis cubes allow those in stasis to move once they are awoken.


 * What year was the events of present day London (with the Zygons)? Assuming it's 2013, Kate Stewart's timeline doesn't quite match with her first appearance in The Power of Three, where she first met the Doctor (she introduced herself and used a scanner to confirm the identity of the Doctor). The Power of Three happened in roughly the year 2020.
 * No year is explicitly given in The Power of Three. We also don't know with certainty that Day of the Doctor was set in 2013.
 * Although there is no set date in The Day of the Doctor due to the fact that Kate is on a friendly basis with the Eleventh Doctor it presumably takes place after the events of The Power of Three, so the date can be determined by dating this story. Amy comments in The Power of Three that it has been ten years since the Doctor and Amy began travelling. If she is counting from the ending scenes of The Eleventh Hour, which takes place in 2010, then it would place this story in 2020 - which is consistent with the events of The Hungry Earth/Cold Blood in which a relatively future version of Amy and Rory are seen in 2020. That would place The Day of the Doctor post-2020. However, in The Name of the Doctor Vastra's letter said that Clara lived in 2013, at least seven years before the dating explained above. The only way around this is if the Doctor shares with Kate a non-linear relationship like he does with River Song, and she first met a later version of the Doctor from The Power of Three sometime prior to 2013 and was told to pretend that The Power of Three was their first meeting.
 * Amy also says that it hasn't been ten years for earth. Just for them. So some lesser amount of time has passed for everyone else, meaning that story is presumably not set in 2020.
 * The Doctor could have taken Amy and Rory to the future to wave at them.
 * One thing that makes the dating of the 50th anniversary special slightly controversial is that the BBc's summary for The Day of the Doctor states that the year is 2013. However, the answers above seem to work as an explanation as well, considering that Amy and Rory did not live linearly through time.


 * Tom Baker is shown supposedly playing the fourth Doctor, but the fourth doctor regenerated when Tom Baker was young so he cannot exist with the present day Doctor. The only way he can exist is if the fourth doctor who appeared in this episode was from another universe where the fourth Doctor hasn't regenerated yet.
 * It was deliberately left ambiguous as to whether it was actually the Fourth Doctor. and as to his age you may remember that in the Tenth Doctor mini-episode Time Crash the Tenth Doctor met the Fifth Doctor and commented that he had aged due to shortening out of the time differential. If this is the Fourth Doctor this would explain why he appears to have aged. In case anyone wonders why his clothes are different if he if the Fourth Doctor, presumably he is incognito.
 * He is not the "Fourth Doctor." Eleven mentions that he could be the curator and someday he would like to settle down and do that.  Then "The Curator" appears and while talking to Eleven mentions that he likes to revisit the old favourites.  So while he looks like Four he is actually "The Curator".
 * The implication being that he may be a future incarnation of the Doctor. This causes a separate continuity issue, however (addressed later).
 * It's easier to think of The Curator as the "Twenty-Fourth Doctor," a far away future incarnation that chooses to 'revisit' his old face of his Fourth incarnation as he retires from time and space adventuring to settle down as a curator.


 * The Doctors plan to use their sonic screwdrivers to destroy the door in the tower. This is possible because the screwdriver has been working on the problem for 400+ years.  In "Smith and Jones" the Doctor's sonic screwdriver was destroyed.  He would have had to get a new one, so how has the screwdriver been working on the problem of the door?
 * * He also lost it again in "The Eleventh Hour"
 * * * Its stated that despite the different appearance its the same technology. Perhaps its like how when you get a new phone you can still see messages from the previous one.
 * * * * It is possible that because the TARDIS creates the sonic screwdriver that the data that the screwdriver receives is directly linked to TARDIS. So, the information stored on the sonic screwdriver is sent to the TARDIS and the information is configured there and when a sonic screwdriver is created, the information of the previous version is put in. This would explain why the Doctor didn't want to give up the sonic screwdriver in Rings of Akhaten.
 * * It was explained in the episode that the scans made by the sonic are implanted in its software as a permanent subroutine so that, no matter which exterior casing the screwdrivers use, they all operate on the same software.
 * * * Basically, think of it as a variation on The Cloud.


