Theory:Doctor Who television discontinuity and plot holes/Heaven Sent

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This page is for discussing the ways in which Heaven Sent doesn't fit well with other DWU narratives. You can also talk about the plot holes that render its own, internal narrative confusing.

Remember, this is a forum, so civil discussion is encouraged. However, please do not sign your posts. Also, keep all posts about the same continuity error under the same bullet point. You can add a new point by typing:

* This is point one.
::This is a counter-argument to point one.
:::This is a counter-argument to the counter-argument above
* This is point two.
::Explanation of point two.
::Further discussion and query of point two.

... and so on. 
  • Why doesn't the Doctor recite the "Bird" speech in his head rather than outloud? It would save him a considerable amount of years.
Well because by this point all his memories of his previous lives in the castle return to him. It would be pretty hard for him to concentrate on it mentally considering how many things would be rattling inside his head at this point. Thus, it would be easier for him to verbally do it.
Why doesn't he just not say it at all though? In each life he could get an extra punch or two if he wasn't trying to finish each sentence.
  • In the following episode, we are told the Doctor has been in the confession dial for 4.5 billion years, yet after just 2 billion years the wall is nearly broken.
In the shot after he says he's 20 million years in, we can see the wall is broken enough for him to stand in, even though it should only have about 2 inched of indentation at that point. It's done more for cinematic purposes of showing the wall wearing down without immediately dropping the times as hundreds of millions.
  • The Doctor paints the portrait of Clara, yet when the castle is reset, the painting is complete. Surely, after a reset, the canvas would be blank?
Things that are changed or added by the Doctor, are not affected by the reset.
Except when the Doctor digs the hole, its filled up when he revisits.
  • In the following episode, Hell Bent, Clara mentions that the Doctor's eyes show he hasn't seen her in a long, long time. But, if the doctor killed each copy and was regenerated anew through the teleporter, only having lived for about a week or so each time, doesn't that mean that the Doctor last saw Clara a week ago in his memory?
No, because the episode establishes that once the Doctor makes the connection to the message "BIRD" all the memories of having repeatedly done this over and over come flooding back (at 37:53-56 he says, "I can remember it all. Every time"). Even though physically the Doctor of "Hell Bent" may only be a week or so older, mentally he feels all 4.5 billion years. Considering how poorly he's taking things at the 7,000-year mark, his clear insanity in the following episode becomes more understandable considering his likely state of mind at the 4.5-billion-year mark.
Yes, because the Doctor himself realises that each new version is a copy. With no new memories. Perhaps, at some point the Doctor realises he has repeated this over and over, but its a different version, who does not age!
  • Can somebody explain exactly what the Confession Dial actually was and how it works?
A general explanation is given in the next episode. It's also indicated that the Time Lords altered the normal behaviour of it here, in order to find out more about the Hybrid.
It's also evident that the dial utilizes some of the same "bigger on the inside" tech as the TARDIS.
The Confession Dial seems a rather odd thing to create. Who would want to torture a weakened Timelord whilst in their final incarnation, just so they can upload their consciousness to the Matrix?
This isn't the normal operation of a Confession Dial; this particular one was modified by the Time Lords.
I remember hearing that a confession dial is meant to allow a dying Timelord to confront their inner demons and make peace. However it could also be modified to torture one for confessions.
  • We see that the Doctor has been repeating for 7000 years, so how come the wall he punches has no dents from the past years?
There are a few bumps on it. It ends up taking 4,500,000,000 years or so to complete, so 7,000 years wouldn't get very far.
This is made evident also in the montage where the Doctor doesn't get very far with the Shepard's Boy monologue until literally tens of millions of years have passed.
If you look very closely you can see a large "dent" in the wall where the tunnel is starting to form.
  • The obvious one. If all the rooms in the castle reset, how is the Doctor able to slowly wear down the diamond wall over multiple incarnations?
At a guess the resetting stops when the Doctor 'dies' and begins again when he 'arrives'. So the settings are as they were when he begins the loop again (all the rooms would have been reset by then to their 'normal' settings). The diamond wall room is occupied when the Doctor dies so the resetting stops when he has done some damage and stays that way until the loop stops with him inside it again. You may ask why, if this is true, do the bloodstains on the floor disappear, to which I can only answer that maybe the floor is independently self cleaning?
But the rooms reset if the Doctor leaves for some time. But I think if this material is harder than diamond it is also hard to regenerate.
I view it as simply as this. Whoever trapped the Doctor in there would never have expected he wouldn't give in, so therefore they never programmed the dial to reset that room, eventually leading to the long battle to destroy it. It's simply the unseen enemy's arrogance that results in the room not resetting. As a side note, how do you replenish something 400x harder than diamond?
I thought the reset was because in the end everything ends up the same way it was before he came, so it seems to reset. Maybe I misunderstood the episode, considering how strange it was.
The wall is the perimeter of the Confession Dial and is not subject to the system that maintains the rooms inside the castle.
  • Every 100 years the bird (got from the writing in the sand) pecks at the wall, therefore what the doctor is doing is pointless.
The writing "bird" in the sand is meant to remind the Doctor of the story. There is no real bird.
Unless I really wasn't paying attention, I thought he was referring to a bird on an alien world that would eventually wear down the mountain or whatever it was, and he wrote it because he got the idea from the alien bird.
I'm afraid you really weren't, nobody mentioned any kind of alien world, and in the episode there was a wall, not a mountain, and as explained above, there was no real bird, the Doctor simply compared himself beating the wall to the bird pecking a mountain from the fairy tale.
The story is about how eventually, the mountain is worn away by the bird. Similarly, the azbantium wall will eventually be worn down by a fist.
As the doctor said, it's based off the Brother's Grimm story "The Shepard's Boy" where an emperor hears talk of a Shepard's boy who knows the answer to every question. The king asks him "How many drops of water in the ocean?" To which he replies that once every river and dam going to the ocean is blocked, then he can count them. The second question was "How many stars in the heavens?" To which he replies by putting dots on a piece of paper till they're indistinguishable from one another and saying that that's the amount of stars in the heavens. The third question, of course, "How many seconds in eternity?" where the Shepard's Boy replies with the famous "Bird" story.
  • Who put the very first costume in the fireplace room? Or the first 12th doctor just put off the wet one, left it, and went on naked? Otherwise there'd be no extra costume for the next 12. And why didn't it disappear when the room reset? Even if it's not supposed to be gone because it's like a part of something alien-not-castle-stuff, still the question stands - who put the first costume in the room?
The most likely answer is the one you give in your question - The Doctor takes off his clothes (possibly leaving on undergarments, as we don't see those there) to dry by the fire. He then goes wandering about, eventually dies and brings in a "new" Doctor. When he gets wet, he finds the previous set of clothes, and swaps them out. The cycle then continues.
This cannot be, as the room resets each time.
What OP means is where would the clothes have come from the first time the Doctor came. This is a good question -- the Doctor finding his clothes there suggest that those are the clothes left by the last Doctor. Thus perpetually the Doctor is putting his clothes there and picking up the wardrobe of his predecessor. But if there were no clothes the first time, the Doctor would and could not have left his clothing there. Various things could explain this, though. There could have been extra clothing in that room and the loop would still work, as this room clearly is one of the ones exempt from the reset. So a clown outfit could have been there and the room wouldn't put the clown outfit back because it doesn't reset. Or maybe there's clothes hidden elsewhere in the room that the Doctor doesn't find in all cases past the first one because he doesn't need to. Or possibly the first time he stripped his clothes down without another wardrobe and spent the rest of the episode after that point naked. I prefer the later possibility, and will now accept it as head canon.