 * Given the events of the next episode, Time of the Doctor, there are two issues raised with regards to regeneration. Given that Eleven knows he's the final Doctor (supposedly), he should be more surprised at meeting the Curator, who is supposedly a future incarnation of himself. And the fact Ten knows the numbering as well, it's odd that no reference is made to the Eleventh Doctor being the last of the line. (We will assume for ease of argument, that Twelve joined of his own volition given that Eleven, under the assumption of being the last Doctor, would have had no reason to seek him out.) Note: although this board usually does not bring up future episodes, I'm breaking the rule here since Name of the Doctor, Day of the Doctor and Time of the Doctor were promoted, marketed, and confirmed by Moffat et al as being a trilogy, not standalone stories. Plus they were all written around the same time by the same writer.
 * Eleven does seem very surprised on seeing the Curator but doesn't really quite know who he is - only that he looks like an older version of his past self, and seems to have some future information. Time is "wibbly-wobbly" enough that there could be many possibilities yet to be known to explain this.
 * A few moments before meeting the Curator, the Eleventh Doctor reminds the War and Tenth Doctors that due to time being in flux, they will not remember anything about meeting their future selves. Why should Eleven be immune? If the Curator is, in fact, a future Doctor, then he likely forgot all about him after the guy left (which would also cover off the fact the "search for Gallifrey" scenario appears to be set aside when the Doctor goes to Trenzalore and stays there). Alternately, people change over time, physically, so Eleven might have thought he was meeting his own incarnation many years down the line. As it is, when Eleven eventually does become elderly he resembles the First Doctor.


 * One thing I'm surprised that no one has picked up on is when Kate tries to destroy London to save the Earth she asks the Doctor how many times has he made that calculation. He replies only once and it is implied he is referring to the supposed destruction of Gallifrey. Yet in Fires of Pompeii (I'm sure there are other examples but this is the best I could think of) The Doctor destroys Pompeii to save the World.
 * The Gallifrey example is the biggest example of such, and, of course, is particularly foremost on his mind at that moment. there wasn't really a need for him to give Kate a detailed list of every time he's had to something kind of similar - plus, if anything, that might embolden her to stand her ground on doing it, which he clearly does not want.
 * Also, a nuclear explosion in the heart of London would kill far more people than died at Pompeii. According to Wikipedia, 16,000 died when Vesuvius blew. A nuke going off in London would kill millions.
 * Arguably, the Doctor had no choice about Pompeii: its destruction was as much an historical event as the ones the First Doctor didn't change. If he hadn't blown Vesuvius, he would have changed history (it's a bit like the Fifth Doctor realising that putting out the fire in the Terrileptil base would prevent the Great Fire of London). That factor doesn't apply in the case of the nuke under London.
 * I think the doctor is talking about a destruction that kills millions of your own people. For instance, the doctor is not from Pompeii, but he is from Gallifrey, therefore this decision to destroy Gallifrey is bigger for him - this is similar to Kate Lethbridge-Stewart in that Kate is from London and threatening to destroy London.
 * Further to the Vesuvius point, clearly the destruction of London by nuke is not a "fixed point in time" and therefore can be prevented, thus saving many lives, including children (a major thread in the Doctor's guilt over his earlier actions).


 * In Full Circle, Romana stated the TARDIS weighed 5 million kg, which is far too heavy to be carried by helicopter the way it was.
 * * In The Evil of the Daleks, it was driven away on the back of a lorry (and so must have been lifted there). The continuity issue would appear to be with Full Circle.
 * It's also been lifted and carried other times as well. Romana may have simply been mistaken, or was talking about the internal mass and not taking into account the effect of the chameleon circuit on the outer shell's characteristics.
 * I believe Romana was talking about the mass of the inside.
 * Otherwise, the TARDIS would sink into the ground, or cut a hole through any vessel's hull it lands on; the airplane it lands in during "The Bells of Saint John" would have plummeted from the sky.
 * In Flatline it was mentioned the TARDIS can change external weight and that its true weight would destroy the Earth


 * The Doctor was unfamiliar with how the Moment worked, but he supposedly had a hand in building it.
 * Nothing in the TV show suggests he had anything to do with building it. They state that it was the ancients of Gallifrey who did so. The production team don't generally seem to consider the comics as "canon".
 * Actually, there's been a few hints that they do consider comics to be canon in some way; regardless, The Moment was created by Steven Moffat for this episode, based on a throwaway line of dialogue in "The End of Time". Any similar weapons that might have been mentioned in other media beforehand are coincidental. Plus, even if he did help design it, there is plenty of evidence that the Doctor doesn't retain all of his memories when he regenerations; he might have simply forgotten, or even repressed the memory.


 * Wouldn't the Zygons be able to tell they were Zygons even if their memories were erased, by figuring out that they were shapeshifters and not in their natural forms?
 * How? The average human wouldn't know how to shapeshift even if they were able to, so none of them would know how to initiate the process.
 * Yeah but they didn't lose their entire memories, surely a subconscious thing such as shapeshifting would be remembered - for example, Osgood and Mcgillop did not forget how to walk and talk. So, how can the zygons not know they are zygons?
 * Why would it? The premise of the question assumes a very detailed knowledge of exactly which areas of memory the Doctors erased from the Zygons & humans. We have no idea how the memory erasing technology works, or how the Doctor modified it. We also don't know how Zygons shapeshift, or where it resides in their memories. Is it instinctive? Is it learned behaviour? The face value of the explanation given in the story seems to stand.
 * that makes almost no sense."The average human wouldn't know how to shapeshift even if they were able to, so none of them would know how to initiate the process." if I'm walking my dog and we are both in some kind of accident where we both have amnesia. (I guess just assume for the dog) since the accident, if my dog isn't able to ride a bike, or tune a banjo, can you assume that I've forgotten how to?
 * The Black Archive has technology that is able to convince someone it's his first day of work year upon year. We cannot assume that it isn't capable (especially with three Doctors interfering) of suppressing such memories, even instinct, for the relatively brief period of time that counts.


 * How come the Zygon shapeshifting could copy clothes but not Osgood's inhaler?
 * The inhaler may be more complex. Or, they may simply not have known of its existence until after copying Osgood.
 * It could also tie in with the two Osgoods pondering what would happen if she lost a shoe, given that Zygon Osgood's clothes are actually part of her. Perhaps there's an object like the inhaler in Zygon Osgood's pocket but it's part of her and so can't be removed.
 * The inhaler is a separate object, not "connected" to the body. We see Zygons replicate clothes, but do we ever actually see them disrobing? It's very possible Zygon!Osgood might have been physically unable to remove her scarf, for example, or her glasses. Of course, this makes the whole "you can't tell who is human and who is Zygon" ploy a bit moot, though, really, the intent of that was just to get the two Kates to stop the countdown. If they discovered the truth a few moments later, it wouldn't have mattered because the countdown was already stopped.


 * The Doctor was stated to have been working on the calculations to save Gallifrey for centuries (presumably starting from his time as the War Doctor), but all the incarnations before the eleventh lost their memories of this event after it happened, so how could they have been working on the calculations?
 * Even longer than that - as indicated by Doctors 1 through 8 showing up to help as well. We know Time Lord minds are very complex, so presumably this was a more or less unconscious process for him. Kind of like the sonic screwdriver doing its thing all that time as a "permanent subroutine" in the software.
 * Or the TARDIS computers have been running the calculations.
 * The screwdrivers had been running the calculations without the Doctor's knowledge, and he wouldn't have known to listen to the screwdriver's bzzzz, so he didn't.
 * There is nothing in the scene to suggest sonic screwdrivers had anything to do with the calculations. It may have been the TARDIS. Note that the First Doctor can clearly be heard uttering the words (recorded by a voice actor for the occasion) "Commencing calculation." The First Doctor is not known to have ever had a sonic screwdriver.
 * Actually, the Eleventh Doctor mentions building in his room instead of having a social life in A Christmas Carol. Although this does seem to contradict his having a granddaughter by 237.  Either way, The Day of the Doctor never says the sonic screwdriver performs the calculation.


 * Also, the First Doctor has a sonic screwdriver in most of his MAs. (Also, the Eighth Doctor in the EDAs explicitly borrows his original screwdriver from out of time from his First incarnation, not his Second.) See Venusian Lullaby (and Alien Bodies) for examples.


 * The 9th, 10th, and 11th Doctors never noticed a weird program running on their sonic screwdrivers that they didn't remember programming?
 * Nope. Why would they? Presumably it has a lot of processes running on a regular basis.
 * Plus the War Doctor could have worked some sort of "masking code" into his subroutine. Ditto for the program used by the Doctors throughout their lives.
 * Would the program work in the first place? With three Doctors together wouldn't the program only work once all the Doctors are back in their own correct time line?
 * Why would that happen? Do computers stop working every time they time travel? Or brains? Why should screwdrivers care about being in a different time if computers and brains don't?