And that's basically what the above explanation says - the first version leaves his clothes there, goes wandering about with out them (possibly naked, possibly still in undergarments), and the next version of the Doctor finds them.
This cannot be, as the Doctor does not know he has the ability to return.
Thanks for the answers, except I think the costume room does reset, as otherwise the fire in the fireplace would've gone out many years ago. I do like the idea of him finding some other clothes somewhere in the room or the castle (there was a bed, and food, could easily be a wardrobe too), and as you said, after leaving his own costume there for the first time, he never needed any other clothes to look for. And the costume doesn't reset because it is indeed something that the Doctor brought with him, foreign material and stuff. Seems legit to me.
Moffat has since stated that the first time the Doctor left his suit in that room, he found some generic clothes there to change into. That outfit got burned with that iteration of the Doctor, so all the ones to follow ended up wearing their predecessors' clothes.
Note, for example, that the Doctor finds food, and presumably the tools to create the portrait of Clara, so some things were provided to him (otherwise the Doctor might have starved to death). Presumably this included a change of clothes - we don't know that the Doctor didn't find them in another room initially.
  • What was the point in taking the panel from the floor, writing on it and burying in the garden? And if all the rooms except the wall one reset, why didn't the garden and the floor reset? The garden only resets to the grave having a stone buried in it, but that's not what it was like when the Doctor first got there. Or in fact he wasn't who buried the stone, the Time Lords were, so the grave with the stone buried in it was a default? Why? To show him the way? But why so complicated?
See point above about the bird pecking on the wall every 100 years.
Sorry, still not getting it. The bird and 100 years is just a metaphor, in fact the Doctor every time beats the wall as often as he can. How does this answer my question? And what the Doctor is doing is the opposite of pointless, the problem is eventually solved exactly because he's been doing it for all this time. And if you mean that all his other actions are pointless because of resetting, I still want to know who dug the grave and why doesn't it reset?
It's 12. In an interview, Moffat explained that "The first time round the castle, the Doctor is there for many years - because there is no clue leading him to room 12. He's ancient by the time he understands that room 12 is important. It's a very old man who starts punching the wall..." (DWM 495.) So I assume it was the first Twelve that drew Clara, wrote the message, and drew the arrows.
If the moment a new Doctor clone is created the base state for the reset is made, then that would solve the problem with the word "bird" not disappearing from the sand.
On the word "bird", see the question below.
But not the Wall, for which I have two theories:
1)The Wall room is non-resettable.
2)The Azbantium is too difficult to reset.
I think the first one is correct. If the Time Lords wanted it to be reset, they would have made the wall of something more 'resettable'. I think they had no idea he'd do something like what he did, and as the wall was actually a gate of sorts, they never intended for it to reset - no need, it's not even technically a part of the castle.
I'm guessing the wall is the perimeter of the confession dial and so doesn't reset because it isn't part of the "World". I imagine that even if the Time Lords altered the castle to be a jungle or a town or whatever, the edge of that world would still be the same impenetrable wall. Therefore, it does not reset.
  • If the rooms reset all the time, why the word 'bird' stayed on the sand for a while for the Doctor to read it, and was gone later? And why the castle started moving and opened a way to the roof when the Doctor saw this word? The Bird clearly means no good for the Time Lords, more like vice versa.
The doctor writes the word 'bird' when he is weak, each new doctor reads it and wipes it away. When the room is reset the word is written there for him to read.
Both questions stand, why doesn't the word reset as everything else and why the way to the roof opened exactly when the Doctor saw the word. As initially, when the Doctor first arrived there (which is, as i understood, the state that the rooms are supposed to reset to) there couldn't be any such word, as there was no Doctor yet to write it.
The hypothesis above suggests that the reset value for the room is determined when the "new" Doctor arrives, or even as the "old" Doctor dies (being before the word has disappeared).
As for the bird thing, I now think that the Doctor's ashes is what the Doctor's basically become, it's a significant part of him, which can't be reset by the castle, which is why he chooses it to leave a message. And well, also because there's nothing else he can possibly reach at that moment. So no matter if the Doctor leaves the room or not, the word stays and it's blown away by the wind later.
The word "Bird" does not disappear because the room reset *before* the doctor wrote the word. At 44:29, as he is crawling toward the teleporter, he says, "The room has reset." The room is already ready to go, in the same state it was in originally, *except* that the teleporter doesn't have enough energy to operate. The Doctor writes the word "Bird" in the sand, gives the teleporter some energy with his body, and the teleporter activates and does what it originally did, making a Doctor copy. The new Doctor copy emerges seconds later, so there hasn't been enough time for another reset, and the word "Bird" is still there.
The way I look at it, everything that arrived on the Doctor's person survives the reset, such as the skull and the clothes. In fact, you could say the rooms don't reset, but rather the objects inside return to their original position and status. They also repair themselves from damage the Doctor caused, such as the broken window. As disturbing as it sounds, that 'sand' isn't actually sand, but rather the Doctor's ashes from burning himself many many many many many many many times.
  • The castle in the state presented in the episode is made up out of a mixture of bread crumbs left behind by the Doctor (and for some reason not reset to the default), bread crumbs that are a default part of the castle (?), and just random stuff, and it's not always obvious which is which. What is clear, though, is that the first time (and possibly a few more after the first one) the Doctor is transported there differed from the sequence occurring ad nauseum in the episode. At what point did the Doctor set up the scenario as we saw it unfold? How much of it was actually set up by him and what parts were already part of the default castle? Also, how was the transporter activated the first time?
The Doctor had 7,000 years' worth of attempts to set up the bread crumbs before we first join the episode. As to the first activation of the teleport, that presumably was set to occur after he was sent away from Ashildr in the previous episode. Each "burned out" version of the Doctor just needed to activate the special rematerialisation of the stored pattern.
Moffat has stated that the first go-around in the dial for the Doctor took years before he worked out the tricks.
However, the Doctor would have been killed long before working out the tricks, and as each new Doctor has no memories, he'd have to start all over again!
The Doctor is very clever. He worked it out the first time and didn't die. How he figured it out the first time we don't know; we only get to see how he works it out in subsequent incarnations.
But he can't have left the clue "BIRD" the first time, because he writes it in the sand, but the sand is created from the destruction of his old body, so the first time through there wouldn't have been any sand. And he says that when he sees the word "BIRD" that's when he remembers, so how would he remember the first few times when there's no word "BIRD" because there's not enough sand yet? And how did he find out about the rooms resetting, because surely he wouldn't have been able to work that out the first time through?
  • Why, for God's sake, doesn't the Doctor figure out something better to hit that wall with than his hands?
Put yourself in his position. If you were trapped inside that room with the Veil coming at you, how else are you going to go back and get that other thing to hit the wall with? Furthermore, I doubt using that other thing would actually get him out of that area faster.
Aren't his shoes a harder surface to hit it with than his hands? Unless he's using some Time-Lordery on his hands to make them really hard or something, it just seems silly. Ideally, he'd force a regeneration into some powerful creature with claws/pincers/what-have-you that can more efficiently chip away at the wall, maybe even hold off the Veil while we're at it.
I don't think he can choose to regenerate into a different species-type of body.
The wall isn't merely a physical object; it's a construct which embodies the boundary between the Confession Dial's pocket dimension and the rest of the universe. It's possible that mundane objects can't damage it at all, but being a Time Lord gives the Doctor the capacity to do so, much like how his Time Lord status let him keep moving when Time was being reversed in "Invasion of the Dinosaurs".
I don't think that is supposed to be the case. The Azbantium is said to be 400x harder than diamond, but it isn't said to be infinitely harder, or impervious to normal objects. And the hypothesis that some special Timelordy material is needed to get through it seems to conflict with the point of the bird story -- the bird isn't some special mountain-destroying object. The point is that a tiny amount of damage from the humblest of sources, if repeated enough times over a long enough period, will eventually destroy the largest and hardest of objects.