 * If the Tenth Doctor forgot everything about this episode, how did he remember his marriage to Elizabeth in The End of Time (TV story)?
 * It's clear that he remembers their courtship at least. Since it's implied that the Ninth Doctor remembers an alternate version of the end of the Time War, it's possible that the Tenth remembers a version of the wedding that didn't include Clara and his other selves. My guess is his mind somehow supplies him with false memories to account for his timelines being out of sync.
 * Regarding the out-of-sync memory, the Tenth Doctor's mind probably "seamed" the "spliced" memories together, not suspecting anything strange. For example, he probably remembered his time until the vortexy portal, and his mind just created a smooth link to the wedding, cutting out the Eleventh Doctor and Clara, replacing them with inconspicuous blank spaces.
 * Makes sense, according to one of the Expanded Universe Novel (Can't remember which but I believe it happens in a short trip) that the Doctor after the event doesn't remember much except for a vague thing. From what I understand, only the latest Doctor remembers what happens and the earlier Doctor's memory of meeting their past self is locked or changed to make sure it doesn't affect what happens or cause the event in question to not happen. A bit Timey-Wimey but makes sense when you stop and REALLY think about it.


 * How did the Tenth and War Doctors forget about the Eleventh Doctor or Clara? Even if the answer is old age, the Doctor has said, on numerous occasions, "I never forget a face", meaning that in The Eleventh Hour, his reaction should have been more like, "Oh, I'm that guy". For Clara, when he first sees her in The Snowmen/The Bells of Saint John, he should have recognized her from this adventure.
 * War and Ten don't remember Eleven's face because, like with most multi-Doctor encounters, their timestreams are unsynchronized and they therefore cannot retain any memory of the encounter. However, the Eleventh Doctor has had Tom Baker's face before, so upon seeing the Curator, he would recognize him from back in the days when he could look in the mirror and look just like Tom Baker. Also, the phrase "I never forget a face" isn't meant in a strictly literal sense.


 * If every Doctor was supposedly helping save Gallifrey, why were there just 13? If the Doctor got a new Regeneration Cycle, not just a new regeneration, then why were there not 26 Doctors there? (Or More?)
 * It is possible that an event in the Doctor's future will allow him to no longer reach that point in time.
 * Another explanation is that they may have only needed 13 Doctors to participate in saving Gallifrey.


 * This is a big plot hole. As most of us can figure out, the reason that the Sonic Screwdrivers went through the wooden door thing was to foreshadow to later in the episode when the Doctors saved Gallifrey. However, in this scene it was proven that the Doctor needed to wait awhile for the sonic screwdriver to finally work. (although, we don't know if it actually worked or not since he has not used his sonic screwdriver on doors yet) Even in the scene before they save Gallifrey, the Doctors and the Time Lord Council talk about how the calculations would take a long time. So, how did any Doctor prior to the one that had it finally working, supposedly the War Doctor, participate in saving Gallifrey? Also, why did any Doctor after the one that had it finally working participate if it only needed to work with one of them?
 * The Doctor who got the calculation working could tell the previous Doctors what to do as the TARDIS will be able to communicate with itself from the past.
 * This doesn't explain anything. The calculations are what make this work. We know this by the screwdriver scene. It explained that it would have to take a long time to work. The calculations are like the process to start any technological machine. You can only tell someone with the same machine to start it, not the end result.
 * You could have the first Doctor start the calculation as a permanent sub routine for the Tardis whilst all of the Doctors follow the instructions of the Doctor who had the finished calculation without a contradiction as doing the calculation and following the instructions of the Doctor who had the finished calculation are separate processes. And to answer the other question "why did any Doctor after the one that had it finally working participate if it only needed to work with one of them?", one of the Doctors (sorry I can't remember which one) said they needed to surround Gallifrey for their plan to work so presumably that is why they needed lots of Doctors.


 * Apparently the earlier Doctors (War and Ten) won't remember anything happened in Day of the Doctor because when two or more incarnations of the same Time Lord cross timestreams, only the latest one (in this case Eleven) will remember it. However, the same writer (Moffat) also wrote Time Crash (TV story) in which the Tenth Doctor remembers what happened from the Fifth Doctor's point of view. There's also the fact that the First and Second Doctors both remember the events of The Three Doctors (TV story) when they meet up again in The Five Doctors (TV story).
 * The previous Doctors (i.e. Ten and War in this example) can remember what happens while it is happening.In Time Crash, Ten can only remember how to fix the TARDIS while the Doctors are together. Five minutes before Time Crash, he could not have remembered.