The shovel wasn't available because the Doctor doesn't remember what he's supposed to do until after he enters Room 12, by which time the Veil is blocking any chance of departure to retrieve the shovel. Also, the Doctor being a Time Lord, he likely does pack a stronger punch than if he'd used his shoes or something.
Time Lords have much greater physical strength than humans, so his punches are stronger than ours. Also, just a reminder, Azbantium is 400x harder than diamond. If he grabs a chair and whacks it against the wall, it'll break on the first hit. If he grabs the shovel, it breaks on the first hit. Anything he could've used would break instantly.
  • At the end we see everything took place inside a confession dial, but was it the Doctor's confession dial? If so, why was this what was inside it and shouldn't he have known?
Perhaps the dial was meant to extract the confessions out of the Doctor
That may be, but the Doctor lies about the Hybrid! He is the Hybrid, not a Timelord/Dalek combination.
He may have lied about being the Hybrid.
It was the Doctor's Confession Dial (that's why Ashildr needed his Confession Dial at the end of the previous episode). However, the Confession Dial was modified by the Time Lords; this is not how it normally operates. Probably they held the Doctor in stasis somewhere while they modified his Confession Dial, then put him in it.
  • Once on Gallifrey, the Doctor casually reveals the secret he was so insistent not to reveal to the Veil just moments earlier. So why did he go through the torturous process of creating and sacrificing billions of clones?
Dialogue states he knows of only the legend of the Hybrid and he did state, just before he punched through that hard wall, that he would no longer be confessing to the Veil his knowledge about the Hybrid - which of course included the confession we heard at the end.
But the point was, apparently, not to not confess specifically to the Veil, but to not confess at all. I think the whole point of keeping the Hybrid secret was to protect Gallifrey. As he had no idea that the Time Lords were those who tortured him (if that's true, things still can be not what they seem), he wanted to protect them and not to let the unknown torturer learn the secret that he could use against the Time Lords. And later, of course, when he realized it was all in vain and they were the ones who tortured him to find out the truth, and they were the reason Clara died (seriously, she was partly the reason for saving them, I hate those guys and would be glad if in the finale it's revealed they're actually innocent), he had no desire to protect them any longer, and thus revealed the secret with a quite clear warning about what now awaits them for everything they've done.
If he'd claimed to be the Hybrid any earlier, whomever was behind it could have just sealed Room 12 permanently and left him trapped in his Hell forever, or chucked the Confession Dial into a black hole. Hybrid menace foiled. But once he's successfully escaped, the Doctor can make that claim with impunity: his captors have been scaring him to death for billions of years, so now he's free to start returning the favor.
This point is answered in "Hell Bent."
Probably his claim to be the hybrid is just a lie meant to scare the Timelords. In "Hell Bent," he seems to disagree with Ashildr's theory that he is the hybrid.
  • This is point four: Too many skulls. In the water the Doctor sees many thousands of skulls. He emerges from the water in the interior of the castle. Billions of skulls being added would eventually inundate the castle. The depth of the water within the castle walls can be estimated. 7000 years in the future gives the point at which we join the story. If he survives in the castle for a week, 52 skulls a year will be deposited. 7000 x 52 = 364,000 skulls. This amount does not rise above the water in the interior of the castle. If he adds the same amount until breaching the crystal wall he will add 104,000,000,000 skulls. The castle would overflow with skulls. Even if the skulls fall exterior to the castle the 'angle of repose' applies. Complicating factors such as currents, storms and the depth of the water exterior to the castle all lead to the same conclusion: too many skulls.
You have to remember that skulls don't last forever. They'll eventually turn to dust, allowing for newer skulls to take their place.
Indeed. Considering that the Doctor appears to live and die at a consistent rate by the time we hit this episode, the bones would decay and add up at a consistent rate leaving a perpetual collection of skulls.
Because the Confession Dial is also one big TARDIS, for all intents and purposes, it might be automatically clearing away the skulls (otherwise the Doctor would at one point land head first into a pile of bone, rendering all the efforts to extract a confession moot).
But why would it leave a collection of thousands of skulls on the bottom?
  • How can each version of the Doctor specifically remember burning the previous ones when, technically, they haven't done it yet? Further, accepting that this is possible, why does nothing else in the entire castle ring a bell?
As I got it, he didn't remember it, he just figured it out. He guessed that's what happens every time, because that's what he was about to do. He says 'burning the old me' right before he actually does it, so. The only thing that confuses me is him saying, 'You don't understand, I can remember it all, every time.' I don't know what he means, as he can't possibly remember something that happened not to him but to his copies. Some say he means 'I remember that no matter what I do you'll still be gone'.
He makes that remark while arguing with imagined-Clara (37:53-56), explaining why he doesn't want to go on. This only makes sense if he is saying that he can remember every cycle (that makes it psychologically worse every time). There is then a longish pause before he says, "And you'll still be gone." He does not appear to be saying that he can remember that she'll still be gone; he seems to be saying he can remember every cycle, and in addition, Clara will still be gone when he gets out.
Exactly how much he remembers is unclear, but by the end of a given body he may well have some recollection of the memories of his previous bodies. We know that Time Lords do have some psychic abilities, and trace memories from the previous versions of the Doctor may linger in the castle.
The "burning myself up to create another" is also a direct metaphor for regeneration, and it's known that the Doctor retains memories of his past incarnations.
  • Moffat has a long history of having episode titles that have very little to do with the story, but this time I'm completely lost. Why is this called Heaven Sent?
At one point the Doctor says, "I'm not scared of Hell - it's just Heaven for bad people." The main reason it's called Heaven Sent is to provide a contrast with the finale's title, in which the Doctor is "hell bent" on saving Clara. The pattern in Series 9 was to come up with titles that echoed one another, e.g., "The Girl Who Died"/"The Woman Who Lived", "The Zygon Invasion"/"The Zygon Inversion", etc.
Yeh, the linking titles seem to be the only real reason. Though I suppose with the confession dial as a place Time Lords go before death, it's somewhat thematically related to "Heaven", albeit kind of ironically, when it was more purgatory than Heaven.
Maybe the castle is being referred to as "Heaven" (as he says, "Heaven for bad people"), and the Doctor gets sent from this "heaven" to Gallifrey at the end. Or, maybe Earth is "heaven", and the Doctor is sent from there to the castle.
  • The Doctor says that the Hybrid is part Dalek, part Time Lord. The Doctor lies, for he is the hybrid. Why does he not die, when he lies?
He said that the legend said it was half Dalek and half Time Lord, but he never said that the legend was correct. So he never technically lied.
  • If the Doctor's memory is reset every visit, why doesn't he make the same mistake and die the first time, every time? Surely, the only way to survive is by learning from the previous mistakes, which is what happens! Therefore, his memories are not reset!
It's possible that he remembers his mistakes subconsciously and that may be enough to overcome them.
Doubtful, as its a "new" Doctor every time.
The first time, he figured out how to get reborn, and he also left clues for himself to make it easier the next time.
  • How did the Confession Dial get to Gallifrey?
Ashildr was contacted by the Time Lords, which set these events in motion, so she presumably gave it to them.
And then they left it in the desert? Doubtful.
  • Where did the child come from who met the Doctor? It's the desert!
There's probably a village nearby. We just don't see it.
Probably that same village where the Doctor was having lunch with a bunch of people later.
  • This might seem like a stupid question, but, when are the scenes in the TARDIS set?
It's all in the Doctors mind. A place of safety when stressed.