 * Why was the rabbit in this episode not brown? Wild rabbits would not be white.
 * The rabbit is brown. Although albinism does occur in wild rabbits.


 * How did Clara see "those big, sad eyes" if the Doctor was looking front and not behind at Clara?
 * Clara may be talking about "those big, sad eyes" she's observed on many previous occasions.
 * Yeah, but as he was looking at the painting, she was talking about his eyes at that current moment and she shouldn't have been able to see them.
 * True, but there's thing this called empathy, which apparently women are supposed to be especially good at, which means that you're sensitive to other people's feelings. She's also just been in his personal timeline and survived so that will probably help that. So she can hear the inflection in his voice, or his body language or a wide variety of things and pick up on his feelings and in her mind sees those "big, sad eyes" that she's learned tend to accompany such feelings.


 * We are told by Kate Lethbridge-Stewart that after leaving the Black Archive, your memory is wiped. Shouldn't this affect Kate Lebridge-Stewart, everytime she leaves?
 * First, if nobody activates the memory eraser, memories don't get erased. It doesn't seem like Sarah Jane's memories got wiped when the Brig smuggled her in a few years earlier. And we saw that Kate had direct control over the machine (until the Doctor took control of it from her), so presumably everyone's memory being erased is just a policy, not an automatic magic thing, meaning she could easily make an exception for herself if necessary.


 * Second, how do you know her memories of what she saw inside aren't erased every time she leaves? (The later Zygon Inversion shows that, at least sometimes if not always, they are.) Sure, that would mean that all she knows about what's in the archive is what's in the secret outside records about what was put in the archive (and any messages she or others sent out), but there's no contradiction there.


 * Its pretty bad security to allow Kate Lethbridge-Stewart to retain her memories. The whole point of the security system is to avoid UNIT being compromised. Why bother having a guards memories wiped, when Kates isn't?


 * On entering the Black Archive, Kate Lethbridge-Stewart exclaims that the guards memory is wiped every day. Why? He's on guard at a closed door. She also says that the guard thinks is his first day. What about his private life?


 * Yes, it's a pretty horrible invasion of his life to wipe his memory so he always thinks he's going in to his first day of work. Presumably, they picked a guy who doesn't have a wife and kids and told him what he'd be volunteering for before wiping his memory of agreeing to it, but still, they're basically taking his entire life from him. But how is that a discontinuity? UNIT regularly does things like violating the UK's (and other nations') sovereignty, operating C19, kidnapping the Doctor and his TARDIS instead of asking him for help, sending soldiers on suicide missions to deal with the Master… They do all that because they think it's necessary, and the same is true here.


 * The Doctors comment that the brigadier always said "science leads" makes no sense. The brig was always a "shoot first, ask questions later" person, most notably in Doctor Who and the Silurians
 * I can only imagine that what the Doctor was intending to suggest was that the brigadier was the sort of man who led with his head rather than his heart, thus doing rather self-serving things, like the blowing up of the Silurians which you mention.
 * I figured that it meant the Brigadier was willing to learn. He starts out tending towards the reliable 'five rounds rapid' and comes to recognize the value of other ways of doing things -- usually because those 'other ways' were well-demonstrated by the Doctor (even if the scriptwriters never really showed this change in attitude). When facing threats that shrug off bullets, use different methods.


 * If the Sonic Screwdriver can now "do" wood, how come The Doctor has never used this new feature?
 * Next time the best way to get through a wooden door is to spend 400 years running calculations, I'm sure he'll do so.


 * If Kate Lethbridge-Stewart and the Zygon thought they were both human, wouldn't they want to continue the countdown?
 * Neither knew if they were human or Zygon, so concluded that it would be wiser to stop the detonation.


 * How did the Doctor and Clara leave the Doctors own time stream?
 * Where did Clara meet the War Doctor whilst inside his own time stream?
 * She didn't meet the War Doctor. See "The Name of the Doctor"
 * Clara does see the War Doctor in "Name of the Doctor", but they don't interact, and we don't know where this scene takes place. But, if the Time War lasted a life time, I'm sure the GI should have met him, and hence, Clara should have met the War Doctor.