  • What is the purpose of the octagonal space in the floor with the arrows pointing to the center, and wouldn't it be reset each time? I can vaguely understand the removed stone being under the dirt (perhaps that helps it avoid the reset), but the room it came from I'd assume would reset and erase the arrows. If it doesn't, why not store more specific information there instead of obscure breadcrumbs?
Because the Doctor's clever enough to figure it out.
He could give helpful directions such as "bring something good for chipping stone to room 12." Maybe shorten the time to escape by a billion or so years.
  • I'm not even sure why the Veil is such a threat. I'll assume it's invulnerable. But since the grave area can be barricaded against it and one time he digs all night, it's clear he can get more than 82 minutes of peace, sleep, or research in. The Veil doesn't have infinite strength, or it could have forced the door open against the Doctor. With time to dig it would seem reasonable that he could lay traps for it, not to hurt it but to impair its movement, perhaps keeping it in the grave area instead of outside. Or let the door open when done, have it walk in, circle around and go back out again since it's not very fast.
  • Does the Doctor die each time he jumps out into the water and see the skulls? Since there doesn't seem to be an obvious way back up to anything. If not that would seem like another location he could ditch the Veil for awhile - go swim for an hour and lazily circle back even if it's swimming after you.
Interesting point. If the Doctor does die every time he jumps into the water, how is he able to get back to the control room to make another copy?
He does not die. He jumped in, saw the skulls, climbed out of the water, then found that room with the fire and the change of clothes, where he left his wet clothes.
  • Why do some room reset while others don't?
  • The woman whose corpse the Doctor saw as a child was presumably a Time Lady, so why didn't she regenerate?
Regeneration can be halted in various ways, such as stabbing both hearts. Alternately, the woman had reached the end of her regeneration cycle.
Shobogans also live on Gallifrey and do not regenerate (this was established in The Deadly Assassin, so it is valid to bring up here). He may have spent time with Shobogans, since the barn he grew up in seems to be outside of the Citadel.
I thought Timelords only got a limited number of regenerations.
  • The doctor was in the Confession Dial for 4.5 billion years. Where was the Confession Dial itself during all this time? Not on Gallifrey, because Gallifrey is gone from the universe during our time - it was moved to the end of time. The Confession Dial must have been somewhere else, and then when it got to the time where Gallifrey is located going "the long way around," somehow someone moved it to Gallifrey?
  • Why don't other parts of the castle wear down before that diamond wall does? Why doesn't he wear holes through the hallways by walking on them, why don't the gears and other mechanisms of the castle wear down to nothing, etc.? Wouldn't those things happen faster than a 20-foot-thick wall 400x harder than diamond being worn down by a fist?
Each room of the castle resets. The Azbantium is the wall of the Confession Dial, technically outside of the castle, and as such does not reset.
  • Where does all the matter come from for all these skulls? When he jumps in the water, there is a huge pile of skulls underwater, clearly containing many times more mass than his own body. How is all this mass coming into the system?
  • How can his body provide enough energy to create a new copy of him? Each time, his skull is left behind, so at best, the teleport machine might have received the amount of mass/energy in his body minus his skull.
When the Doctor burns himself up, he's trying to summon (or re-print, as he puts it) the version of himself that is stored in the teleporter, not create a new version from scratch. The amount of energy required for this task, presumably, is less than the amount provided by his total body mass.
  • Where is the energy coming from to keep the whole mechanism of the castle running for 4.5 billion years? And if the system has such a vast energy source, how come the Doctor has to burn his own body to provide enough energy to run the teleporter?
It's very clever Time Lord technology, i.e. so intricate that it would be far too difficult for the dying Doctor to understand and re-purpose on the spot, if it's possible at all from the inside.
It's possible the Time Lords, similar to the Logopolitans, have come up with ways to avoid/prevent/reverse the loss of energy over time.
  • What was the Confession Dial doing for 4.5 billion years? Just sitting in the desert, in that place where the Doctor emerged and met a little boy? And no one tampered with it during that time? Nor did its walls get worn down by weather, nor was it buried as continents moved, mountains turned to ocean floors, and similar geologic changes occurred?
Considering this whole thing was a setup by the Time Lords, it naturally follows that they intended for him to end up on Gallifrey, so it's likely that they ensured the the dial would end up on the planet, if not specifically the region. Furthermore, with it being Time Lord tech and all, maybe it was kept in some kind of pocket space or something for those 4.5 billion years, keeping it safe from the physical changes you describe.
It's also possible that time passes faster inside the dial. Heck,

that 4.5 billion years he spent inside the dial could have only been a few days outside.

  • Why would the Doctor bury a cryptic message to himself underground, rather than a very informative, explicit message that was easy to access?
  • Are the new copies of the Doctor that appear in each cycle actually the same person - or did the Doctor we know simply die, and then a series of clones of him lived and died, until finally one lucky clone emerged at the end?
Depends on your philosophy, I suppose. When Super Mario dies and respawns, do you consider that the same Mario, or a clone? I'd say it was the same Doctor.
Definitely the clone.
  • Why did the Time Lords make it difficult for the Doctor to figure out what he was supposed to do? It was only by accident that he figured out that he was supposed to tell secrets to the Veil, because he accidentally confessed "I'm afraid of dying." If he didn't happen to say that, out loud (and very oddly), he wouldn't have known, and the Veil would have just killed him.
It could be possible that the Veil would actually only kill him once he started breaking down the defences, for fear that he'd eventually get through.
In that case why didn't the Veil just start running at him as soon as he started punching the wall?
  • Why would the Time Lords have put a creature in there that would probably just kill the Doctor? Then they'd never find out anything.
  • Why does the Doctor assume from the start that the Veil is going to kill him? And especially once he figures out why the Veil is there, shouldn't the Doctor assume that the Veil won't really kill him?
Think about it this way, you have your childhood nightmare following your every movement after being teleported to a strange place. You'd probably think that it was going to kill you.
  • When he gets to the Azbantium wall (at 35:45), the Doctor says, "Of course. The last square on the board. What else would it be? The Tardis. One confession away." What did he mean? Was the Tardis supposed to be on the other side of the Azbantium wall? But then how come, when he got through the wall, he wound up on Gallifrey, with no Tardis? And if the Azbantium wall is the edge of the Confession Dial, how could the Tardis be on the other side of it anyway?
I don't understand how the Doctor thinks the TARDIS is on the other side. The TARDIS is nowhere near the Confessional Dial in the previous episode!
The wall says "Home". The TARDIS is the Doctor's home so that is obviously what he would expect to find behind a wall saying "Home".
  • At the end of each cycle, why is there a skull left behind with electrodes attached to it? Since the electrodes are attached to the head, wouldn't the Doctor's head be the first part of him to get destroyed, if any part of his body did? It would make more sense that, say, his feet would be left, because they were farther away. And since the electrodes were attached to his skin, wouldn't they have fallen off when the skin burned away, instead of winding up stuck to the bone?
  • When the Doctor is shown punching at the Azbantium wall at a couple million years and past, the top of the tunnel appears to be WAY taller than his head, almost an arm's length taller than he is. Why didn't he dig a bit lower and duck through toward the exit? That would have saved him a billion years at least.
  • When he punches the Azbantium wall the last time, the entire thing just shatters and falls. It looks like it was a lot more than paper-thin, so how did he crack so much in the last punch?
Crystaline structures fracture differently to you might expect, as the structure is ordered and... structured. If you've ever seen a glass break, you can see the entire structure can crack/shatter even if the crack was previously small. It's simply how crystals work- it's known as Cleavage.
  • How were the Sisterhood of Karn able to get to Gallifrey, if it was time locked?
Ask this on the Hell Bent discontinuity discussion.